gebhart/patrepeval huggingface dataset:
Novosphingobium ginsenosidimutans sp. nov., with the Ability to Convert Ginsenoside (2013)

A Gram-negative, strictly aerobic, non-motile, non-sporeforming, and rod-shaped bacterial strain designated FW-6T was isolated from a freshwater sample and its taxonomic position was investigated by using a polyphasic approach. Strain FW-6T grew optimally at 10-42 degrees C and at pH 7.0 on nutrient and R2A agar. Strain FW-6T displayed beta- glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to Rd. On the basis of 16S rRNA gene sequence similarity, strain FW-6T was shown to belong to the family Sphingomonadaceae and was related to Novosphingobium aromaticivorans DSM 12444T (98.1% sequence similarity) and N. subterraneum IFO 16086T (98.0%). The G+C content of the genomic DNA was 64.4%. The major menaquinone was Q-10 and the major fatty acids were summed feature 7 (comprising C18:1 omega9c/ omega12t/omega7c), summed feature 4 (comprising C16:1 omega7c/iso- C15:0 2OH), C16:0, and C14:0 2OH. DNA and chemotaxonomic data supported the affiliation of strain FW-6T to the genus Novosphingobium. Strain FW-6T could be differentiated genotypically and phenotypically from the recognized species of the genus Novosphingobium. The isolate that has ginsenoside converting ability therefore represents a novel species, for which the name Novosphingobium ginsenosidimutans sp. nov. is proposed, with the type strain FW-6T (= KACC 16615T = JCM 18202T).
Carnivorous Nutrition in Pitcher Plants (Nepenthes spp.) via an Unusual Complement of Endogenous Enzymes (2016)

Plants belonging to the genus Nepenthes are carnivorous, using specialized pitfall traps called “pitchers” that attract, capture, and digest insects as a primary source of nutrients. We have used RNA sequencing to generate a cDNA library from the Nepenthes pitchers and applied it to mass spectrometry-based identification of the enzymes secreted into the pitcher fluid using a nonspecific digestion strategy superior to trypsin in this application. This first complete catalog of the pitcher fluid subproteome includes enzymes across a variety of functional classes. The most abundant proteins present in the secreted fluid are proteases, nucleases, peroxidases, chitinases, a phosphatase, and a glucanase. Nitrogen recovery involves a particularly rich complement of proteases. In addition to the two expected aspartic proteases, we discovered three novel nepenthensins, two prolyl endopeptidases that we name neprosins, and a putative serine carboxypeptidase. Additional proteins identified are relevant to pathogen-defense and secretion mechanisms. The full complement of acid-stable enzymes discovered in this study suggests that carnivory in the genus Nepenthes can be sustained by plant-based mechanisms alone and does not absolutely require bacterial symbiosis.
The Söderfors Project : Construction of an Experimental Hydrokinetic Power Station (2011)

Orexins are excitatory neuropeptides that have a critical role in maintaining wakefulness. Orexin receptor antagonists promote sleep in animals and humans. Indeed, small molecule orexin receptor antagonists have demonstrated clinical proof-of-concept in the treatment of primary insomnia. This review describes optimization of orexin receptor antagonists across diverse structural classes with a focus on how molecules were designed to optimize potency, physicochemical properties, pharmacokinetics, brain penetration, and in vivo activity.
The geometry of the representation of decision variable and stimulus difficulty in the parietal cortex (2021)

Summary Lateral intraparietal (LIP) neurons represent formation of perceptual decisions involving eye movements. In circuit models for these decisions, neural ensembles that encode actions compete to form decisions. Consequently, decision variables (DVs) are represented as partially potentiated action plans, where ensembles increase their average responses for stronger evidence supporting their preferred actions. As another consequence, DV representation and readout are implemented similarly for decisions with identical competing actions, irrespective of input and task context differences. Here, we challenge those core principles using a novel face-discrimination task, where LIP firing rates decrease with supporting evidence, contrary to conventional motion-discrimination tasks. These opposite response patterns arise from similar mechanisms in which decisions form along curved population-response manifolds misaligned with action representations. These manifolds rotate in state space based on task context, necessitating distinct readouts. We show similar manifolds in lateral and medial prefrontal cortices, suggesting a ubiquitous representational geometry across decision-making circuits.
ChemInform Abstract: Laser‐Induced Dehydrochlorination of 1,2‐Dichloropropane. (1989)

Abstract Dehydrochlorination of 1,2‐dichloropropane (I) according to A) is found to be considerably accelerated compared to B).
Lack of Response to Supplemental Tin, Vanadium, Chromium and Nickel when added to a Purified Crystalline Amino Acid diet for Chicks (1975)

An experiment was conducted to ascertain if supplementing a completely purified diet with tin, vanadium chromium and nickel would enhance chick performance between hatching and 27-days posthatching. No effects on rate and efficiency of gain or on feather development were noted. A level of 350 p.p.m. magnesium, all in inorganic form, was found adequate for chick growth during this period.
Tristetraprolin expression by keratinocytes protects against skin carcinogenesis (2021)

Cancer is caused primarily by genomic alterations resulting in deregulation of gene regulatory circuits in key growth, apoptosis, or DNA repair pathways. Multiple genes associated with the initiation and development of tumors are also regulated at the level of mRNA decay, through the recruitment of RNA-binding proteins to AU-rich elements (AREs) located in their 3'-untranslated regions. One of these ARE-binding proteins, tristetraprolin (TTP; encoded by Zfp36), is consistently dysregulated in many human malignancies. Herein, using regulated overexpression or conditional ablation in the context of cutaneous chemical carcinogenesis, we show that TTP represents a critical regulator of skin tumorigenesis. We provide evidence that TTP controlled both tumor-associated inflammation and key oncogenic pathways in neoplastic epidermal cells. We identify Areg as a direct target of TTP in keratinocytes and show that EGFR signaling potentially contributed to exacerbated tumor formation. Finally, single-cell RNA-Seq analysis indicated that ZFP36 was downregulated in human malignant keratinocytes. We conclude that TTP expression by epidermal cells played a major role in the control of skin tumorigenesis.
Interleukin 7 generates antitumor cytotoxic T lymphocytes against murine sarcomas with efficacy in cellular adoptive immunotherapy. (1991)

Interleukin 7 (IL-7) is a 25-kD cytokine that was initially described as a pre-B cell growth factor. This cytokine has also been shown to have T cell proliferative and differentiation effects. In this report, we demonstrate that antitumor cytotoxic T lymphocytes (CTL) generated by secondary in vitro sensitization of draining lymph node cells in IL-7 are effective in treating 3-day syngeneic methylcholanthrene (MCA) sarcoma pulmonary metastases in mice. In vivo titrations comparing IL-7 to IL-2 antitumor CTL show that they have equivalent potency in adoptive immunotherapy. IL-7 antitumor CTL generated against MCA sarcomas of weak immunogeneity are also tumor specific in their in vivo efficacy. This study represents the first successful use of a cytokine other than IL-2 for the generation of cells with in vivo efficacy in cellular adoptive transfer.
Supplementary Figure 1 from Development of an Fc-Enhanced Anti–B7-H3 Monoclonal Antibody with Potent Antitumor Activity (2023)

&lt;p&gt;PDF file, 204KB, Panel A: Representative reactivity of anti-B7-H3 mAb BRCA84D with frozen tissue sections of prostate, breast, colon, lung, gastric and renal cancer. Panel B: Reactivity of anti-B7-H3 mAb BRCA69D on formalin-fixed paraffin embedded normal human spleen and lymph node tissues.&lt;/p&gt;
Vertical ground reaction force 2 years after anterior cruciate ligament reconstruction predicts 10‐year patient‐reported outcomes (2021)

Disruptions in knee biomechanics during walking following anterior cruciate ligament (ACL) injury have been suggested to lead to the development of premature knee osteoarthritis (OA) and to be potential markers of OA risk and targets for intervention. This study investigated if side-to-side differences in early stance peak vertical ground reaction force (vGRF) during walking 2 years after ACL reconstruction are associated with longer-term (10 years post-reconstruction) changes in patient-reported outcomes. Twenty-eight participants (mean age: 28.7 ± 6.4 years) with primary unilateral ACL reconstruction underwent gait analysis for assessment of peak vGRF and completed Knee Injury and Osteoarthritis Outcome Score (KOOS) and International Knee Documentation Committee (IKDC) surveys at 2 years post-surgery (2.2 ± 0.3 years) and completed surveys at follow-up 10 years post-surgery (10.5 ± 0.9 years). Associations between changes (10-2 years) in patient-reported outcomes and between limb-differences in vGRF were assessed with Pearson or Spearman's ρ correlation coefficients and exploratory backwards elimination multiple linear regression analyses. Differences in vGRF between symptomatic progressors and non-progressors were also assessed. The side-to-side difference in vGRF was related to the variability in longer-term changes in patient-reported outcome metrics and distinguished symptomatic progressors from non-progressors. Participants with higher vGRF in the reconstructed (ACLR) limb versus the contralateral limb had worsening of IKDC (R = -0.391, p = 0.040), KOOS pain (ρ = -0.396, p = 0.037), KOOS symptoms (ρ = -0.572, p = 0.001), and KOOS quality of life (R = -0.458, p = 0.014) scores at follow-up. Symptomatic progressors had greater vGRF in the ACLR limb as compared to the contralateral limb at baseline than non-progressors (p = 0.023). These data highlight associations between a simple-to-measure gait metric and the development of long-term clinical symptoms after an ACL injury.
Inhibition of Epidermal Growth Factor Receptor-associated Tyrosine Kinase Blocks Glioblastoma Invasion of the Brain<subtitle>Experimental Studies</subtitle> (1997)

OBJECTIVE: Glioblastoma multiforme is a malignant primary brain tumor associated with short patient survival despite aggressive treatment, in part because of its propensity to aggressively infiltrate into brain tissue. Glioblastoma multiforme is also unique because it is the only nonepithelial human tumor for which excessive activation of epidermal growth factor receptor (EGFR) has been consistently linked to tumor growth and patient survival, and EGFR activation promotes glioblastoma multiforme infiltration in vitro. METHODS: Cocultures of human glioblastoma spheroids (derived from three separate patients) and fetal rat brain aggregates were examined for infiltration using confocal microscopy, in the presence of 0 to 100 µmol/L genistein, a tyrosine kinase (TK) inhibitor, and 3 µmol/L tyrphostin A25, a specific EGFR-TK inhibitor. RESULTS: Infiltration (not attachment) was completely inhibited by genistein at 10µmol/L, the IC20 for monolayer growth inhibition in two cell lines. Tyrphostin A25 at 3 µmol/L (the IC20 for monolayers) reduced invasion in a third cell line from 38.8 ± 6.1% invasion-hour per hour (n = 5) to 2.9 ± 1.2% invasion-hour per hour (n = 6)(P = 0.0002, two-tailed t test, 93% inhibition), and from 0.54 ± 0.065% per hour (slope) to 0.028 ± 0.018% per hour(P = 0.00001, 95% inhibition). Maximal percent invasion was reduced from 100 ± 0 to 7.4 ± 5.6% of the fetal rat brain aggregate. No change was detected in EGFR-associated tyrosine phosphorylation at those doses in monolayers by 32P immunolabeling, consistent with the known effects of low concentrations of TK inhibitors. An increase in expression of wild-type and truncated EGFR was demonstrated by Western blotting. Invasion was equally well inhibited by a monoclonal antibody to the high-affinity ligand binding domain of EGFR and not by antibody to an inactive domain. CONCLUSION: Our observations support the role of EGFR activation as a determinant by which glioblastoma invades normal brain tissue, and we show that invasion can be effectively inhibited at much lower concentrations of TK inhibitors than are necessary for growth suppression.
The impact of intrinsic device fluctuations on CMOS SRAM cell stability (2001)

Reductions in CMOS SRAM cell static noise margin (SNM) due to intrinsic threshold voltage fluctuations in uniformly doped minimum-geometry cell MOSFETs are investigated for the first time using compact physical and stochastic models. Six sigma deviations in SNM due to intrinsic fluctuations alone are projected to exceed the nominal SMM for sub-100-nm CMOS technology generations. These large deviations pose severe barriers to scaling of supply voltage, channel length, and transistor count for conventional 6T SRAM-dominated CMOS ASICs and microprocessors.
Role of the interleukin 5 receptor system in hematopoiesis: Molecular basis for overlapping function of cytokines (1992)

Interleukin 5 (IL-5) is a kind of peptide hormone released from T lymphocytes of mammals infected with microorganisms or parasites. It is an acidic glycoprotein with a molecular mass of 40 to 50 kDa that consists of a homodimer of polypeptides. It controls hematopoiesis so that it increases natural immunity. In the mouse, IL-5 acts on committed B cells to induce differentiation into Ig-producing cells and on common progenitors for CD5+ pre-B cells and CD5+ macrophages to support their survival. The antibodies secreted by CD5+ B cells seem to be responsible for the primary protection against the infection with microorganisms or parasites. It also supports the growth and/or differentiation of eosinophil precursor and mature eosinophils, which can be effective for the removal of parasites in combination with the antibodies against them. Murine IL-5 receptor (IL-5R) consists of two different polypeptide chains; alpha chain and beta chain. The IL-5R alpha chain is 60 kDa protein that binds IL-5 with low affinity. The IL-5R beta chain is a 130 kDa protein which does not bind IL-5 by itself but is necessary to form the high affinity IL-5R. The beta chain was identified by using one of the anti-IL-5R mAb and anti-IL-3R mAb as the IL-3R homologue. This beta chain is also used as the beta chain of GM-CSF receptor. This fact suggests that there is a common signaling mechanism among these cytokines and efficient cooperation among them. At the same time, these findings may explain the overlapping role of these cytokines in the development of granulocytes.
P2‐106: UBAP1 is a risk factor for frontotemporal lobar degeneration (2008)

Frontotemporal lobar degeneration (FTLD) is a heterogeneous neurodegenerative syndrome that includes the clinical syndromes of frontotemporal dementia, semantic dementia, progressive nonfluent aphasia, and progressive apraxia. Approximately 30 – 50% of cases are thought to be familial in origin. Mutations in MAPT and PGRN account for up to 20% of familial FTLD, and rare forms result from mutations of CHMP2B. Recently, linkage to chr9p was reported in families with FTLD and motor neuron disease. Based on published linkage data the chr9p minimal candidate region was defined from D9S2154 to D9S1874. Using a gene-centric approach we genotyped 190 haplotype tagging SNP's covering this region in the Manchester FTLD cohort (N=214) and 286 normal controls using the Sequenom MassArray genotyping technology. Using a case-control approach and sliding window haplotype analysis, UBAP1 (Ubiquitin associated protein 1) was found to be associated with a maximum sliding window P value of 0.00025. A further 12 tagging SNPs covering UBAP1 were genotyped for validation. Of the 10 SNPs that make up the haplotype block covering UBAP1, 7 were associated with FTLD with a P value of ≤0.05, the haplotype block itself associated with disease status with a global P value of 0.008, a finding that translates to maximum increased risk for FTLD of OR 1.71 (95% CI 1.20–2.44, P=0.003). A replication cohort of Dutch FTLD cases (N=230), and controls (N=484) were also genotyped for these tagging SNPs. 3 of the UBAP1 SNPs associated with FTLD in the Dutch data, with a maximum haplotype association of OR 1.39 (95% CI 1.02–1.89, P= 0.033). Combined analysis resulted in a haplotype association of P=0.014, with a maximum haplotype risk of OR 1.42 (95% CI 1.12–1.80, P=0.003). These data suggest that UBAP1 is a risk factor for FTLD in at least two different populations. Analysis of UBAP1 in chr9p-linked families is required. Molecular and biochemical characterisation of UBAP1 is underway to determine the biological basis of this association.
Hypoxia signaling pathways in cancer metabolism: the importance of co-selecting interconnected physiological pathways (2014)

Both tumor hypoxia and dysregulated metabolism are classical features of cancer. Recent analyses have revealed complex interconnections between oncogenic activation, hypoxia signaling systems and metabolic pathways that are dysregulated in cancer. These studies have demonstrated that rather than responding simply to error signals arising from energy depletion or tumor hypoxia, metabolic and hypoxia signaling pathways are also directly connected to oncogenic signaling mechanisms at many points. This review will summarize current understanding of the role of hypoxia inducible factor (HIF) in these networks. It will also discuss the role of these interconnected pathways in generating the cancer phenotype; in particular, the implications of switching massive pathways that are physiologically 'hard-wired' to oncogenic mechanisms driving cancer.
Characterization of overlay mark fidelity (2003)

In this publication we introduce a new metric for process robustness of overlay metrology in microelectronic manufacturing. By straightforward statistical analysis of overlay metrology measurements on an array of adjacent, nominally identical overlay targets the Overlay Mark Fidelity (OMF) can be estimated. We present the results of such measurements and analysis on various marks, which were patterned using a DUV scanner. The same reticle set was used to pattern wafers on different process layers and process conditions. By appropriate statistical analysis, the breakdown of the total OMF into a reticle-induced OMF component and a process induced OMF component was facilitated. We compare the OMF of traditional box-in-box overlay marks with that of new gratingbased overlay marks and show that in all cases the grating marks are superior. The reticle related OMF showed an improvement of 30 % when using the new grating-based overlay mark. Furthermore, in a series of wafers run through an STI-process with different Chemical Mechanical Polish (CMP) times, the random component of the OMF of the new grating-based overlay mark was observed to be 40% lower and 50% less sensitive to process variation compared with Box in Box marks. These two observations are interpreted as improved process robustness of the grating mark over box in box, specifically in terms of reduced site by site variations and reduced wafer to wafer variations as process conditions change over time. Overlay Mark Fidelity, as defined in this publication, is a source of overlay metrology uncertainty, which is statistically independent of the standard error contributors, i.e. precision, TIS variability, and tool to tool matching. Current overlay metrology budgeting practices do not take this into consideration when calculating total measurement uncertainty (TMU). It is proposed that this be reconsidered, given the tightness of overlay and overlay metrology budgets at the 70 nm design rule node and below.
Naval application of storage devices for loads protection in micro-grids dominated by solid state converters (2014)

The correct operating mode of protection systems is a fundamental aspect in order to guarantee a good quality of service to loads connected to a distribution grid. This paper deals with naval plants that, being dominated by power electronic converters can lead to malfunctioning of protection systems due to limited fault currents. The solution proposed by the authors consists in introducing a storage systems in order to increase the fault level of the grid. Three control strategies to drive the intervention of the storage device have been studied. These strategies have been tested by means of numerical simulations and their effectiveness has been proved. Finally, some considerations for the choice of the optimal technology for realizing the storage unit have been given and some guidelines for the sizing of this unit have been provided.
Understanding the Benefits of Musical Training (2009)

A number of studies suggest that musical training has benefits for other cognitive domains, such as language and mathematics, and studies of children and adults indicate structural as well as functional differences between the brains of musicians and nonmusicians. The induced gamma-band response has been associated with attentional, expectation, memory retrieval, and integration of top-down, bottom-up, and multisensory processes. Here we report data indicating that the induced gamma-band response to musical sounds is larger in adult musicians than in nonmusicians and that it develops in children after 1 year of musical training beginning at age 4.5 years, but not in children of this age who are not engaged in musical lessons. We conclude that musical training affects oscillatory networks in the brain associated with executive functions, and that superior executive functioning could enhance learning and performance in many cognitive domains.
Polymerized ionic liquid block copolymers for electrochemical energy (2015)

Polymerized ionic liquid (PIL) block copolymers are an emerging class of polymers that synergistically combine the benefits of both ionic liquids (ILs) and block copolymers into one, where the former possesses a unique set of physiochemical properties and the latter self assembles into a range of nanostructures.
GaN Selective Area Metal–Organic Vapor Phase Epitaxy: Prediction of Growth Rate Enhancement by Vapor Phase Diffusion Model (2007)

Thickness profiles of GaN grown by selective area metal–organic vapor phase epitaxy (SA-MOVPE) were successfully reproduced by a vapor phase diffusion model that employs only one parameter–effective diffusion length D/ks. The value of D/ks of Ga-containing precursors changes from 10 to 50 µm under growth temperature of 1000–1250 °C and reactor total pressure of 100 mbar. It was confirmed that, in the wide-stripe SA-MOVPE of GaN, the vapor phase diffusion of Ga-containing precursors govern the profile of growth rate. Numerical simulation using the vapor phase diffusion model is of great help for the design and control of thickness profiles in the SA-MOVPE of GaN.