gebhart/patrepeval huggingface dataset:
Screening for C. elegans male copulation-defective mutants by the mating plug phenotype (2017)

We describe an efficient screen for male mating defective mutants in Caenorhabditis elegans. We report the isolation of 20 alleles that confer specific mating defects. In a previously reported screen (Hajdu-Cronin et al, 2017), we isolated 19 Cod (for copulation defective) strains in which morphologically wild-type males fail to mate. Failure to mate could conceivably result from defects in any step of the mating process: response, turning, vulva location, spicule insertion, and sperm transfer. By observation, we identified mutants defective in each of these steps except for vulva location. We believe that this was due to both redundancy of sensory structures mediating this step and our stringent screening conditions. To address this, we modified the Cod screen, using the strain plg-1(e2001d); him-5(e1490), in which the presence of a copulatory "plug" over the hermaphrodite vulva provides a visible marker for successful mating (Hodgkin and Doniach, 1997). We backcrossed plg-1(e2001d) four times into him-5(e1490) to make strain PS1395, the parent of our initial screen (sy4xx series). We subsequently repeated our screen after re-isolating a plg-1(e2001d); him-5(e1490) strain PS3696 that had consistent mating behavior and brood size (PS3696 is the parental background for the sy6xx series). Since we select for whether males are able to mate with their moving siblings as opposed to paralyzed hermaphrodites, we expected to isolate more subtle Cod mutants (such as incompletely penetrant vulva location defects). The screen would also allow for the identification of plug formation defective and hermaphrodite-specific mating defective strains. In one PS3696 screen, of 1400 F2 clones, 5% were non-Plg, 280 were then examined for behavior; we kept 69 as candidates; eight had strong phenotypes and normal morphology and were given allele names (sy678, sy680, sy681, sy682, sy683, sy684, sy685, and sy678). sy681 turned out to have the same molecular lesion as sy680 and was discarded. Overall, we isolated 20 Cod mutants from several screens including several pilot screens (Table 1). sy671 was isolated in this screen and found to be an allele of unc-18 (Schindelman et al., 2006).
Genetic associations with micronutrient levels identified in immune and gastrointestinal networks (2014)

The discovery of vitamins and clarification of their role in preventing frank essential nutrient deficiencies occurred in the early 1900s. Much vitamin research has understandably focused on public health and the effects of single nutrients to alleviate acute conditions. The physiological processes for maintaining health, however, are complex systems that depend upon interactions between multiple nutrients, environmental factors, and genetic makeup. To analyze the relationship between these factors and nutritional health, data were obtained from an observational, community-based participatory research program of children and teens (age 6-14) enrolled in a summer day camp in the Delta region of Arkansas. Assessments of erythrocyte S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), plasma homocysteine (Hcy) and 6 organic micronutrients (retinol, 25-hydroxy vitamin D3, pyridoxal, thiamin, riboflavin, and vitamin E), and 1,129 plasma proteins were performed at 3 time points in each of 2 years. Genetic makeup was analyzed with 1 M SNP genotyping arrays, and nutrient status was assessed with 24-h dietary intake questionnaires. A pattern of metabolites (met_PC1) that included the ratio of erythrocyte SAM/SAH, Hcy, and 5 vitamins were identified by principal component analysis. Met_PC1 levels were significantly associated with (1) single-nucleotide polymorphisms, (2) levels of plasma proteins, and (3) multilocus genotypes coding for gastrointestinal and immune functions, as identified in a global network of metabolic/protein-protein interactions. Subsequent mining of data from curated pathway, network, and genome-wide association studies identified genetic and functional relationships that may be explained by gene-nutrient interactions. The systems nutrition strategy described here has thus associated a multivariate metabolite pattern in blood with genes involved in immune and gastrointestinal functions.
Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery (2020)

Although the etiology of obesity is not well-understood, genetic, environmental, and microbiome elements are recognized as contributors to this rising pandemic. It is well documented that Roux-en-Y gastric bypass (RYGB) surgery drastically alters the fecal microbiome, but data are sparse on temporal and spatial microbiome and metabolome changes, especially in human populations. We characterized the structure and function (through metabolites) of the microbial communities in the gut lumen and structure of microbial communities on mucosal surfaces in nine morbidly obese individuals before, 6 months, and 12 months after RYGB surgery. Moreover, using a comprehensive multi-omic approach, we compared this longitudinal cohort to a previously studied cross-sectional cohort (n = 24). In addition to the expected weight reduction and improvement in obesity-related comorbidities after RYGB surgery, we observed that the impact of surgery was much greater on fecal communities in comparison to mucosal ones. The changes in the fecal microbiome were linked to increased concentrations of branched-chain fatty acids and an overall decrease in secondary bile acid concentrations. The microbiome and metabolome data sets for this longitudinal cohort strengthen our understanding of the persistent impact of RYGB on the gut microbiome and its metabolism. Our findings highlight the importance of changes in mucosal and fecal microbiomes after RYGB surgery. The spatial modifications in the microbiome after RYGB surgery corresponded to persistent changes in fecal fermentation and bile acid metabolism, both of which are associated with improved metabolic outcomes.
Preoperative superselective arteriolar embolization: a new approach to enhance resectability of spinal tumors. (1990)

The extent of surgical resection of spinal tumors is frequently limited by blood loss and technical difficulty associated with the vascularity of the tumors. We report here the use of superselective percutaneous arterial embolization to reduce the rate of blood loss at the time of surgical resection and enhance resectability. The types of tumors treated were metastatic renal carcinoma, metastatic thyroid carcinoma, metastatic melanoma, and giant cell tumor of the sacrum. Two of the patients required repeated embolization and surgery for recurrent symptoms. The estimated blood loss in seven of nine procedures performed on the six patients ranged from 300 to 800 ml, after which no transfusion was required. In two procedures, extensive resection of very large tumors resulted in larger losses of blood, and postoperative transfusion was necessary. No significant complications of embolization or surgery occurred. A key factor in our embolization technique is the use of microfibrillar collagen, which allows occlusion of tumor vessels as small as 20 microns and may prevent reconstitution of the embolized vessels by collateral flow. We conclude that preoperative arterial embolization enhances the resectability of a variety of spinal tumors by reducing intraoperative blood loss. This may provide an additional benefit by reducing the risk related to postoperative transfusion. By permitting a more aggressive surgical approach, the use of preoperative embolization also has the potential to improve outcome in patients with spinal tumors.
Safety and serum distribution of anti-SARS-CoV-2 monoclonal antibody MAD0004J08 after intramuscular injection (2022)

The emerging threat represented by SARS-CoV-2 variants, demands the development of therapies for better clinical management of COVID-19. MAD0004J08 is a potent Fc-engineered monoclonal antibody (mAb) able to neutralize in vitro all current SARS-CoV-2 variants of concern (VoCs) including the omicron variant even if with significantly reduced potency. Here we evaluated data obtained from the first 30 days of a phase 1 clinical study (EudraCT N.: 2020-005469-15 and ClinicalTrials.gov Identifier: NCT04932850). The primary endpoint evaluated the percentage of severe adverse events. Secondary endpoints evaluated pharmacokinetic and serum neutralization titers. A single dose administration of MAD0004J08 via intramuscular (i.m.) route is safe and well tolerated, resulting in rapid serum distribution and sera neutralizing titers higher than COVID-19 convalescent and vaccinated subjects. A single dose administration of MAD0004J08 is also sufficient to effectively neutralize major SARS-CoV-2 variants of concern (alpha, beta, gamma and delta). MAD0004J08 can be a major advancement in the prophylaxis and clinical management of COVID-19.
Attosecond Transient Absorption Spectroscopy for Real-Time Observation of Valence Electron Motion (2010)

Combining attosecond technology and x-ray absorption spectroscopy further expands the horizon of attosecond science. In a proof-of-principle experiment we traced valence electron motion in real time and completely reconstructed the strong-field initiated spin-orbit wavepacket coherence.
Synthesis of New and Potent Analogues of anti‐Tuberculosis Agent 5‐Nitro‐furan‐2‐carboxylic Acid 4‐(4‐Benzyl‐piperazin‐1‐yl)‐benzylamide with Improved Bioavailability. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Mild heat shock induces cyclin D1 synthesis through multiple Ras signal pathways (2002)

Hyperthermia such as that occurring during fever may improve cell survival during infection, although its mechanism of action is largely unknown. Here we show that acute exposure to mild, but not severe, heat shock induces the synthesis of cyclin D1 that plays a critical role(s) in G1 progression of the cell cycle. This induction seemed to be regulated through multiple Ras signal pathways involving extracellular signal-regulated kinase, phosphatidylinositol 3-kinase, and Rac1/NADPH oxidase, all of which have well been documented to be responsible for growth factor-induced cyclin D1 expression. In a physiological sense, mild heat shock may regulate cell proliferation through inducing cyclin D1 along with growth factors.
Apoptotic degeneration induction in retinal cells by acute ocular hypertension and neuroprotection by troxolol (1999)

Summary The effects of acute experimental ocular hypertension on retinal cells have been studied. IOP levels and degree of cell damage have been evaluated by cytochemical and DNA analysis, by which the degeneration, necrotic and apoptotic modalities were observed. Possible pharmacological approaches, e.g. neuroprotection with troxol, have been determined for the prevention of the degenerative events that may be ascribed, at least in part, to oxidizing processes.
Baseline Acute Myeloid Leukemia Prognosis Models using Transcriptomic and Clinical Profiles by Studying the Impacts of Dimensionality Reductions and Gene Signatures on Cox-Proportional Hazard (2022)

Abstract Gene marker extraction to evaluate risk in cancer can refine the diagnosis process and lead to adapted therapies and better survival. These survival analyses can be done through computer systems and Machine Learning (ML) algorithms such as the Cox-Proportional-Hazard model from gene expression (GE) RNA-Seq data. However, optimal tuning of CPH from genome-wide GE data is challenging and poorly assessed so far. In this work we propose to interrogate an Acute Myeloid Leukemia (AML) dataset (Leucegene) to derive key components of the CPH driving down its performance and discovering its sensitivity to various factors in hoping to ameliorate the system. In this study, we compare the projection and selection data reduction techniques, mainly the PCA and LSC17 gene signature in combination with the CPH in a ML framework. Results reveals that CPH performs better with a combination of clinical and genetic expression features. We determine that projections performs better than selections without clinical information. We ascertain that CPH is affected by overfitting and that this overfitting is linked to the number and the content of input covariables. We show that PCA links clinical features via ability to learn from the input data directly and generalizes better than LSC17 on Leucegene. We postulate that projection are preferred than selection on harder task such as assessing risk in the intermediate subset of Leucegene. We extrapolate that these findings apply in the more general context of risk detection via machine learning in cancer. We see that higher capacity models such as CPH-DNNs systems can be improved via survival-derived projections and combat overfitting through heavy regularization. Author summary This study aims to investigate the feasibility of using gene expression to evaluate risk in cancer, and to compare the projection and selection data reduction techniques. The study used the Leucegene dataset to compare the PCA method and a previously published 17 genes signature in combination with the Cox-Proportional-Hazard model in a machine learning framework. Results showed that CPH was affected by overfitting and that this overfitting was linked to the number and the content of input covariables. The study found that PCA links clinical features via ability to learn from the input data directly and generalizes better than LSC17 on Leucegene. The study concluded that projections are preferred than selection on harder task such as assessing risk in the intermediate subset of Leucegene and can be tuned to improve their performance. Data availability statement Source code for pipelines and algorithms, as well as gene expression matrices, are available here: https://github.com/lemieux-lab/dimensions_coxph . Access to the Leucegene cohort’s survival times can be granted upon request and following ethical review.
A multi-campus virtual corporate laboratory (2000)

The US Semiconductor Industries Association, Semiconductor Equipment Manufacturing Institute and Department of Defense have jointly established a pioneering new long range research effort identified as the Focus Center Research Program (FCRP). In late 1998 the Interconnect Focus Center (IFC) was established at MIT, Stanford University, Rensselaer Polytechnic Institute, State University of New York at Albany, Cornell University and Georgia Institute of Technology (GIT) with GIT serving as the prime contracting university. The overarching goal of the IFC is to discover and invent new solutions that will enable the US semiconductor industry to transcend known limits on interconnections (between billions of transistors in a single silicon microchip) that would otherwise decelerate or halt the historical rate of progress of semiconductor technology.
Acoustic super models for large scale video event detection (2011)

Given the exponential growth of videos published on the Internet, mechanisms for clustering, searching, and browsing large numbers of videos have become a major research area. More importantly, there is a demand for event detectors that go beyond the simple finding of objects but rather detect more abstract concepts, such as "feeding an animal" or a "wedding ceremony". This article presents an approach for event classification that enables searching for arbitrary events, including more abstract concepts, in found video collections based on the analysis of the audio track. The approach does not rely on speech processing, and is language-indepent, instead it generates models for a set of example query videos using a mixture of two types of audio features: Linear-Frequency Cepstral Coefficients and Modulation Spectrogram Features. This approach can be used in complement with video analysis and requires no domain specific tagging. Application of the approach to the TRECVid MED 2011 development set, which consists of more than 4000 random "wild" videos from the Internet, has shown a detection accuracy of 64% including those videos which do not contain an audio track.
<title>Experiments on jet array cooling modules for high heat flux removal</title> (1997)

Experimental studies of impinging liquid jet-array cooling modules are described. Heat fluxes have reached 7.2 MW/m<SUP>2</SUP> over an area of 10.3 cm<SUP>2</SUP>. Heat loads are applied to a metallic faceplate by a plasma-sprayed resistance heater. Faceplates are a few millimeters thick and area made from either copper or molybdenum alloys. The faceplate is cooled by an array of 14 small diameter water jets operating at speeds of 46 m/s. Cooling is believed to be entirely convective, without boiling. The construction of the plasma sprayed heaters presents several challenges, including unpredictable thermal and electrical properties, high thermal resistances, and fracture at high temperatures. Thermal resistances are quantified and our experience with the heaters is described.
SPRNG: A SCALABLE LIBRARY FOR PSEUDORANDOM NUMBER GENERATION (1999)

. In this article we outline some methods for parallel pseudorandom number generation. We will focus on methods based on parameterization, meaning that we will not consider splitting methods. We describe parameterized versions of the following pseudorandom number generators: (i) linear congruential generators, (ii) shift-register generators, and (iii) lagged-Fibonacci generators. We briefly describe the methods, detail some advantages and disadvantages of each method and recount results from number theory that impact our understanding of their quality in parallel applications. Finally, we present a short description of a scalable library for pseudorandom number generation, called SPRNG. The description contained within this document is meant only to outline the rationale behind and the capabilities of SPRNG. Much more information, including examples and detailed documentation aimed at helping users with putting and using SPRNG on scalable systems is available at the URL: http://www.ncs...
Performance analysis of the scalable video coding standard (2007)

The emerging Scalable Video Coding extends the H.264/AVC video coding standard with new tools designed to efficiently support temporal, spatial and SNR scalability. This paper gives a comprehensive overview of the new features of the SVC standard, providing at the same time an evaluation of their Rate-Distortion performance as well as of the computational complexity.
An Investigation Of Anomalous Scatter From Beryllium Mirrors (1990)

Scatter from Beryllium mirrors often seems to be higher than would be expected based on mirror surface roughness data. This paper verifies the effect and shows that it is more severe in the IR than in the visible. The implication is that the excess scatter is caused by mirror defects that are non-topographic in nature. The conclusion is that profile, or roughness specifications should not be used when low scatter is the requirement of concern.
Publisher Correction: On the issue of transparency and reproducibility in nanomedicine (2019)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Lyophilised Full Spectrum Microbiota Capsules for Treatment of Severe Clostridium difficile Infection in 2 Patients in ICU: A Case Study (2018)

Clostridium difficile infection (CDI) is the most common cause of pseudomembranous colitis and in extreme cases may also result in death. CDI symptoms range in severity from loose stools to severe bloody diarrhoea in conjunction with colonic ulceration and life threatening peritonitis. Encapsulated Lyophilized Fecal Microbiota Transplantation (LFMT) for the treatment of severe CDI has not been used before and we report two such cases admitted to Australian Intensive Care Units (ICU). Patient A: Male patient, age 79 years, diagnosed with CDI Colitis in December 2017 with elevated inflammatory markers, white cell count (WCC) 60, C-reactive protein (CRP) 380. The patient was treated with metronidazole and oral vancomycin. In January 2018, he experienced severe diarrhoea with associated left side abdominal pain and was admitted to ICU for septic shock with presumed pseudomembranous colitis. He was administered 80 LFMT capsules over 7 days. The patient's inflammatory markers were reduced (WCC 14, CRP 105), however abdominal pain and distension continued. Bowel motions improved to formed stool. Stool test for culture and polymerase chain reaction (PCR) for C. difficile toxin was negative. The Patient was able to leave ICU. He later died of unrelated respiratory disease. Patient B: Male patient, age 68 years, was admitted into ICU for non-gastrointestinal related symptoms and developed abdominal distension, bowel dilatation and thickening. He also experienced left sided abdominal tenderness, pain and loose bowel motions. The patient was diagnosed with pseudo-obstruction and CDI colitis. Inflammatory markers were high (WCC 20, CRP 65). He commenced on oral metronidazole and vancomycin followed by 36 LFMT capsules administered over 3 days via nasogastric tube. His bowel motions and abdominal tenderness improved and WCC was reduced to 9. Stool test for culture and PCR for C. difficile toxin was negative. The patient was able to leave ICU but died later due to respiratory illness. Treatment with encapsulated LFMT can eradicate CDI and improve symptoms in patients suffering from severe CDI colitis. More studies are required to examine the efficacy and route of delivery in ICU of FMT for severe CDI.
Cone-beam volumetric CT imagers: simulations for rapid prototype system design and prediciton of image quality (2001)

A framework for rapid and reliable design of Volumetric Computed Tomography (VCT) systems is presented. This work uses detailed system simulation tools to model standard and anthropomorphic phantoms in order to simulate the CT image and choose optimal system specifications. CT systems using small-pitch, 2-D flat area detectors, initially developed for x-ray projection imaging, have been proposed to implement Volume CT for clinical applications. Such systems offer many advantages, but there are also many trade-offs not fully understood that affect image quality. Although many of these effects have been studied in the literature for traditional CT applications, there are unique interactions for very high-resolution flat-panel detectors that are proposed for volumetric CT. To demonstrate the process we describe an example that optimizes the parameters to achieve high detectability for thin slices. The VCT system was modeled over a range of operating parameters, including: tube voltage, tube current, tube focal spot size, detector cell size, number of views, and scintillator thickness. The response surface, which captures the effects of system components on image quality, was calculated. Optimal and robust designs can be achieved by determining an operating point from the response equations, given the constraints. We verify the system design with images from standard and low contrast phantoms. Eventually this design tool could be used, in conjunction with clinical researchers, to specify VCT scanner designs, optimize imaging protocols, and quantify image accuracy and repeatability.