gebhart/patrepeval huggingface dataset:
Transplantation of Human Skin Microbiota in Models of Atopic Dermatitis (2017)

Abstract Atopic dermatitis (AD) is characterized by reduced barrier function, reduced innate immune activation, and susceptibility to Staphylococcus aureus. Host susceptibility factors are suggested by monogenic disorders associated with AD-like phenotypes, and can be medically modulated. S. aureus contributes to AD pathogenesis and can be mitigated by antibiotics. Recent work has revealed that the skin microbiome differs significantly between healthy controls and patients with AD, including decreased Gram-negative bacteria in AD. However, little is known about the potential therapeutic benefit of microbiome modulation. To evaluate if parameters of AD pathogenesis are altered after exposure to different culturable Gram-negative (CGN) bacteria collected from human skin. CGN bacteria were collected from healthy controls and patients with AD. Impacts on cellular and culture-based models of immune, epithelial, and bacterial function were evaluated. Representative strains were evaluated in the MC903 mouse model of AD. We found that CGN bacteria taken from healthy volunteers but not from patients with AD were associated with enhanced barrier function, innate immunity activation, and control of S. aureus. Treatment with CGN from healthy controls improved outcomes in a mouse model of AD. These findings suggest that a live-biotherapeutic approach may hold promise for treatment of patients with AD.
BMD regulation on mouse distal chromosome 1, candidate genes, and response to ovariectomy or dietary fat (2010)

The distal end of mouse chromosome 1 (Chr 1) harbors quantitative trait loci (QTLs) that regulate bone mineral density (BMD) and share conserved synteny with human chromosome 1q. The objective of this article was to map this mouse distal Chr 1 region and identify gene(s) responsible for BMD regulation in females. We used X-ray densitometry [ie, dual-energy X-ray Absorptiometry (DXA), micro-computed tomography (µCT), and peripheral quantitative computed tomography (pQCT)] to phenotype a set of nested congenic strains constructed from C57BL/6BmJ (B6/Bm) and C3H/HeJ (C3H) mice to map the region associated with the BMD QTL. The critical region has been reduced to an interval of 0.152 Mb that contributes to increased BMD when C3H alleles are present. Histomorphometry and osteoblast cultures indicated that increased osteoblast activity was associated with increased BMD in mouse strains with C3H alleles in this critical region. This region contains two genes, Aim2, which binds with cytoplasmic dsDNA and results in apoptosis, and AC084073.22, a predicted gene of unknown function. Ovariectomy induced bone loss in the B6/Bm progenitor and the three congenic strains regardless of the alleles present in the critical BMD region. High dietary fat treatment (thought to suppress distal Chr 1 QTL for BMD in mice) did not induce bone loss in the congenics carrying C3H alleles in the critical 0.152 Mb carrying the AIM2 and AC084073.22 genes. Gene expression studies in whole bone of key congenics showed differential expression of AC084073.22 for strains carrying B6/Bm versus C3H alleles but not for Aim2. In conclusion, our data suggest that osteoblasts are the cellular target of gene action and that AC084073.22 is the best candidate for female BMD regulation in the distal region of mouse Chr 1.
Artifact of "Learning nonlinear hybrid automata from input-output time-series data" (2023)

Artifact of "Learning nonlinear hybrid automata from input-output time-series data"
The Presence and Potential Role of ALDH1A2 in the Glioblastoma Microenvironment (2021)

Glioblastoma (GBM) is the most aggressive malignant glioma. Therapeutic targeting of GBM is made more difficult due to its heterogeneity, resistance to treatment, and diffuse infiltration into the brain parenchyma. Better understanding of the tumor microenvironment should aid in finding more effective management of GBM. GBM-associated macrophages (GAM) comprise up to 30% of the GBM microenvironment. Therefore, exploration of GAM activity/function and their specific markers are important for developing new therapeutic agents. In this study, we identified and evaluated the expression of ALDH1A2 in the GBM microenvironment, and especially in M2 GAM, though it is also expressed in reactive astrocytes and multinucleated tumor cells. We demonstrated that M2 GAM highly express ALDH1A2 when compared to other ALDH1 family proteins. Additionally, GBM samples showed higher expression of ALDH1A2 when compared to low-grade gliomas (LGG), and this expression was increased upon tumor recurrence both at the gene and protein levels. We demonstrated that the enzymatic product of ALDH1A2, retinoic acid (RA), modulated the expression and activity of MMP-2 and MMP-9 in macrophages, but not in GBM tumor cells. Thus, the expression of ALDH1A2 may promote the progressive phenotype of GBM.
Effects of auditory streaming on voicing judgment of Japanese intervocalic stop consonants. (1991)

An intervocalic voiceless stop consonant is perceived as voiced when the silence duration of its closure is reduced. The present study tries to clarify effects of auditory streaming of the sounds before and after the silence on this phenomenon. Phonetic identification tests are conducted for natural VCV (C=/p,t,k/) sequences (1) and those with three different types of preclosure portion of reduced streaming while varying silence duration. The degraded preclosure portions are those pronounced by the same talker but in isolation (2), one pronounced by a different talker (3), and noise burst with spectrum and amplitude envelopes resembling the original. The result with natural sequences indicates that perception of the consonant is shifted to voiced as silence duration is reduced. For stimuli whose preclosure portion is replaced, stream segregation (overlapping illusion) is observed and silence duration shows no effect on consonant perception at all. The present results indicate that silence duration can be a voicing cue only when sounds before and after the silence are interpreted as one speech event. Since masking ability of the sound before the silence is almost the same for all types of stimuli, the present result cannot be explained by the masking hypothesis.
Terrain Partial Obstruction LOS Path Loss Model for Rural Environments (2011)

The first Fresnel zone of direct path interacts differently with various terrain profiles, resulting in different partial obstruction losses. This letter presents a new model for partial obstruction of descending terrain extracted from a large number of terrain profiles representing various terrain characteristics and base-station antenna heights. The model is simple enough to be effectively used in system-level simulations and RF predictions without excessive analysis of the underlying terrain data.
3 mJ All-Fiber MOPA With a Short-Length Highly Er<sup>3+</sup>-Doped Phosphate Fiber (2020)

A very large mode-area 2 wt% erbium-doped double-clad phosphate fiber with a core diameter of 60 μm and core numerical aperture of 0.03 was fabricated and used for the last stage amplifier of an all-fiber pulsed laser master-oscillator power amplifier (MOPA) at 1550 nm. The Er <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> double-clad phosphate fiber has a cladding-core ratio of 2.17 and a V number of 3.6 at 1550 nm. 3 mJ pulses with 21.5 ns duration were obtained with Gaussian-like spatial beam profile with only a 75 cm long phosphate gain fiber.
Separation of carrier-free <sup>90</sup>Y from <sup>90</sup>Sr using flat sheet supported liquid membranes containing multiple diglycolamide-functionalized calix[4]arenes (2015)

Five diglycolamide-appended calix[4]arene (C4DGA) ligands, viz. C4DGA with no substituent (L-I), n-propyl (L-II), 3-pentyl (L-III), n-octyl (L-IV) and both side (L-V) substituents were evaluated for the separation of carrier free 90Y from a 90Y–90Sr mixture using the flat sheet supported liquid membrane technique. Based on the results of earlier batch studies, the transport properties of the C4DGA ligands towards Y(III) and Sr(II) were monitored at two different feed acidities. The transport rates were significantly lower for 6 M HNO3 as compared to 3 M HNO3 as the feed. After 6 h, the observed trend of Y(III) transport with the C4DGA ligands using a feed of 3 M HNO3 was: L-I ~ L-III > L-V > L-IV > L-II which changed to L-III > L-I > L-IV > L-V > L-II for 6 M HNO3 as the feed. With 3 M HNO3 as feed, >97% Y(III) transport was obtained with L-I and L-III in 6 h. Comparative Sr(II) transport was negligible resulting in high decontamination factors. In a one-step separation process, using L-I as the carrier ligand, pure 90Y was obtained as the respective complex with either EDTA or DOTA. The highlights of this liquid membrane-based separation method comprise: its easiness, one-step separation, low ligand inventory, relatively pure product and continuous method.
Critical Assessment of EPA's Weight-of-Evidence Approach to Nutrient Criteria Development (2009)

Critical Assessment of EPA's Weight-of-Evidence Approach to Nutrient Criteria DevelopmentEPA has developed a series of nutrient TMDLs for southeastern Pennsylvania watersheds that rely on a new method to establish nutrient criteria for phosphorus. This method, the weight-of-evidence approach, is not based on cause and effect relationships. Rather, it depends upon a collection of evaluations with dubious ties to nutrient-related use impairments. These “lines of evidence”...Author(s)William T. HallJohn C. HallSourceProceedings of the Water Environment FederationSubjectSession 10 - Nutrient Criteria and the TMDL ProcessDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2009ISSN1938-6478SICI1938-6478(20090101)2009:6L.761;1-DOI10.2175/193864709793958345Volume / Issue2009 / 6Content sourceTMDLS ConferenceFirst / last page(s)761 - 777Copyright2009Word count134Subject keywordsNutrientsPhosphorusWater Quality StandardTMDLMacroinvertebratesConditional Probability AnalysisWeight of EvidenceNuisance Algal Growth
Differential involvement of COX1 and COX2 in the vasculopathy associated with the α-galactosidase A-knockout mouse (2009)

The lysosomal storage disorder Fabry disease is characterized by excessive globotriaosylceramide (Gb3) accumulation in major organs such as the heart and kidney. Defective lysosomal alpha-galactosidase A (Gla) is responsible for excessive Gb3 accumulation, and one cell sensitive to the effects of Gb3 accumulation is vascular endothelium. Endothelial dysfunction is associated with Fabry disease and excessive cellular Gb3. We previously demonstrated that excessive vascular Gb3 in a mouse model of Fabry disease, the Gla-knockout (Gla(-/0)) mouse, results in abnormal vascular function, which includes abnormal endothelium-dependent contractions, a vascular phenomenon known to involve cyclooxygenase (COX). Therefore, we hypothesized that the vasculopathy in the Gla knockout mouse may be due to a vasoactive COX-derived product. To test this hypothesis, vascular reactivity experiments were performed in aortic rings from wild-type (Gla(+/0)) and Gla(-/0) mice in the presence and absence of specific and nonspecific COX inhibitors. Specific inhibition of COX1 or COX2 in endothelium-intact rings from Gla(-/0) mice decreased overall phenylephrine contractility compared with untreated Gla(-/0) rings, whereas COX inhibitors had no effect on contractility in endothelium-denuded rings. Nonspecific inhibition of COX with indomethacin (10 micromol/l) or COX1 inhibition with valeryl salicylate (3 mmol/l) improved endothelial function in rings from Gla(-/0) mice, but COX2 inhibition with NS-398 (1 micromol/l) further increased endothelial dysfunction in rings from Gla(-/0) mice. These results suggest that, in the Gla(-/0) mice, COX1 and COX2 activity are increased and localized in the endothelium, producing vasopressor and vasorelaxant products, which contribute to the Fabry-related vasculopathy.
Pyruvate Oxidase Influences the Sugar Utilization Pattern and Capsule Production in Streptococcus pneumoniae (2013)

Pyruvate oxidase is a key function in the metabolism and lifestyle of many lactic acid bacteria and its activity depends on the presence of environmental oxygen. In Streptococcus pneumoniae the protein has been suggested to play a major role in metabolism and has been implicated in virulence, oxidative stress survival and death in stationary phase. Under semi-aerobic conditions, transcriptomic and metabolite profiling analysis of a spxB mutant grown on glucose showed minor changes compared to the wild type, apart from the significant induction of two operons involved in carbohydrate uptake and processing. This induction leads to a change in the sugar utilization capabilities of the bacterium, as indicated by the analysis of the growth profiles of the D39 parent and spxB mutant on alternative carbohydrates. Metabolic analysis and growth experiments showed that inactivation of SpxB has no effect on the glucose fermentation pattern, except under aerobic conditions. More importantly, we show that mutation of spxB results in the production of increased amounts of capsule, the major virulence factor of S. pneumoniae. Part of this increase can be attributed to induction of capsule operon (cps) transcription. Therefore, we propose that S. pneumoniae utilizes pyruvate oxidase as an indirect sensor of the oxygenation of the environment, resulting in the adaption of its nutritional capability and the amount of capsule to survive in the host.
Determination of persistent organochlorine residues in a commercial fresh water catfish by GLC and study of their accumulation pattern. (2012)

Concentrations of various organochlorine pesticides in a commercial fresh water catfish, Heteropneustes fossilis, were measured. This study reveals possible toxicological exposure of human beings by way of consuming such fish containing pesticide and that will amount to possible exposure. Tissue extracts obtained by Soxhlet apparatus were used for analysis and the concentrations of analytes were determined by gas chromatography with electron capture detection. The major organochlorines found in blood sample were Endosulfan, Alpha-HCH, Beta-HCH and Gamma-HCH. However, the organochlorines found in edible portion of fish (i.e.flesh) were mainly--Endosulfan, Delta-HCH, Aldrine, pp-DDE etc. The concentrations of these organochlorines were at or above the theoretical threshold limit and hence are supposed to be effectively toxic to fish eaters, due to biomagnification.
Loss of sperm in juvenile spermatogonial depletion (<i>jsd</i>) mutant mice is ascribed to a defect of intratubular environment to support germ cell differentiation (1992)

C57BL/6(B6)-jsd/jsd mice are sterile due to the defective spermatogenesis in the testes. To know the cause of the deficient spermatogenesis in B6-jsd/jsd mice, we examined whether the problem is within or outside the seminiferous tubules by transplanting tubules from cryptorchid testes of B6- +/+ mice into B6-jsd/jsd testes or tubules from B6-jsd/jsd mice into testes of (WB x C57BL/6)F1-W/Wv (hereafter, WBB6F1-W/Wv) mice. Type A spermatogonia differentiated into spermatids in seminiferous tubules from cryptorchid testes transplanted into B6-jsd/jsd testes. In contrast, in B6-jsd/jsd tubules transplanted into WBB6F1-W/Wv testes, type A spermatogonia were stimulated to mitotic proliferation, but didn't proceed to any differentiated germ cells. The present results suggest that the cause of the deficient spermatogenesis in B6-jsd/jsd mice is a defect of intratubular environment to support germ cell differentiation.
R2d2 Drives Selfish Sweeps in the House Mouse (2020)

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution.
AmpC Disk Test for Detection of Plasmid-Mediated AmpC β-Lactamases in <i>Enterobacteriaceae</i> Lacking Chromosomal AmpC β-Lactamases (2005)

Although plasmid-mediated AmpC beta-lactamases were first reported in the late 1980s, many infectious disease personnel remain unaware of their clinical importance. These enzymes are typically produced by isolates of Escherichia coli, Klebsiella spp., Proteus mirabilis, and Salmonella spp. and are associated with multiple antibiotic resistance that leaves few therapeutic options. Plasmid-mediated AmpC beta-lactamases have been associated with false in vitro susceptibility to cephalosporins. Many laboratories do not test for this resistance mechanism because current tests are inconvenient, subjective, lack sensitivity and/or specificity, or require reagents that are not readily available. In this study a new test, the AmpC disk test, based on filter paper disks impregnated with EDTA, was found to be a highly sensitive, specific, and convenient means of detection of plasmid-mediated AmpC beta-lactamases in organisms lacking a chromosomally mediated AmpC beta-lactamase. Using cefoxitin insusceptibility as a screen, the test accurately distinguished AmpC and extended-spectrum beta-lactamase production and differentiated AmpCs from non-beta-lactamase mechanisms of cefoxitin insusceptibility, such as reduced outer membrane permeability. The test is a potentially useful diagnostic tool. It can provide important infection control information and help to ensure that infected patients receive appropriate antibiotic therapy.
Bone and Soft-tissue Sarcomas: Epidemiology, Radiology, Pathology and Fundamentals of Surgical Treatment (2006)

An understanding of the basic biology and pathology of bone and soft-tissue tumors is essential for appropriate planning of their treatment. This chapter reviews the unique biological behavior of soft-tissue and bone sarcomas. which underlies the basis for their staging, resection, and the use of appropriate adjuvant treatment modalities. A detailed description of the clinical, radiographic, and pathological characteristics for the most common sarcomas is presented.
Can Essential Oils Provide an Alternative Adjuvant Therapy for COVID-19 Infections and Pain Management at the Same Time? (2022)

The active compounds from essential oils have been an important asset in treating different diseases for many centuries. Nowadays, there are various available formulations used as food supplements to stimulate the immune system. In light of the current pandemic and the large amount of fake news circulating the internet, it is important to analyze which of the active compounds from essential oils can be successfully used in the treatment of COVID-19 infections. We analyzed the current literature on the effects of essential oils against the new SARS-CoV-2 virus to gain a better understanding of the underlying mechanisms of these compounds and establish their possible antiviral efficacy. The available studies have highlighted the antiviral potential of active compounds from essential oils, indicating that they could be used as adjuvants in treating various viral infections, including COVID-19, leading to a milder course of the disease, and improving patients' outcomes. At the same time, these compounds relieve pain and lift the mood in comorbid patients suffering from opioid addiction. Essential oils might be useful as adjuvant tools, not only against SARS-CoV-2 but also for a subset of especially vulnerable patients affected with both COVID-19 and opioid addiction. However, randomized clinical trials are needed to determine their efficacy and develop standardized high-quality preparations that can be safely administered to the general population.
Adaptive Tutoring on a Virtual Reality Driving Simulator (2018)

We propose a system for a Virtual Reality (VR) driving simulator including an Intelligent Tutoring System (ITS) to train the user's driving skills. The VR driving simulator comprises a detailed model of a city, Artificial Intelligence (AI) traffic, and a physical driving engine, interacting with the driver. In a physical mockup of a car cockpit, the driver operates the vehicle through the virtual environment by controlling a steering wheel, pedals, and a gear lever. Using a Head-Mounted Display (HMD), the driver observes the scene from within the car. The realism of the simulation is enhanced by a 6 Degrees of Freedom (DOF) motion platform, capable of simulating forces experienced when accelerating, braking, or turning the car. Based on a pre-defined list of driving-related activities, the ITS permanently assesses the quality of driving during the simulation and suggests an optimal path through the city to the driver in order to improve the driving skills. A user study revealed that most drivers experience presence in the virtual world and are proficient in operating the car.
Automated Facial Expression and Speech Emotion Recognition App Development on Smart Phones using Cloud Computing (2018)

Because emotions are such a significant and integral part of being human, understanding them and knowing how to react to the emotions of others is a fundamental requirement for successful social interaction. We recognize emotions primarily through speech and facial expression. The topic is gaining importance in academic research triggered by research in new techniques such as identifying emotions based on speech context. This investigates the relationship between emotions and the content of our speech. This paper proposes how emotion in speech and facial expression can be recognized in real time using a framework consisting of mobile phone technology backed by cloud computing. This functionality was developed and built into a mobile phone application. Currently, the application works on any Android smartphone to detect and identify emotions in real time. The results are expressed as a percentage of all the possible emotions, such as sad, happy, fear, surprise, anger and so on. The results of the experiment confirm that face and speech emotion recognition was conducted successfully using a smartphone. It was correct in 97.26% of instances when used with standard corpora: a.Ryerson Audio-Visual Database of Emotional Speech and Song (RAVDESS) b.the Surrey Audio-Visual Expressed Emotion (SAVEE).