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A comprehensive software suite for protein family construction and functional site prediction

David Renfrew Haft, Daniel H. Haft, Olivier Lespinet
2017 PLoS ONE  
OPEN ACCESS Citation: Haft DR, Haft DH (2017) A comprehensive software suite for protein family construction and functional site prediction. PLoS ONE 12(2): e0171758.  ... 
doi:10.1371/journal.pone.0171758 pmid:28182651 pmcid:PMC5300114 fatcat:ecvewabc5nbergziywcmoxzsou

An Assessment of the Impact of Hafting on Paleoindian Point Variability

Briggs Buchanan, Michael J. O'Brien, J. David Kilby, Bruce B. Huckell, Mark Collard, John P. Hart
2012 PLoS ONE  
It has long been argued that the form of North American Paleoindian points was affected by hafting.  ...  According to this hypothesis, hafting constrained point bases such that they are less variable than point blades.  ...  One is that Clovis points were hafted in such a way that the haft did not constrain the base characters.  ... 
doi:10.1371/journal.pone.0036364 pmid:22666320 pmcid:PMC3364334 fatcat:4j4zoaumlrhg5ogg3awm4ph7qe

In vivo bone strain and finite-element modeling of the craniofacial haft in catarrhine primates

Callum F. Ross, Michael A. Berthaume, Paul C. Dechow, Jose Iriarte-Diaz, Laura B. Porro, Brian G. Richmond, Mark Spencer, David Strait
2010 Journal of Anatomy  
The behavior of this model is then used to test hypotheses regarding the overall deformation regime in the craniofacial haft of macaques.  ...  Introduction Primates exhibit a diverse range of morphology in the craniofacial haft -the structures joining the rostrum to the braincase.  ...  The behavior of this model is then used to test hypotheses regarding the overall deformation regime in the craniofacial haft of macaques.  ... 
doi:10.1111/j.1469-7580.2010.01322.x pmid:21105871 fatcat:tkilfnuy3nex3cxljiwalltq2y

In Vitro Testing of a Novel Blood Pump Designed for Temporary Extracorporeal Support

David J. Spurlock, David N. Raney, Emilia M. Fracz, Daniel E. Mazur, R.H. Bartlet, Jonathan W. Haft
2012 ASAIO journal (1992)  
Acknowledgments This work was sponsored by the National Institute of Health, R42HL096168 David Spurlock is the recipient of an NIH sponsored T32HL076123 Vascular Surgery: Research Training in Vascular  ... 
doi:10.1097/mat.0b013e318245d356 pmid:22236624 pmcid:PMC3296523 fatcat:ocpetxd67fce7aemcqjtoxjzmm

COVID-19 in Africa: a comparative analysis of early policy responses

David Olusegun Sotola, Pregala Pillay, Hafte Gebreselassie
2021 Revista de Administração Pública  
They are to conduct preliminary checks and send those perceived as potential cases for test (David & Mash, 2020) . This may prove to be a useful strategy in checking community transmission.  ... 
doi:10.1590/0034-761220200427 fatcat:yf75ab2rffccvar3v3wzoii5by

Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics [article]

Amanda N Shelton, Erica C Seth, Kenny C Mok, Andrew W Han, Samantha N Jackson, David R Haft, Michiko E Taga
2018 bioRxiv   pre-print
., 2016; Haft et al., 2012; 122 Galperin et al., 2015; Markowitz et al., 2012) for cobamide biosynthesis, cobamide-dependent 123 enzymes, and cobamide-independent alternative functions were chosen.  ...  and Haft, 2017).160 All six HMMs have not been assigned TIGRFAM accessions at the time of publication, but will 161 be included in the next TIGRFAM release, and are included as Supplementary Files.  ... 
doi:10.1101/342006 fatcat:6ag7oxqr5ngarl7bwxivtc25ua

PLASMA LIPOPROTEIN METABOLISM IN PERFUSED RAT LIVERS. I. PROTEIN SYNTHESIS AND ENTRY INTO THE PLASMA*

David E. Haft, Paul S. Roheim, Abraham White, Howard A. Eder
1962 Journal of Clinical Investigation  
PROTEIN SYNTHESIS AND ENTRY INTO THE PLASMA* By DAVID E. HAFT, PAUL S. ROHEIM, ABRAHAM WHITE AND HOWARD A.  ... 
doi:10.1172/jci104541 pmid:13903558 pmcid:PMC290986 fatcat:l6bfwoauh5ctffo5v4dveet3a4

Preliminary In Vivo Testing of a Novel Pump for Short-Term Extracorporeal Life Support

David J. Spurlock, Kelly Koch, Daniel E. Mazur, Emilia M. Fracz, Robert H. Bartlett, Jonathan W. Haft
2012 Annals of Thoracic Surgery  
Background-Blood pumps used for temporary circulatory support have limitations. We propose a novel device designed for short-term extracorporeal support which is intrinsically volume responsive, afterload insensitive, and incapable of cavitation or excessive hemolysis. After in vitro testing, we performed the initial in vivo implantations and assessments. Methods-The BioVAD prototype (MC3, Inc, Ann Arbor, MI) was implanted in six adult male sheep (60.2 +/− 2.8 kg) via the left ventricular apex
more » ... nd descending thoracic aorta. Arterial, left and right atrial, pump inlet and outlet pressures and BioVAD flow were measured and recorded. The animals were volume loaded to assess volume responsiveness, and the inlet lines were abruptly clamped during maximum support to observe for cavitation. An acute heart failure model was created with rapid ventricular pacing, and the animals were supported for 4 hours. Results-Peak flow was 3.19 +/− 0.56 L/min, and increased with 20 mmHg vacuum assisted drainage to 3.71 +/− 0.53 L/min. Without manual changes in pump settings, pump flow increased 17.5% with volume loading. During acute venous line occlusion, there was no evidence of cavitation and inlet suction was minimal. Hemodynamics were maintained for 4 hours during acute heart failure. Conclusions-The BioVAD provided adequate flow in an acute in vivo model. Its design may be superior for short-term extracorporeal support.
doi:10.1016/j.athoracsur.2011.09.014 pmid:22115336 pmcid:PMC3244559 fatcat:ds55ajyvz5fnniixb6uzqehkfm

A strategy to combine pathway-targeted low toxicity drugs in ovarian cancer

Joe R Delaney, Chandni Patel, Katelyn E McCabe, Dan Lu, Mitzie-Ann Davis, Isabelle Tancioni, Tami von Schalscha, Alena Bartakova, Carley Haft, David D Schlaepfer, Dwayne G Stupack
2015 OncoTarget  
Serous Ovarian Cancers (SOC) are frequently resistant to programmed cell death. However, here we describe that these programmed death-resistant cells are nonetheless sensitive to agents that modulate autophagy. Cytotoxicity is not dependent upon apoptosis, necroptosis, or autophagy resolution. A screen of NCBI yielded more than one dozen FDA-approved agents displaying perturbed autophagy in ovarian cancer. The effects were maximized via combinatorial use of the agents that impinged upon
more » ... points of autophagy regulation. Autophagosome formation correlated with efficacy in vitro and the most cytotoxic two agents gave similar effects to a pentadrug combination that impinged upon five distinct modulators of autophagy. However, in a complex in vivo SOC system, the pentadrug combination outperformed the best two, leaving trace or no disease and with no evidence of systemic toxicity. Targeting the autophagy pathway in a multi-modal fashion might therefore offer a clinical option for treating recalcitrant SOC.
doi:10.18632/oncotarget.5093 pmid:26418751 pmcid:PMC4741591 fatcat:tyfvwgbfejeilbbwhw4d2kluqe

Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics

Amanda N. Shelton, Erica C. Seth, Kenny C. Mok, Andrew W. Han, Samantha N. Jackson, David R. Haft, Michiko E. Taga
2018 The ISME Journal  
The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level.
more » ... 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway. These predictions highlight the importance of cobamide and cobamide precursor salvaging as examples of nutritional dependencies in bacteria.
doi:10.1038/s41396-018-0304-9 pmid:30429574 pmcid:PMC6461909 fatcat:jqqxonybyzg4pik6tqurcuqgcm

PLASMA LIPOPROTEIN METABOLISM IN PERFUSED RAT LIVERS. II. TRANSFER OF FREE AND ESTERIFIED CHOLESTEROL INTO THE PLASMA*

Paul S. Roheim, David E. Haft, Lewis I. Gidez, Abraham White, Howard A. Eder
1963 Journal of Clinical Investigation  
In a previous paper (1), the synthesis and entry into the plasma of the protein moiety of the different lipoprotein classes has been described. The present studies deal with the metabolism of the free and esterified cholesterol of the lipoproteins. Relatively little is known of the metabolism of the plasma lipids as they exist in the various lipoprotein fractions. Study of certain lipids is difficult, if not impossible, because exchange occurs among different lipoprotein fractions, and useful
more » ... servations can be made only with those lipids not undergoing exchange (2). Previous studies (3-5) have shown that the in vitro exchange of ester cholesterol is slow relative to that of free cholesterol. In the present study, we labeled free and esterified cholesterol of the plasma biosynthetically and measured their equilibration between various lipoprotein fractions. After we established that there was virtually no exchange of esterified cholesterol in vitro, we examined the metabolism of this lipid fraction of the various lipoproteins. METHODS Animals. Male rats of the Wistar strain 1 weighing 300 to 500 g were used as blood and liver donors in all studies except the two shown in Tables VI, VII, and VIII, in which Sprague-Dawley rats 2 were used. The standard diet was one of Rockland Farm mouse pellets.
doi:10.1172/jci104812 pmid:14057857 pmcid:PMC289398 fatcat:f6txcah63bcirlb6h4hipgoriu

In Vivo Testing of a Novel Blood Pump for Short-Term Extracorporeal Life Support

Nicholas R. Teman, David S. Demos, Benjamin S. Bryner, Bradley Faliks, Emilia M. Jahangir, Daniel E. Mazur, Alvaro Rojas-Pena, Robert H. Bartlett, Jonathan W. Haft
2014 Annals of Thoracic Surgery  
Background. Centrifugal pumps are used increasingly for temporary mechanical support for the treatment of cardiogenic shock. However, centrifugal pumps can generate excessive negative pressure and are afterload sensitive. A previously developed modified roller pump mitigates these limitations both in vitro and in preliminary animal experiments. We report the results of intermediateterm testing of our evolving pump technology, known as the BioVAD. Methods. The BioVAD was implanted in 6 adult
more » ... sheep (62.5 ± 3.9 kg), with drainage from the left atrium and reinfusion into the descending aorta. The sheep were monitored for 5 days. Heparin was given during the initial implantation, but no additional anticoagulants were given. Data collected included hemodynamic status, pump flow and pressures, laboratory values to monitor end-organ function and hemolysis, pathologic specimens to evaluate for thromboembolic events and organ ischemia, and explanted pump evaluation results.
doi:10.1016/j.athoracsur.2014.04.027 pmid:24856794 pmcid:PMC4097385 fatcat:pt3is7d6wbgixkekqf3vrsppwi

Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes

Lorna J Richardson, Neil D Rawlings, Gustavo A Salazar, Alexandre Almeida, David R Haft, Gregory Ducq, Granger G Sutton, Robert D Finn
2018 Nucleic Acids Research  
Automatic annotation of protein function is routinely applied to newly sequenced genomes. While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes. Genome Properties (GPs) define such functional entities as a series of steps, originally described by either TIGRFAMs or Pfam entries. To increase the scope of coverage, we have migrated GPs to function as a companion
more » ... esource utilizing InterPro entries. Having introduced GPs-specific versioned releases, we provide software and data via a GitHub repository, and have developed a new web interface to GPs (available at https://www.ebi.ac.uk/ interpro/genomeproperties). In addition to exploring each of the 1286 GPs, the website contains GPs pre-calculated for a representative set of proteomes; these results can be used to profile GPs phylogenetically via an interactive viewer. Users can upload novel data to the viewer for comparison with the precalculated results. Over the last year, we have added ∼700 new GPs, increasing the coverage of eukaryotic systems, as well as increasing general coverage through automatic generation of GPs from related resources. All data are freely available via the website and the GitHub repository.
doi:10.1093/nar/gky1013 pmid:30364992 fatcat:cfganwexh5b5dhq53n2xzypxv4

Long-Term Animal Model of Venovenous Extracorporeal Membrane Oxygenation with Atrial Septal Defect as a Bridge to Lung Transplantation

Daniele Camboni, Alvaro Rojas, Peter Sassalos, David Spurlock, Kelly L. Koch, Sarah Menchak, Jennifer Singleton, Erika Boothman, Jonathan W. Haft, Robert H. Bartlett, Keith E. Cook
2013 ASAIO journal (1992)  
This study evaluated the effectiveness of an atrial septal defect (ASD) with veno-venous extracorporeal membrane oxygenation (vvECMO) as a bridge to transplantation. Sheep (56 ± 3 kg; n = 7) underwent a right sided thoracotomy to create the ASD (diameter = 1 cm) and place instrumentation and a pulmonary artery (PA) occluder. After recovery, animals were placed on ECMO, and the PA was constricted to generate a two-fold rise in right ventricular systolic pressure. Sheep were then maintained for
more » ... hours on ECMO, and data were collected hourly. Five sheep survived 60 hours. One sheep died due to a circuit clot extending into the RV, and another died presumably due to an arrhythmia. Mean right ventricular pressure (mRVP) was 19±3 mmHg at baseline, averaged 27±7 mmHg over the experiment, but was not statistically significant (p = 0.27) due to one sheep without an increase. Cardiac output (CO) was 6.8±1.2 L/min at baseline, averaged 6.0±1.0 L/min during the experiment, and was statistically unchanged (p = 0.34). Average arterial oxygen saturation and pCO 2 over the experiment were 96.8 ± 1.4% and 31.8 ± 3.4 mmHg, respectively. In conclusion, an ASD combined with vvECMO maintains normal systemic hemodynamics and arterial blood gases during a long-term increase in right ventricular afterload. Keywords right ventricular failure; pulmonary failure; ECLS; lung transplant; septostomy Correspondence: Daniele Camboni, MD, Franz-Josef-Strauss-Allee, 11 93053 Regensburg, daniele.camboni@ukr.de, phone: 0941 944 9801, fax: 0941 944 9802. Disclosures: none NIH Public Access
doi:10.1097/mat.0b013e3182a91ddb pmid:24172261 pmcid:PMC3836596 fatcat:7ko4qvywtnar5mmg6b236iqjxq

Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer

Joe Ryan Delaney, Chandni B. Patel, Katelyn McCabe Willis, Mina Haghighiabyaneh, Joshua Axelrod, Isabelle Tancioni, Dan Lu, Jaidev Bapat, Shanique Young, Octavia Cadassou, Alena Bartakova, Parthiv Sheth (+6 others)
2017 Nature Communications  
Identification of specific oncogenic gene changes has enabled the modern generation of targeted cancer therapeutics. In high-grade serous ovarian cancer (OV), the bulk of genetic changes is not somatic point mutations, but rather somatic copy-number alterations (SCNAs). The impact of SCNAs on tumour biology remains poorly understood. Here we build haploinsufficiency network analyses to identify which SCNA patterns are most disruptive in OV. Of all KEGG pathways (N ¼ 187), autophagy is the most
more » ... ignificantly disrupted by coincident gene deletions. Compared with 20 other cancer types, OV is most severely disrupted in autophagy and in compensatory proteostasis pathways. Network analysis prioritizes MAP1LC3B (LC3) and BECN1 as most impactful. Knockdown of LC3 and BECN1 expression confers sensitivity to cells undergoing autophagic stress independent of platinum resistance status. The results support the use of pathway network tools to evaluate how the copy-number landscape of a tumour may guide therapy.
doi:10.1038/ncomms14423 pmid:28198375 pmcid:PMC5316854 fatcat:7pz4b3q4anazxg234moc5ezzfq
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