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ThyNVM

Jinglei Ren, Jishen Zhao, Samira Khan, Jongmoo Choi, Yongwei Wu, Onur Mutlu
2015 Proceedings of the 48th International Symposium on Microarchitecture - MICRO-48  
Emerging byte-addressable nonvolatile memories (NVMs) promise persistent memory, which allows processors to directly access persistent data in main memory. Yet, persistent memory systems need to guarantee a consistent memory state in the event of power loss or a system crash (i.e., crash consistency). To guarantee crash consistency, most prior works rely on programmers to (1) partition persistent and transient memory data and (2) use specialized software interfaces when updating persistent
more » ... y data. As a result, taking advantage of persistent memory requires significant programmer effort, e.g., to implement new programs as well as modify legacy programs. Use cases and adoption of persistent memory can therefore be largely limited. In this paper, we propose a hardware-assisted DRAM+NVM hybrid persistent memory design, Transparent Hybrid NVM (ThyNVM), which supports softwaretransparent crash consistency of memory data in a hybrid memory system. To efficiently enforce crash consistency, we design a new dual-scheme checkpointing mechanism, which efficiently overlaps checkpointing time with application execution time. The key novelty is to enable checkpointing of data at multiple granularities, cache block or page granularity, in a coordinated manner. This design is based on our insight that there is a tradeoff between the application stall time due to checkpointing and the hardware storage overhead of the metadata for checkpointing, both of which are dictated by the granularity of checkpointed data. To get the best of the tradeoff, our technique adapts the checkpointing granularity to the write locality characteristics of the data and coordinates the management of multiple-granularity updates. Our evaluation across a variety of applications shows that ThyNVM performs within 4.9% of an idealized DRAM-only system that can provide crash consistency at no cost. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from Permissions@acm.org.
doi:10.1145/2830772.2830802 dblp:conf/micro/RenZKCWM15 fatcat:mqjy754ojrceniah2lebbgrj2y

A Lightweight System for Detecting and Tolerating Concurrency Bugs

Mingxing Zhang, Yongwei Wu, Shan Lu, Shanxiang Qi, Jinglei Ren, Weimin Zheng
2016 IEEE Transactions on Software Engineering  
Along with the prevalence of multi-threaded programs, concurrency bugs have become one of the most important sources of software bugs. Even worse, due to the non-deterministic nature of concurrency bugs, these bugs are both difficult to detect and fix even after the detection. As a result, it is highly desired to develop an all-around approach that is able to not only detect them during the testing phase but also tolerate undetected bugs during production runs. However, existing bug-detecting
more » ... d bug-tolerating tools are usually either 1) constrained in types of bugs they can handle or 2) requiring specific hardware supports for achieving an acceptable overhead. In this paper, we present a novel program invariant, name Anticipating Invariant (AI), that can detect most types of concurrency bugs. More importantly, AI can be used to anticipate many concurrency bugs before any irreversible changes have been made. Thus it enables us to develop a software-only system that is able to forestall failures with a simple thread stalling technique, which does not rely on execution roll-back and hence has good performance. Experiments with 35 real-world concurrency bugs demonstrate that AI is capable of detecting and tolerating many important types of concurrency bugs, including both atomicity and order violations. It has also exposed two new bugs (confirmed by developers) that were never reported before in the literature. Performance evaluation with 6 representative parallel programs shows that AI incurs negligible overhead (<1%) for many nontrivial desktop and server applications.
doi:10.1109/tse.2016.2531666 fatcat:gexbi7xouzc6bpuildc4vhs7we

DudeTM

Mengxing Liu, Mingxing Zhang, Kang Chen, Xuehai Qian, Yongwei Wu, Weimin Zheng, Jinglei Ren
2017 Proceedings of the Twenty-Second International Conference on Architectural Support for Programming Languages and Operating Systems - ASPLOS '17  
Emerging non-volatile memory (NVM) offers non-volatility, byte-addressability and fast access at the same time. To make the best use of these properties, it has been shown by empirical evidence that programs should access NVM directly through CPU load and store instructions, so that the overhead of a traditional file system or database can be avoided. Thus, durable transactions become a common choice of applications for accessing persistent memory data in a crash consistent manner. However,
more » ... ting durable transaction systems employ either undo logging, which requires a fence for every memory write, or redo logging, which requires intercepting all memory reads within transactions. This paper presents DUDETM, a crash-consistent durable transaction system that avoids the drawbacks of both undo logging and redo logging. DUDETM uses shadow DRAM to decouple the execution of a durable transaction into three fully asynchronous steps. The advantage is that only minimal fences and no memory read instrumentation are required. This design also enables an out-of-the-box transactional memory (TM) to be used as an independent component in our system. The evaluation results show that DUDETM adds durability to a TM system with only 7.4% ∼ 24.6% throughput degradation. Compared to the existing durable transaction systems, DUDETM provides 1.7× to 4.4× higher throughput. Moreover, DUDETM can be implemented with existing hardware TMs with minor hardware modifications, leading to a further 1.7× speedup.
doi:10.1145/3037697.3037714 dblp:conf/asplos/LiuZCQWZR17 fatcat:5vqrfqdt4vferptfsl5fykwhwe

Sparse coding reveals greater functional connectivity in female brains during naturalistic emotional experience

Yudan Ren, Jinglei Lv, Lei Guo, Jun Fang, Christine Cong Guo, Weiming Zeng
2017 PLoS ONE  
Author Contributions Investigation: Yudan Ren. Methodology: Yudan Ren, Jinglei Lv. Supervision: Christine Cong Guo. Writing -original draft: Yudan Ren.  ...  Writing -review & editing: Yudan Ren, Lei Guo, Jun Fang, Christine Cong Guo.  ...  (DOCX) Ren Y, Lv J, Guo L, Fang J, Guo CC (2017) Sparse coding reveals greater functional connectivity in female brains during naturalistic emotional experience.  ... 
doi:10.1371/journal.pone.0190097 pmid:29272294 pmcid:PMC5741239 fatcat:5agxedi5wjeorajfefoq2qcy4u

Effective connectivity of the anterior hippocampus predicts recollection confidence during natural memory retrieval

Yudan Ren, Vinh T. Nguyen, Saurabh Sonkusare, Jinglei Lv, Tianji Pang, Lei Guo, Simon B. Eickhoff, Michael Breakspear, Christine C. Guo
2018 Nature Communications  
Human interactions with the world are influenced by memories of recent events. This effect, often triggered by perceptual cues, occurs naturally and without conscious effort. However, the neuroscience of involuntary memory in a dynamic milieu has received much less attention than the mechanisms of voluntary retrieval with deliberate purpose. Here, we investigate the neural processes driven by naturalistic cues that relate to, and presumably trigger the retrieval of recent experiences. Viewing
more » ... e continuation of recently viewed clips evokes greater bilateral activation in anterior hippocampus, precuneus and angular gyrus than naïve clips. While these regions manifest reciprocal connectivity, continued viewing specifically modulates the effective connectivity from the anterior hippocampus to the precuneus. The strength of this modulation predicts participants' confidence in later voluntary recall of news details. Our study reveals network mechanisms of dynamic, involuntary memory retrieval and its relevance to metacognition in a rich context resembling everyday life.
doi:10.1038/s41467-018-07325-4 fatcat:og5vxcchdbh3xl4aa75ifxj24m

Structure-based dynamic analysis of the glycine cleavage system suggests key residues for control of a key reaction step

Han Zhang, Yuchen Li, Jinglei Nie, Jie Ren, An-Ping Zeng
2020 Communications Biology  
AbstractMolecular shuttles play decisive roles in many multi-enzyme systems such as the glycine cleavage system (GCS) for one-carbon (C1) metabolism. In GCS, a lipoate swinging arm containing an aminomethyl moiety is attached to protein H and serves as a molecular shuttle among different proteins. Protection of the aminomethyl moiety in a cavity of protein H and its release induced by protein T are key processes but barely understood. Here, we present a detailed structure-based dynamic analysis
more » ... of the induced release of the lipoate arm of protein H. Based on molecular dynamics simulations of interactions between proteins H and T, four major steps of the release process showing significantly different energy barriers and time scales can be distinguished. Mutations of a key residue, Ser-67 in protein H, led to a bidirectional tuning of the release process. This work opens ways to target C1 metabolism in biomedicine and the utilization of formate and CO2 for biosynthesis.
doi:10.1038/s42003-020-01401-6 pmid:33311647 fatcat:bwmph23d35eulet2jgyi4jkt5q

AI: a lightweight system for tolerating concurrency bugs

Mingxing Zhang, Yongwei Wu, Shan Lu, Shanxiang Qi, Jinglei Ren, Weimin Zheng
2014 Proceedings of the 22nd ACM SIGSOFT International Symposium on Foundations of Software Engineering - FSE 2014  
Concurrency bugs are notoriously difficult to eradicate during software testing because of their non-deterministic nature. Moreover, fixing concurrency bugs is time-consuming and error-prone. Thus, tolerating concurrency bugs during production runs is an attractive complementary approach to bug detection and testing. Unfortunately, existing bug-tolerating tools are usually either 1) constrained in types of bugs they can handle or 2) requiring roll-back mechanism, which can hitherto not be fully
more » ... achieved efficiently without hardware supports. This paper presents a novel program invariant, called Anticipating Invariant (AI), which can help anticipate bugs before any irreversible changes are made. Benefiting from this ability of anticipating bugs beforehand, our software-only system is able to forestall the failures with a simple thread stalling technique, which does not rely on execution roll-back and hence has good performance Experiments with 35 real-world concurrency bugs demonstrate that AI is capable of detecting and tolerating most types of concurrency bugs, including both atomicity and order violations. Two new bugs have been detected and confirmed by the corresponding developers. Performance evaluation with 6 representative parallel programs shows that AI incurs negligible overhead (< 1%) for many nontrivial desktop and server applications.
doi:10.1145/2635868.2635885 dblp:conf/sigsoft/ZhangWLQRZ14 fatcat:43o5j3cgsjhq7keq45dnbg3su4

Dephosphorization of Vanadate Leaching Solution by Chloride-Free Dephosphorizing Agent

Jinglei Zhang, Yanli Ren, Changlin Liu, Jianming Li, Jinyang Zhang
2013 International journal of chemical Engineering and Applications  
CaCl 2 was generally used as dephosphorizing agent during the sodiumization-vanadium extraction process. However, a large number of chloride ions were brought into wastewater from vanadium precipitation, which increased the corrosion of the evaporation-concentration equipments of wastewater treatment. Then, the chloride-free dephosphorizing agent (CFDA) was developed, and the dephosphorizing effect was compared with that of CaCl 2 . The results showed that, with the chloride-free
more » ... agent, the dephosphorizing ratio≥99 %, clarification time of 120 min, vanadium loss≤3.5 %, and vanadate leaching solution dephosphorized by the CFDA could meet the demand of high density vanadium precipitation. Index Terms-Chloride-free dephosphorizing agent, dephosphorization, vanadate leaching solution, vanadium precipitation. since 2010. He is engaged in treatment of wastes during production of vanadium and titanium, including treatment of wastewater from vanadium precipit-ation, resource utilization of the slag from molten salt chlorination, etc.
doi:10.7763/ijcea.2013.v4.335 fatcat:gejdlkobkzcivbqes2bdfipvby

Fixing, preventing, and recovering from concurrency bugs

DongDong Deng, GuoLiang Jin, Marc de Kruijf, Ang Li, Ben Liblit, Shan Lu, ShanXiang Qi, JingLei Ren, Karthikeyan Sankaralingam, LinHai Song, YongWei Wu, MingXing Zhang (+2 others)
2015 Science China Information Sciences  
Concurrency bugs are becoming widespread with the emerging ubiquity of multicore processors and multithreaded software. They manifest during production runs and lead to severe losses. Many effective concurrency-bug detection tools have been built. However, the dependability of multi-threaded software does not improve until these bugs are handled statically or dynamically. This article discusses our recent progresses on fixing, preventing, and recovering from concurrency bugs.
doi:10.1007/s11432-015-5315-9 fatcat:qx6mwxqhazaoror6whqhbauoi4

Pre- and post-selected measurements with coupling-strength-dependent modulation

Zhaoxue Li, Jiangdong Qiu, Linguo Xie, Lan Luo, Xiong Liu, Zhiyou Zhang, Changliang Ren, JingLei Du
2019 Chinese Physics B  
Pre- and post-selected (PPS) measurement, especially the weak PPS measurement, is a useful protocol for amplifying small physical parameters. However, it is difficult to retain both the attainable highest measurement sensitivity and precision with the increase of the parameter to be measured. Here, a modulated PPS measurement scheme based on coupling-strength-dependent modulation is presented with the highest sensitivity and precision retained for an arbitrary coupling strength. This idea is
more » ... onstrated by comparing the modulated PPS measurement scheme with standard PPS measurementv scheme, respectively, in the cases of balanced pointer and unbalanced pointer. By using the Fisher information metric, we derive the optimal pre- and post-selected states, as well as the optimal coupling-strength-dependent modulation without any restriction on the coupling strength. We also give the specific strategy of performing the modulated PPS measurement scheme, which may promote practical application of this scheme in precision metrology.
doi:10.1088/1674-1056/28/3/030602 fatcat:sekbixeu4ve2rjaybhsqdc5m6a

An Innovative Prone Position Using a Body-Shape Plaster Bed and Skull Traction for Posterior Cervical Spine Fracture Surgeries

Zhiyu Ding, Yijun Ren, Hongqing Cao, Yuezhan Li, Shijie Chen, Jinglei Miao, Jinsong Li
2022 Frontiers in Surgery  
BackgroundAn innovative prone cervical spine surgical position using a body-shape plaster bed with skull traction (BSPST) was compared with the traditional prone surgical position with horseshoe headrests.MethodsA total of 47 patients, undergoing posterior cervical spine surgery for cervical spine fracture, were retrospectively classified into two groups, the BSPST group (n = 24) and the traditional group (n = 23), and underwent a posterior instrumented fusion with or without decompression.
more » ... iple indicators were used to evaluate the advantages of the BSPST compared with the traditional position.ResultsAll the operations went smoothly. The mean recovery rate was 56.30% in the BSPST group and 48.55% in the traditional group (p = 0.454), with no significant difference. The intraoperative blood loss (177.5 ml vs. 439.1 ml, p = 0.003) and the total incidence of complications (8.3 vs. 47.8%, p = 0.004) were significantly less in the BSPST group than in the traditional group. In addition, the BSPST position provided a greater comfort level for the operators and allowed convenient intraoperative radiography.ConclusionsThis is the first study to describe a combined body-shape plaster bed and skull traction as an innovative cervical spine-prone surgical position that is simple, safe, and stable, intraoperative traction direction adjustable, reproducible, and economical for posterior cervical spine fracture surgery, and potentially other cervical and upper dorsal spine surgeries in the prone position. Additionally, this position provides the surgeons with a comfortable surgical field and can be easily achieved in most orthopedic operation rooms.
doi:10.3389/fsurg.2022.649421 pmid:35356505 pmcid:PMC8960061 fatcat:7256ebd5erfyjgcv4srz64zno4

A non-structural pure enzyme protein forms an LCST type of stimuli-responsive and reversible hydrogel with novel structure and catalytic activity [article]

Jinglei Nie, Xinyi Zhang, Yongfei Liu, Martin Schroer, Wei Wang, Jie Ren, Dmitri I. Svergun, An-Ping Zeng
2021 bioRxiv   pre-print
Hydrogels have a wide range of applications such as in biomedicine, cosmetics and soft electronics. Compared to polymer hydrogels based on covalent bonding, protein hydrogels offer distinct advantages owing to their biocompatibility and better access to molecular engineering. However, pure and natural protein hydrogels have been seldom reported except for structural proteins like collagen and silk fibrin. Here, we report the unusual ability and mechanism of a unique natural enzyme,
more » ... in ligase A (LplA) of E. coli to self-assemble into a stimuli-responsive and reversible hydrogel of the low critical solution temperature (LCST) type. This is the first globular and catalytic protein found to form a hydrogel in response to temperature, pH and the presence of ions. Protein structure based analysis reveals the key residues responsible for the gel formation and mutational studies confirms the essential roles of hydrogen bonding between the C-terminal domains and electrostatic interactions in the N-terminal domains. Characterization of phase transitions of wild type LplA and its mutants using small angle X-ray scattering (SAXS) yields details of the gelation process from initial dimer formation over a pre-gel-state to full network development. Further electron microscopic analyses and modeling of SAXS data suggest an unusual interlinked ladder-like structure of the macroscopic crosslinking network with dimers as ladder steps. The unique features of this first reported protein hydrogel may open up hitherto inaccessible applications, especially those taking advantage of the inherent catalytic activity of LplA.
doi:10.1101/2021.02.07.430034 fatcat:uqp2jejsjra3ncjifqae4tg7ke

Identification of gene modules associated with survival of diffuse large B-cell lymphoma treated with CHOP-based chemotherapy

YongChao Gao, Bao Sun, JingLei Hu, Huan Ren, HongHao Zhou, Ling Chen, Rong Liu, Wei Zhang
2020 The Pharmacogenomics Journal  
Diffuse Large B-cell Lymphoma (DLBCL), a heterogeneous disease, is influenced by complex network of gene interactions. Most previous studies focused on individual genes, but ignored the importance of intergenic correlations. In current study, we aimed to explore the association between gene networks and overall survival (OS) of DLBCL patients treated with CHOP-based chemotherapy (cyclophosphamide combination with doxorubicin, vincristine and prednisone). Weighted gene co-expression network
more » ... sis was conducted to obtain insights into the molecular characteristics of DLBCL. Ten co-expression gene networks (modules) were identified in training dataset (n = 470), and their associations with patients' OS after chemotherapy were tested. The results were validated in four independent datasets (n = 802). Gene ontology (GO) biological function enrichment analysis was conducted with Metascape. Three modules (purple, brown and red), which were enriched in T-cell immune, cell-cell adhesion and extracellular matrix (ECM), respectively, were found to be related to longer OS. Higher expression of several hub genes within these three co-expression modules, for example, LCP2 (HR = 0.77, p = 5.40 × 10-2), CD2 (HR = 0.87, p = 6.31 × 10-2), CD3D (HR = 0.83, p = 6.94 × 10-3), FYB (HR = 0.82, p = 1.40 × 10-2), GZMK (HR = 0.92, p = 1.19 × 10-1), FN1 (HR = 0.88, p = 7.06 × 10-2), SPARC (HR = 0.82, p = 2.06 × 10-2), were found to be associated with favourable survival. Moreover, the associations of the modules and hub genes with OS in different molecular subtypes and different chemotherapy groups were also revealed. In general, our research revealed the key gene modules and several hub genes were upregulated correlated with good survival of DLBCL patients, which might provide potential therapeutic targets for future clinical research.
doi:10.1038/s41397-020-0161-6 pmid:32042095 pmcid:PMC7502356 fatcat:eibwebuvnjbazfajj5c2hrilcq

Stand-alone lipoylated H-protein of the glycine cleavage system enables glycine cleavage and the synthesis of glycine from one-carbon compounds in vitro [article]

Yingying Xu, Yuchen Li, Han Zhang, Jinglei Nie, Jie Ren, Wei Wang, An-ping Zeng
2021 bioRxiv   pre-print
H-protein, one of the four component proteins (H, T, P and L) of glycine cleavage system (GCS), is generally considered a shuttle protein interacting with the other three GCS-proteins via a lipoyl swinging arm. We report that without P-, T- and L-proteins, lipoylated H-protein (Hlip) enables GCS reactions in both glycine cleavage and synthesis directions in vitro. This apparent catalytic activity is closely related to the cavity on the H-protein surface where the lipoyl arm is attached. Heating
more » ... or mutation of selected residues in the cavity destroys or reduces the stand-alone activity of Hlip, which can be restored by adding the other three GCS-proteins. Systematic study of the Hlip-catalyzed overall GCS reactions and the individual reaction steps provides a first step towards understanding the stand-alone function of Hlip. The results in this work provide some inspiration for further understanding the mechanism of the GCS and give some interesting implications on the evolution of the GCS.
doi:10.1101/2021.03.28.437365 fatcat:acgs4rlh7nh7zd6rl3bs3tg4pi

T1 mapping and feature tracking imaging of left ventricular extracellular remodeling in severe aortic stenosis

Xiaoyu Wei, Xuhua Jian, Jiajun Xie, Rui Chen, Xiaodan Li, Zhicheng Du, Xiaomei Zhong, Jinglei Li, Xiaobing Zhou, Guanmin Ren, Yingjie Mei, Hui Liu
2020 Cardiovascular Diagnosis and Therapy  
Left ventricular (LV) extracellular remodeling is a critical process in aortic stenosis (AS), which is related to functional abnormalities. Data regarding the use of combined T1 mapping and feature tracking (FT) to assess LV extracellular remodeling in severe AS are scarce. This study aimed to investigate the ability of T1-derived and FT-derived parameters to identify and assess the changes in process of LV extracellular remodeling in patients with severe AS. A total of 49 patients with severe
more » ... S and 20 healthy volunteers were prospectively recruited. Modified look-locker inversion-recovery T1 mapping and FT imaging were performed in all participants using 3.0-T cardiac magnetic resonance imaging. The degree of myocardial fibrosis was quantified using Masson trichrome stain in biopsy specimens obtained intraoperatively from 13 patients and expressed as collagen volume fraction (CVF). Patients were divided into subgroups according to preserved LV ejection fraction (LVEF) (LVEF ≥50%) or reduced LVEF (LVEF <50%). Regarding the diffuse fibrosis burden, extracellular volume (ECV) was statistically insignificant between patients with preserved LVEF) and controls (28.0%±3.3% vs. 26.5%±2.3%, P>0.05). ECV in the reduced LVEF group (n=20) was significantly higher than that in the preserved LVEF group (n=29) (30.4%±3.9% vs. 28.0%±3.3%, P<0.05). Regarding the myocardial strain, global longitudinal strain (GLS) showed increasing impairment from the control group to the preserved LVEF AS group to the reduced LVEF AS group (-23.4%±3.3% vs. -18.6%±3.8% vs. -11.2%±4.8%, P<0.05). A significant correlation was found between ECV and CVF (r=0.64, P=0.020), whereas the correlation between GLS and CVF was insignificant. Significant correlations were observed between GLS and LV mass index (r=0.72, P=0.006) and LVEF (r=0.82, P<0.001). However, no correlations were found between ECV and LV mass index (P=0.172) and between ECV and LVEF (P=0.339). Discrimination of patients with preserved LVEF from controls, GLS yielded the best diagnostic performance as defined by the area of under the curve (-0.83), and GLS, ECV, and post-T1 were significant discriminators after regression analysis. In the process of LV extracellular remodeling in severe AS, ECV is the structural marker of extracellular fibrosis burden, and GLS is the functional marker before the fibrosis burden intensifies.
doi:10.21037/cdt-20-803 pmid:33381429 pmcid:PMC7758754 fatcat:k4x3eiy7djgq7lhd52m4ryilni
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