gebhart/patrepeval huggingface dataset:
Primary Amyloidosis: A Rare Cause of Cholestatic Liver Disease (2011)

Purpose: Amyloidosis is a series of diseases that occur following alterations in protein folding that result in the eventual deposition of insoluble amyloid fibrils in extracellular spaces and soft tissue. The disease is classified by the composition of the protein involved, with the most common type being Primary Amyloidosis (AL). The fibrils are monoclonal immunoglobulin light chains (κ or λ) with this type. The liver is a common site of deposition, however the development of clinically significant disease is rare. A 75 year-old man presented with a six week history of worsening jaundice. The patient denied any associated abdominal pain, fever, nausea or vomiting, but did report anorexia and a 30 lbs. weight loss over the previous six months. He had a history of end-stage renal disease requiring peritoneal dialysis for the previous four years. He denied history of prior inflammatory or autoimmune disease. The patient had been evaluated six months prior to presentation for worsening renal function at an outside facility with a renal biopsy that demonstrated amyloid infiltration. Urine and serum protein electrophoresis (UPEP/SPEP) were performed at that time and were negative. On physical exam, scleral icterus was present and his abdomen was benign. Laboratory evaluation showed elevated total bilirubin of 9.9 mg/dL and alkaline phosphatase of 888 IU/L. Transaminase levels showed AST of 84 IU/L and ALT of 47 IU/L. Albumin was 2.3 g/dL and coagulation profile was normal. BUN and creatinine were abnormal at 37 mg/dL and 4.48 mg/dL, respectively. ESR was 13 mm/hr. Ferritin was elevated at 1204 ng/ml. Viral hepatitis panel and ANA were negative. Ferritin was elevated at 1204. CA19-9 was elevated at 392 U/mL with a normal AFP of 2.0 IU/mL. Imaging including abdominal ultrasound, contrast CT scan and MRCP. Collectively these studies found splenomegaly and hepatomegaly without dilation of the hepatic or biliary ducts. Wedge biopsy of the liver was performed. Biopsy results showed staining and polarization with Congo red consistent with amyloidosis. The hepatic architecture was distorted by amyloid deposition, however the portal tracts showed intact bile ducts. No findings suggested other causes of liver disease or cholestasis. Immunohistologic staining was nonspecific for immunoglobulin light chains. Repeat SPEP/UPEP showed minor nonspecific findings without identification of monoclonal paraproteins. Taking into account the previous renal biopsy and new hepatic involvement, a diagnosis of probable systemic amyloidosis was made. This case illustrates hepatic amyloid deposition as a rare cause of cholestatic liver disease.
<i>In Vitro </i>and <i>In Vivo </i>Results of Brodimoprim and Analogues Alone and in Combination against <i>E. coli </i>and Mycobacteria (1993)

New diaminodiphenylsulfone inhibitors of dihydropteroate synthase are described with increased inhibitory activity against mycobacteria and plasmodia, whereas their side effect of methemoglobin formation could be suppressed. The optimization of diaminobenzylpyrimidines, inhibitors of dihydrofolate reductase, led to derivatives with increased inhibitory effect against mycobacteria, especially M. leprae and plasmodia. Some of these derivatives show autosynergism. Finally the combination of brodimoprim (BDP) and dapsone (DDS) was developed for the treatment of leprosy. First clinical trials in Paraguay and Ethiopia show that combinations of BDP/DDS and BDP/DDS plus rifampicin were highly effective and may become an alternative multi-drug therapy for the treatment of leprosy. The tolerance of the regimens used was generally good.
Understanding Unequal Gender Classification Accuracy from Face Images (2018)

Recent work shows unequal performance of commercial face classification services in the gender classification task across intersectional groups defined by skin type and gender. Accuracy on dark-skinned females is significantly worse than on any other group. In this paper, we conduct several analyses to try to uncover the reason for this gap. The main finding, perhaps surprisingly, is that skin type is not the driver. This conclusion is reached via stability experiments that vary an image's skin type via color-theoretic methods, namely luminance mode-shift and optimal transport. A second suspect, hair length, is also shown not to be the driver via experiments on face images cropped to exclude the hair. Finally, using contrastive post-hoc explanation techniques for neural networks, we bring forth evidence suggesting that differences in lip, eye and cheek structure across ethnicity lead to the differences. Further, lip and eye makeup are seen as strong predictors for a female face, which is a troubling propagation of a gender stereotype.
A Gamified Mobile System for Crowdsourcing Video for Autism Research (2018)

Autism Spectrum Disorder (ASD) is a condition affecting 70 million children worldwide. Due to delays in diagnosis and imbalances in coverage, it is necessary to develop new methods of care delivery for use outside of clinical settings., We present a mobile charades-style game, Guess What?, used for acquisition of structured video from children with ASD for behavioral disease research. By analyzing facial affect in response to various prompts, we demonstrate that engagement and facial affect can be quantified and measured using real-time image processing algorithms: an important step for future therapies, diagnostics, and outcome measures based on home video. Our study of thirteen subjects reveals that game sessions displaying "faces" to the player produced the most emotive facial expressions in the player by a considerable margin. Videos from the younger neurotypical group contained 73.9% more frames with emotion in this category, compared to the older group with ASD. Moreover, results from all categories indicated 20.7% less facial engagement among older children with ASD compared to younger children with no diagnosis.
Preliminary vibration and flutter studies on P-47 tail (1943)

Report presenting a report illustrated by photographs and vibration records on the failure of the P-47 rudder in the high-speed tunnel at a true speed of 468 miles per hour and a density corresponding to 9000 feet altitude. The fin-rudder unit was tested as being at least representative of the tail design of the P-47 airplane.
QUANTIFICATION OF BABOON THYMOPOIESIS IN PORCINE THYMOKIDNEY XENOGRAFTS BY A SIGNAL JOINING TCR EXCISION CIRCLE (SJTREC) ASSAY (2010)

Tena, A.; Vallabhajousula, P.; Hawley, R. J.; Griesemer, A.; Yamada, K.; Sachs, D. H. Author Information
Unsupervised feature optimization (UFO): Simultaneous selection of multiple features with their detection parameters (2009)

Class learning, both supervised and unsupervised, requires feature selection, which includes two main components. The first is the selection of a discriminative subset of features from a larger pool. The second is the selection of detection parameters for each feature to optimize classification performance. In this paper we present a method for the discovery of multiple classification features, their detection parameters and their consistent configurations, in the fully unsupervised setting. This is achieved by a global optimization of joint consistency between the features as a function of the detection parameters, without assuming any prior parametric model. We demonstrate how the proposed framework can be applied for learning different types of feature parameters, such as detection thresholds and geometric relations, resulting in the unsupervised discovery of informative configurations of objects parts. We test our approach on a wide range of classes and show good results. We also demonstrate how the approach can be used to unsupervisedly separate and learn visually similar sub-classes of a single category, such as facial views or hand poses. We use the approach to compare various criteria for feature consistency, including Mutual Information, Suspicious Coincidence, L2 and Jaccard index. Finally, we compare our approach to aparametric consistency optimization technique such as pLSA and show significantly better performance.
Heterochromatin-Like Regions as Ecological Niches for Avirulence Genes in the <i>Leptosphaeria maculans</i> Genome: Map-Based Cloning of <i>AvrLm6</i> (2007)

Map-based cloning of avirulence genes of the AvrLml-2-6 cluster was recently undertaken in Leptosphaeria maculans and led to the identification of AvrLm1. The ensuing chromosome walk toward AvrLm6 resulted in the delineation of a 562-kb bacterial artificial chromosome (BAC) clone contig in an avirulent isolate. Following sequencing of the contig and sequence comparison with a virulent isolate, four AvrLm6 candidate genes were identified. Complementation of the virulent isolate with the four candidates was performed and one gene was found to fully restore the avirulent phenotype on Rlm6 oilseed rape genotypes. AvrLm6 was found to be located in the same genome context as AvrLml, because it is a solo gene surrounded by 85 and 48 kb of degenerated repeats on its 5' and 3' sides, respectively. AvrLm6 is an orphan gene encoding a small, potentially secreted, cysteine-rich protein. Comparison of AvrLm1 and AvrLm6 expressions by quantitative reverse-transcription polymerase chain reaction revealed that both genes are highly overexpressed during primary leaf infection. Using RNA interference, decreasing expression of AvrLm6 was shown to result in virulence toward Rlm6 genotypes whenever the expression was reduced by more than 60% compared with the wild-type isolate.
The expanding indications for virtual histology intravascular ultrasound for plaque analysis prior to carotid stenting. (2008)

Complications of carotid artery stenting (CAS), including stroke, remain relatively high when compared with carotid endarterectomy (CEA). Current selection criteria for patients undergoing CAS are based predominately on surgical risk related to other comorbidities. Little attention is given to the morphology of the atherosclerotic plaque, although studies have shown that extensive variability exists which confers certain risks for plaque vulnerability. Virtual Histology intravascular ultrasound (VH IVUS) offers a unique method of assessing plaque morphology prior to CAS. Herein, the authors review the concepts of atherosclerotic plaque morphology and discuss the background of VH IVUS and illustrate its use in the carotid system. With selection of the appropriate patient and the appropriate plaque, more favorable outcomes of CAS may be achieved which will solidify its place as a frontline treatment of carotid vascular disease.
Heat-killed body of lactobacillus brevis SBC8803 ameliorates intestinal injury in a murine model of colitis by enhancing the intestinal barrier function (2011)

The administration of heat-killed L. brevis SBC8803 helps to successfully maintain intestinal homeostasis, while also curing intestinal inflammation. A therapeutic strategy using heat-killed bacteria is expected to be beneficial for human health even in conditions unsuitable for live probiotics because the heat-killed body is able to exhibit its effects without the requirement of colonization.
DNA micro-array-based identification of bile-responsive genes in Lactobacillus plantarum (2006)

The data presented here provide valuable clues towards the defence mechanisms that play a role during bile stress in Lact. plantarum.
Surface properties and catalytic activity of a Mo-fixed catalyst. Structure of the active site and mechanism for selective oxidation of ethyl alcohol (1978)

The physico-chemical properties of the surface of a Mo-fixed catalyst obtained by a ready reaction between Mo(π-C3H5)4 and surface OH groups of SiO2 were investigated by X-ray photoelectron spectroscopy, photoluminescence technique, u.v. diffuse reflectance spectroscopy, i.r. spectrometry and H2/O2 uptake. The difference between the surface properties of the fixed catalyst and the conventional impregnation catalyst is discussed. The Mo-fixed catalyst showed higher activity and selectivity than the conventional impregnation catalyst in the ethyl alcohol oxidation. Selective oxidation to form acetaldehyde proceeded by a two-stage redox (Mo6+⇌ Mo4+) mechanism. Coordinatively unsaturated dioxomolybdenum of uniform nature in a tetrahedral coordination is the active species in the selective oxidation of ethyl alcohol.
Characterizing process variation in nanometer CMOS (2007)

The correlation of a statistical analysis tool to hardware depends on the accuracy of underlying variation models. The models should represent actual process behavior as measured in silicon. In this paper, we present an overview of test structures for characterizing statistical variation of process parameters. We discuss the test structure design and characterization strategy for calibrating random and layout dependent systematic components of process variation. We also show measurement results from several fabricated structures in 65-nm CMOS technologies.
Transcriptional Regulation of <i>CD1D1</i> by Ets Family Transcription Factors (2005)

CD1 molecules are MHC class I-like glycoproteins specialized in presenting lipid/glycolipid Ags to T cells. The distinct cell-type specific expression of CD1D1 plays an important role in the development and function of NKT cells, a unique subset of immunoregulatory T cells. However, the mechanisms regulating CD1D1 expression are largely unknown. In this study, we have characterized the upstream region of the CD1D1 gene and identified a minimal promoter region within 200 bp from the translational start site of CD1D1 that exhibits cell-type specific promoter activity. Analysis of this region revealed an Ets binding site critical for CD1D1 promoter activity. Gel shift assays and chromatin immunoprecipitation experiments showed that Elf-1 and PU.1 bind to the CD1D1 promoter. Furthermore, we found that gene disruption of Elf-1 resulted in decreased CD1D1 expression on B cells but not other cell types, whereas conditional activation of PU.1 negatively regulated CD1D1 expression in PU.1-deficient myeloid cells. These findings are the first to demonstrate that Ets proteins are involved in the transcriptional regulation of CD1D1 and that they may function uniquely in different cell types.
Implementing real time packet forwarding policies using streams (1995)

This paper describes an implementation of the class based queueing (CBQ) mechanisms proposed by Sally Floyd and Van Jacobson [1] [2] to provide real time policies for packet forwarding. CBQ allows the flows sharing a data link to be guaranteed a share of the bandwidth when the link is congested yet allows flexible sharing of the unused bandwidth when the link is unloaded. In addition, it provides mechanisms which give flows requiring low delay priority over other flows. In this way, links can be shared by multiple flows yet still meet the policy and Quality of Service (QoS) requirements of the flows. We present a brief description of the implementation and some preliminary performance measurements. The problems of packet classification are addressed in a flexible and extensible yet efficient manner, and whilst the Streams implementation cannot cope with very high speed interfaces, it can cope with the serial link speeds that are likely to be loaded.
Trigonal level splittings of chromium(3+)-doped sodium magnesium tris(oxalato)aluminate octahydrate single crystals (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTrigonal level splittings of chromium(3+)-doped sodium magnesium tris(oxalato)aluminate octahydrate single crystalsT. Schoenherr, J. Spanier, and H. H. SchmidtkeCite this: J. Phys. Chem. 1989, 93, 16, 5969–5972Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://pubs.acs.org/doi/10.1021/j100353a006https://doi.org/10.1021/j100353a006research-articleACS PublicationsRequest reuse permissionsArticle Views153Altmetric-Citations20LEARN 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 options Get e-Alerts
Influence of lactose hydrolysis and solids concentration on alcohol production by yeast in acid whey ultrafiltrate (1977)

Abstract Alcohol yields of 6.5% were obtained with Saccharomyces cerevisiae in lactasehydrolyzed acid whey permeate containing 30–35% total solids. Maximum alcohol yields obtained with Kluyveromyces fragilis were 4.5% in lactase‐hydrolyzed acid whey permeate at a solids concentration of 20% and 3.7% in normal permeate at a solids concentration of 10%. Saccharomyces cerevisiae efficiently converted the glucose present in lactase‐hydrolyzed whey permeates containing 5–30% total solids (2–13% glucose) to alcohol. However, the galactose, which comprised about half the available carbohydrate in lactase‐hydrolyzed whey, was not utilized by S. cerevisiae , so that even though alcohol yields were higher when this organism was used, the process was wasteful in that a substantial proportion of the substrate was not fermented. For the process to become commercially feasible, an efficient means of rapidly converting both the galactose and glucose to alcohol must be found.
Vivid Memories of Sercarz's Traineeship and Am Indebted to Him for My Professional Career (2020)

I am writing this chapter to reflect of my memories spanning at the time that I have first met the late Eli Sercarz and succeeded to earn my PhD degree under his titulage and traineeship. My first experience was at the time when Eli was recruited at UCLA as a new Assistant Professor in Immunology and I was in my undergraduate senior year. His teaching course in Fundamental Immunology was revolutionary at the time as prior teaching in immunology was primarily basic serology. I was mesmerized by the subject and decided that my professional career will be in immunology and received my PhD in Eli's laboratory. My research thesis consisted of two related topics. 1. Characterization of the immunogenic, tolerogenic and cryptic epitopes in selectively fragmented hen egg-white lysozyme (HEL) peptide fragments. 2. Analyzing and characterizing human and rabbit tear lysozymes as well as investigating the transport of various antibody isotypes from the serum to the tear. In addition, isolating and characterizing a novel specific tear prealbumin in the tear. This review describes my journey in Eli Sercarz's laboratory and my sincere indebtness of my academic career which was the result of his input and care.
Anisotropic growth of single-crystal graphite plates by nickel-assisted microwave-plasma chemical-vapor deposition (2000)

Growth of single-crystal graphite free-standing plates has been achieved by a microwavehydrogen-plasma etching of graphite powder and nickel mesh. The plates resemble a knife blade and grow in the 〈11̄00〉 direction with long crystals exceeding 100 μm. Hexagonal growth features at the edges and electron diffraction patterns confirm the single-crystal nature of these ultrathin plates. Electron microprobe and Raman spectroscopy indicate the presence of graphite. Diamond crystals nucleate on these plates and they grow simultaneously. We suggest that the paradoxical growth of graphite in a hydrogen plasma, under conditions in which graphite is usually etched away, is possible because of a protective coating by a Ni–C–H phase. This thin coating allows for transport of carbon atoms from the gas phase to the growing graphite surface.
Measles Virus Hemagglutinin Protein Establishes a Specific Interaction With the Extreme N-Terminal Region of Human Signaling Lymphocytic Activation Molecule to Enhance Infection (2020)

Measles virus (MV) is a human pathogen that is classified in the genus <i>Morbillivirus</i> in the family <i>Paramyxoviridae</i> together with several non-human animal morbilliviruses. They cause severe systemic infections by using signaling lymphocytic activation molecule (SLAM) and poliovirus receptor-like 4 expressed on immune and epithelial cells, respectively, as receptors. The viral hemagglutinin (H) protein is responsible for the receptor-binding. Previously determined structures of MV-H and SLAM complexes revealed a major binding interface between the SLAM V domain and MV-H with four binding components (sites 1-4) in the interface. We studied the MV-H and human SLAM (hSLAM) complex structure in further detail by <i>in silico</i> analyses and determined missing regions or residues in the previously determined complex structures. These analyses showed that, in addition to sites 1-4, MV-H establishes a unique interaction with the extreme N-terminal region (ExNTR) of hSLAM. The first principles calculation-based fragment molecular orbital computation method revealed that methionine at position 29 (hSLAM-Met29) is the key residue for the interaction. hSLAM-Met29 was predicted to establish a CH-π interaction with phenylalanine at position 549 of MV-H (MVH-Phe549). A cell-cell fusion assay showed that the hSLAM-Met29 and MVH-Phe549 interaction is important for hSLAM-dependent MV membrane fusion. Furthermore, Jurkat cell lines expressing hSLAM with or without Met29 and recombinant MV possessing the H protein with or without Phe549 showed that the hSLAM-Met29 and MVH-Phe549 interaction enhanced hSLAM-dependent MV infection by ~10-fold. We speculate that in the evolutionary history of morbilliviruses, this interaction may have contributed to MV adaptation to humans because this interaction is unique for MV and only MV uses hSLAM efficiently among morbilliviruses.
Structure and Dynamics of the Lantibiotic Mutacin 1140 (2003)

Mutacin 1140 is a member of a family of ribosomally synthesized peptide bacteriocins called lantibiotics (lanthionine-containing antibiotics) and is produced by the Gram-positive bacterium Streptococcus mutans. Mutacin 1140 has been shown to be effective against a broad array of Gram-positive bacteria. Chromatography and mass spectroscopy data suggested that mutacin 1140 forms a small compact structure. Nuclear magnetic resonance (NMR) data and restrained molecular dynamics simulations showed that mutacin 1140 interconverts between multiple structures. Calculations of scalar (J) coupling constants showed the best agreement with experimental values when the entire population-weighted ensemble of structures was used, providing independent support for the ensemble. Representative structures from each major group in the ensemble had a common feature in which they are all kinked around the hinge region forming a horseshoe-like shape, and the regions of flexibility of the molecule were limited and well-defined. The structures determined in this study provide a starting point for modeling the mutacin 1140-membrane interactions and pore formation.