gebhart/patrepeval huggingface dataset:
Alport Syndrome in Women and Girls (2016)

Alport syndrome is an inherited disease characterized by progressive renal failure, hearing loss, and ocular abnormalities. Inheritance is X-linked (85%) or autosomal recessive (15%). Many renal physicians think of Alport syndrome as primarily affecting men. However, twice as many women are affected by the X-linked diseases. Affected women are commonly undiagnosed, but 15%-30% develop renal failure by 60 years and often hearing loss by middle age. Half of their sons and daughters are also affected. Autosomal recessive Alport syndrome is less common, but is often mistaken for X-linked disease. Recessive inheritance is suspected where women develop early-onset renal failure or lenticonus. Their family may be consanguineous. The prognosis for other family members is very different from X-linked disease. Other generations, including parents and offspring, are not affected, and on average only one in four of their siblings inherit the disease. All women with Alport syndrome should have their diagnosis confirmed with genetic testing, even if their renal function is normal, because of their own risk of renal failure and the risk to their offspring. Their mutations indicate the mode of inheritance and the likelihood of disease transmission to their children, and the mutation type suggests the renal prognosis for both X-linked and recessive disease. Women with X-linked Alport syndrome should be tested at least annually for albuminuria and hypertension. The "Expert guidelines for the diagnosis and management of Alport syndrome" recommend treating those with albuminuria with renin-angiotensin-aldosterone system (RAAS) blockade (and adequate birth control because of the teratogenic risks of angiotensin converting enzyme inhibitors), believing that this will delay renal failure. Current recommendations are that women with autosomal recessive Alport syndrome should be treated with RAAS blockade from the time of diagnosis. In addition, women should be offered genetic counseling, informed of their reproductive options, and monitored closely during pregnancy for the development of hypertension.
Sex-related Clinicopathologic Differences in Patients with Adenocarcinoma of the Lung (2007)

Background: The incidence of adenocarcinoma of the lung has been increasing worldwide, and it has been generally been accepted to be relatively unrelated to smoking with a female preponderance. The aim of this study was to examine the gender-related pathological and survival differences in patients with an adenocarcinoma of the lung. Material and Method: A retrospective review of the clinical information of patients diagnosed with an adenocarcinoma of the lung at Kosin Medical Center from January 1999 to September 2005 was performed. The patient's demographics (age, gender), smoking history, stage, serum tumor marker, pathology classification, EGFR mutation, K-ras mutation, treatment methods, and survival time were analyzed. Result: Of the 438 patients, 179 (40.9%) were female. The median age at the diagnosis was 58 years for females and 59 years for males. However, 25.8% of women and only 17.7% of men were under 50 years of age (p=0.02). The distribution of the disease stage was similar in both men and women. The bronchioloalveolar carcinoma component was diagnosed more often in women (11.2%) than in men (5.0%). The overall survival rate was higher in women than in men (p=0.01), and women had a superior therapeutic response to a combined treatment of surgery and chemotherapy. Conclusion: This study showed significant genders differences in terms of the smoking history, bronchioloalveolar carcinoma component, overall survival, and survival after combined treatment of surgery and chemotherapy. Therefore, gender differences should be considered when diagnosing and treating adenocarcinomas of the lung.
Intracoronary Bone Marrow–Derived Progenitor Cells in Acute Myocardial Infarction (2006)

Intracoronary administration of BMC is associated with improved recovery of left ventricular contractile function in patients with acute myocardial infarction. Large-scale studies are warranted to examine the potential effects of progenitor-cell administration on morbidity and mortality.
Convex and Semi-Nonnegative Matrix Factorizations (2008)

We present several new variations on the theme of nonnegative matrix factorization (NMF). Considering factorizations of the form X=FG(T), we focus on algorithms in which G is restricted to containing nonnegative entries, but allowing the data matrix X to have mixed signs, thus extending the applicable range of NMF methods. We also consider algorithms in which the basis vectors of F are constrained to be convex combinations of the data points. This is used for a kernel extension of NMF. We provide algorithms for computing these new factorizations and we provide supporting theoretical analysis. We also analyze the relationships between our algorithms and clustering algorithms, and consider the implications for sparseness of solutions. Finally, we present experimental results that explore the properties of these new methods.
A Biosensor Platform for Rapid Antimicrobial Susceptibility Testing Directly From Clinical Samples (2010)

This biosensor based antimicrobial susceptibility test, in concert with our previously described pathogen identification assay, can provide culture and susceptibility information directly from a urine sample within 3.5 hours.
Negative methylation status ofVimentinpredicts improved prognosis in pancreatic carcinoma (2014)

In our study, Vimentin methylation status can predict the prognosis of pancreatic cancer patients. However, additional experiments and clinical trials are needed to accurately validate this observation.
All-Atom Numerical Studies of Self-Assembly of Zwitterionic Peptide Amphiphiles (2004)

We present an approach to study the self-assembly of organic macromolecules, based on all-atom empirical force field calculations. The approach is applied to self-assemblies of zwitterionic peptide amphiphiles possessing large dipoles in their hydrophilic headgroups. The assembly is built from the bottom up by first optimizing the diad amphiphile, which is then used as a basic unit to subsequently first build quartets, and then 4 × 4 supercells of molecules to be studied in periodic boundary conditions. Explicit water solvent is added to the surface of the periodic structures and molecular dynamics simulations are performed on them. The calculations reveal an interesting structure of the resulting assemblies: the dipoles in the upper parts of the headgroups are aligned in an antiparallel fashion with respect to each other and along one of the periodic axes, while hydrogen bonds in the lower, rigid parts of the headgroups form a parallel beta sheet along the same direction. It is shown that the structure exhibits the tendency to curve around an axis parallel to the direction of the dipoles and the hydrogen bonds, forming a cylindrical micelle.
Kallistatin in human ocular tissues: reduced levels in vitreous fluids from patients with diabetic retinopathy (1996)

Kallistatin is produced endogenously in the eye and the decrease in the vitreous kallistatin levels may be involved in diabetic retinopathy.
Bend loss in highly multimode fibres (2008)

We investigate the bend loss of highly multimode air-clad microstructured polymer optical fibre which displays low bend loss for small bend radii. After repeated bending the loss approached a plateau, decreasing significantly after a characteristic length. The loss at a particular point depended on the configuration of the fibre preceding that point. A simple analytical model based on a transfer-matrix method is derived to explain this behaviour in terms of the power distribution amongst different mode groups. This model allows the effect of a particular fibre configuration to be predicted.
High tunnel magnetoresistance in epitaxial Fe/MgO/Fe tunnel junctions (2003)

We report on spin-polarized tunneling in fully epitaxial Fe/MgO/Fe/Co tunnel junctions. By increasing the thickness of the insulating layer (tMgO), we have strongly enhanced the tunnel magnetoresistance. Values up to ∼100% at 80 K (∼67% at room temperature) have been observed with tMgO=2.5 nm. This tunnel magnetoresistance ratio, which is much larger than the one predicted by the Jullière’s model, can be understood in the framework of ab initio calculations.
Real-world applications of visualization solutions (1990)

Visual data analysis (VDA) is a visualization approach that combines vector and raster graphics to provide insights into various aspects of multidimensional datasets. VDA methods have found application in aerospace engineering research, VDA is being used to develop nondestructive evaluation testing techniques for graphite epoxy composites by providing insights into stress waves propagating through them. Visual data analysis was used to analyze stress wave propagation, determine the origin of an unexplained wave distortion, and create a theoretical model to eliminate the distortion utilizing mathematical modeling. >
Perturbation of nifT expression in Klebsiella pneumoniae has limited effect on nitrogen fixation (1996)

In the nitrogenase system of Klebsiella pneumoniae, nifT is located between nifDK, the structural genes for dinitrogenase, and nifY, whose product is involved in nitrogenase maturation. It is, therefore, a reasonable hypothesis that the NifT protein might also have a role in the maturation of nitrogenase. However, the phenotypic characterization of nifT and nifT-overexpressing strains for effects on the regulation, maturation, and activity of nitrogenase identified no properties that were distinct from those of the wild type. We conclude that the K. pneumoniae NifT protein is not essential for nitrogen fixation under the conditions examined.
Improvement in the uniformity and the thermal stability of Hf-silicate gate dielectric by plasma-nitridation (2003)

In this study, we used HfSiO/sub x/ with Hf concentration of 60% in order to obtain a EOT less than 1.5nm, and the influence of nitrogen concentration on the electrical properties was examined.
Restoration of competency to stand trial: a training program for persons with mental retardation. (2003)

This article describes the development and use of a formal training tool for restoration of competency in clients with mental retardation who are incompetent to stand trial. The program was developed at Eleanor Slater Hospital within the Rhode Island Department of Mental Health, Retardation and Hospitals. This article describes the development of The Slater Method, the training tool format, the procedure for use of the Slater Method, and the duration of treatment to restore competency to stand trial in clients with mental retardation. Although the developmentally disabled population is not limited to persons with mental retardation, we have used the phrase mental retardation instead of developmentally disabled because the judicial system more commonly uses mental retardation.
Clinical Experience With Gabapentin in Patients With Bipolar or Schizoaffective Disorder (1999)

Gabapentin was effective in the treatment of mania and hypomania in patients with bipolar and schizoaffective disorders. If confirmed in controlled studies, these findings suggest that gabapentin represents a well-tolerated, rapidly acting antimanic agent.
Decellularization and Recellularization of Rat Livers With Hepatocytes and Endothelial Progenitor Cells (2015)

Whole-organ decellularization has been identified as a promising choice for tissue engineering. The aim of the present study was to engineer intact whole rat liver scaffolds and repopulate them with hepatocytes and endothelial progenitor cells (EPCs) in a bioreactor. Decellularized liver scaffolds were obtained by perfusing Triton X-100 with ammonium hydroxide. The architecture and composition of the original extracellular matrix were preserved, as confirmed by morphologic, histological, and immunolabeling methods. To determine biocompatibility, the scaffold was embedded in the subcutaneous adipose layer of the back of a heterologous animal to observe the infiltration of inflammatory cells. Hepatocytes were reseeded using a parenchymal injection method and cultured by continuous perfusion. EPCs were reseeded using a portal vein infusion method. Morphologic and functional examination showed that the hepatocytes and EPCs grew well in the scaffold. The present study describes an effective method of decellularization and recellularization of rat livers, providing the foundation for liver engineering and the development of bioartificial livers.
PLuTo: A Practical and Fully Automatic Polyhedral Program Optimization System (2015)

We present the design and implementation of a fully automatic polyhedral source-to-source transformation framework that can optimize regular programs (sequences of possibly imperfectly nested loops) for parallelism and locality simultaneously. Through this work, we show the practicality of analytical model-driven automatic transformation in the polyhedral model – far beyond what is possible by current production compilers. Unlike previous works, our approach is an end-to-end fully automatic one driven by an integer linear optimization framework that takes an explicit view of finding good ways of tiling for parallelism and locality using affine transformations. We also address generation of tiled code for multiple statement domains of arbitrary dimensionalities under (statement-wise) affine transformations – an issue that has not been addressed previously. Experimental results from the implemented system show very high speedups for local and parallel execution on multi-cores over state-of-the-art compiler frameworks from the research community as well as the best native compilers. The system also enables the easy use of powerful empirical/iterative optimization for general arbitrarily nested loop sequences.
Stat 6-Dependent Induction of Myeloid Derived Suppressor Cells After Physical Injury Regulates Nitric Oxide Response to Endotoxin (2009)

This study shows that induction of CD11b+/Gr1+ cells after physical injury play an essential role in the regulation of nitric oxide production after a septic challenge. The accumulation and induction of arginase 1 in TIMSC is Th2 cytokine dependent. To our knowledge, the role of TIMSC in the regulation of nitric oxide is a novel finding. This observation adds to the possibility that TIMSC could play an important role in immunosuppression observed after physical injury.
Characterization of d‐boroAla as a Novel Broad‐Spectrum Antibacterial Agent Targeting d‐Ala‐d‐Ala Ligase (2011)

d-boroAla was previously characterized as an inhibitor of bacterial alanine racemase and d-Ala-d-Ala ligase enzymes (Biochemistry, 28, 1989, 3541). In this study, d-boroAla was identified and characterized as an antibacterial agent. d-boroAla has activity against both Gram-positive and Gram-negative organisms, with minimal inhibitory concentrations down to 8 μg / mL. A structure-function study on the alkyl side chain (NH(2) -CHR-B(OR')(2) ) revealed that d-boroAla is the most effective agent in a series including boroGly, d-boroHomoAla, and d-boroVal. l-boroAla was much less active, and N-acetylation completely abolished activity. An LC-MS / MS assay was used to demonstrate that d-boroAla exerts its antibacterial activity by inhibition of d-Ala-d-Ala ligase. d-boroAla is bactericidal at 1× minimal inhibitory concentration against Staphylococcus aureus and Bacillus subtilis, which each encode one copy of d-Ala-d-Ala ligase, and at 4× minimal inhibitory concentration against Escherichia coli and Salmonella enterica serovar Typhimurium, which each encode two copies of d-Ala-d-Ala ligase. d-boroAla demonstrated a frequency of resistance of 8 × 10(-8) at 4× minimal inhibitory concentration in S. aureus. These results demonstrate that d-boroAla has promising antibacterial activity and could serve as the lead agent in a new class of d-Ala-d-Ala ligase targeted antibacterial agents. This study also demonstrates d-boroAla as a possible probe for d-Ala-d-Ala ligase function.
Application of the Three-Dimensional Structures of Protein Target Molecules in Structure-Based Drug Design (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplication of the Three-Dimensional Structures of Protein Target Molecules in Structure-Based Drug DesignJonathan Greer, John W. Erickson, John J. Baldwin, and Michael D. VarneyCite this: J. Med. Chem. 1994, 37, 8, 1035–1054Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/jm00034a001https://doi.org/10.1021/jm00034a001research-articleACS PublicationsRequest reuse permissionsArticle Views2143Altmetric-Citations225LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effects of Intracoronary Radiation on Thrombosis After Balloon Overstretch Injury in the Porcine Model (1999)

These results suggest that IR induces thrombosis but does not necessarily compromise the lumen. Strategies for reducing TR may further decrease intimal area as well as increasing the safety of this therapy.
Efficacy of L-ornithine-L-aspartate as an adjuvant therapy in cirrhotic patients with hepatic encephalopathy. (2011)

In cirrhotic patients with advanced hepatic encephalopathy treatment with LOLA was safe and associated with relatively rapid improvement and shorter hospital stay.
Development of type 2 diabetes following intrauterine growth retardation in rats is associated with progressive epigenetic silencing of Pdx1 (2008)

Intrauterine growth retardation (IUGR) has been linked to the onset of diseases in adulthood, including type 2 diabetes, and has been proposed to result from altered gene regulation patterns due to epigenetic modifications of developmental genes. To determine whether epigenetic modifications may play a role in the development of adult diabetes following IUGR, we used a rodent model of IUGR that expresses lower levels of Pdx1, a pancreatic and duodenal homeobox 1 transcription factor critical for beta cell function and development, which develops diabetes in adulthood. We found that expression of Pdx1 was permanently reduced in IUGR beta cells and underwent epigenetic modifications throughout development. The fetal IUGR state was characterized by loss of USF-1 binding at the proximal promoter of Pdx1, recruitment of the histone deacetylase 1 (HDAC1) and the corepressor Sin3A, and deacetylation of histones H3 and H4. Following birth, histone 3 lysine 4 (H3K4) was demethylated and histone 3 lysine 9 (H3K9) was methylated. During the neonatal period, these epigenetic changes and the reduction in Pdx1 expression could be reversed by HDAC inhibition. After the onset of diabetes in adulthood, the CpG island in the proximal promoter was methylated, resulting in permanent silencing of the Pdx1 locus. These results provide insight into the development of type 2 diabetes following IUGR and we believe they are the first to describe the ontogeny of chromatin remodeling in vivo from the fetus to the onset of disease in adulthood.
Ubiquitin Homeostasis Is Critical for Synaptic Development and Function (2011)

The ubiquitin-proteasome system (UPS) controls protein abundance and is essential for many aspects of neuronal function. In ataxia (ax(J)) mice, profound neurological and synaptic defects result from a loss-of-function mutation in the proteasome-associated deubiquitinating enzyme Usp14, which is required for recycling ubiquitin from proteasomal substrates. Here, we show that transgenic complementation of ax(J) mice with neuronally expressed ubiquitin prevents early postnatal lethality, restores muscle mass, and corrects developmental and functional deficits resulting from the loss of Usp14, demonstrating that ubiquitin deficiency is a major cause of the neurological defects observed in the ax(J) mice. We also show that proteasome components are normally induced during the first 2 weeks of postnatal development, which coincides with dramatic alterations in polyubiquitin chain formation. These data demonstrate a critical role for ubiquitin homeostasis in synaptic development and function, and show that ubiquitin deficiency may contribute to diseases characterized by synaptic dysfunction.
Genetically Encoded Synthesis of Protein-Based Polymers with Precisely Specified Molecular Weight and Sequence by Recursive Directional Ligation:  Examples from the Elastin-like Polypeptide System (2002)

We report a new strategy for the synthesis of genes encoding repetitive, protein-based polymers of specified sequence, chain length, and architecture. In this stepwise approach, which we term "recursive directional ligation" (RDL), short gene segments are seamlessly combined in tandem using recombinant DNA techniques. The resulting larger genes can then be recursively combined until a gene of a desired length is obtained. This approach is modular and can be used to combine genes encoding different polypeptide sequences. We used this method to synthesize three different libraries of elastin-like polypeptides (ELPs); each library encodes a unique ELP sequence with systematically varied molecular weights. We also combined two of these sequences to produce a block copolymer. Because the thermal properties of ELPs depend on their sequence and chain length, the synthesis of these polypeptides provides an example of the importance of precise control over these parameters that is afforded by RDL.
Quality Control Mechanisms During Translation (1999)

Translation uses the genetic information in messenger RNA (mRNA) to synthesize proteins. Transfer RNAs (tRNAs) are charged with an amino acid and brought to the ribosome, where they are paired with the corresponding trinucleotide codon in mRNA. The amino acid is attached to the nascent polypeptide and the ribosome moves on to the next codon. The cycle is then repeated to produce a full-length protein. Proofreading and editing processes are used throughout protein synthesis to ensure the faithful translation of genetic information. The maturation of tRNAs and mRNAs is monitored, as is the identity of amino acids attached to tRNAs. Accuracy is further enhanced during the selection of aminoacyl-tRNAs on the ribosome and their base pairing with mRNA. Recent studies have begun to reveal the molecular mechanisms underpinning quality control and go some way to explaining the phenomenal accuracy of translation first observed over three decades ago.