gebhart/patrepeval huggingface dataset:
Proteomic Landscape of Human Sperm in Patients with Different Spermatogenic Impairments (2023)

Although the proteome of sperm has been characterized, there is still a lack of high-throughput studies on dysregulated proteins in sperm from subfertile men, with only a few studies on the sperm proteome in asthenozoospermic and oligoasthenozoospermic men. Using liquid chromatography-mass spectrometry (LC-MS/MS) along with bioinformatics analyses, we investigated the proteomic landscape of sperm collected from subfertile men (<i>n</i> = 22), i.e., asthenozoospermic men (<i>n</i> = 13), oligoasthenozoospermic men (<i>n</i> = 9) and normozoospermic controls (<i>n</i> = 31). We identified 4412 proteins in human sperm. Out of these, 1336 differentially abundant proteins were identified in 70% of the samples. In subfertile men, 32 proteins showed a lower abundance level and 34 showed a higher abundance level when compared with normozoospermic men. Compared to normozoospermic controls, 95 and 8 proteins showed a lower abundance level, and 86 and 1 proteins showed a higher abundance level in asthenozoospermic and oligoasthenozoospermic men, respectively. Sperm motility and count were negatively correlated with 13 and 35 and positively correlated with 37 and 20 differentially abundant proteins in asthenozoospermic and oligoasthenozoospermic men, respectively. The combination of the proteins APCS, APOE, and FLOT1 discriminates subfertile males from normozoospermic controls with an AUC value of 0.95. Combined APOE and FN1 proteins discriminate asthenozoospermic men form controls with an AUC of 1, and combined RUVBL1 and TFKC oligoasthenozoospermic men with an AUC of 0.93. Using a proteomic approach, we revealed the proteomic landscape of sperm collected from asthenozoospermic or oligoasthenozoospermic men. Identified abundance changes of several specific proteins are likely to impact sperm function leading to subfertility. The data also provide evidence for the usefulness of specific proteins or protein combinations to support future diagnosis of male subfertility.
Table S3 from Inhibition of BET Bromodomain Proteins with GS-5829 and GS-626510 in Uterine Serous Carcinoma, a Biologically Aggressive Variant of Endometrial Cancer (2023)

&lt;p&gt;Groups and dosing description of the in vivo drug study on USC-ARK1 xenograft.&lt;/p&gt;
Heterogeneous chemistry related to Antarctic ozone depletion: Reaction of ClONO2 and N2O5 on ice surfaces (1988)

Laboratory studies of heterogeneous reactions of possible importance for Antarctic ozone depletion were performed. In particular, the reactions of chlorine nitrate (ClONO2) and dinitrogen pentoxide (N2O5) were investigated on ice and HCl/ice surfaces. These reactions occur on the surfaces of polar stratospheric clouds (PSCs) over Antarctica. One reaction transforms the stable chlorine reservoir species (ClONO2 and HCl) into photochemically active chlorine in the form of HOCl and Cl2. Condensation of HNO3 in the reactions removes odd nitrogen from the stratosphere, a requirement in nearly all models of Antarctic ozone depletion. Other reactions may also be important for Antarctic ozone depletion. Like the reactions of chlorine nitrate, these reactions deplete odd nitrogen through HNO3 condensation. In addition, one reaction converts a stable chlorine reservior species (HCl) into photochemically active chlorine (ClNO2). These reactions were studied with a modified version of a Knudsen cell flow reactor.
THROOM : Running POSIX Multithreaded Binaries on a Cluster (2003)

Most software distributed shared memory systems (SW-DSMs) lack industry standard interfaces that limit their applicability to a small set of shared-memory applications. In order to gain general acceptance, SW-DSMs should support the same look-and-feel of shared memory as hardware DSMs. This paper presents a runtime system concept that enables unmodified POSIX P1003.1c (Pthreads) compliant binaries to run transparently on clustered hardware. The key idea is to extend the single process model of multi-threading to a multi-process model where threads are distributed to processes executing in remote nodes. The distributed threads execute in a global shared address space made coherent by a fine-grain SW-DSM layer. We also present THROOM, a proof-of-concept implementation that runs unmodified Pthread binaries on a virtual cluster modeled as standard UNIX processes. THROOM runs on top of the DSZOOM fine-grain SW-DSM system with limited OS support. 1
EFFECTS OF FLUOXETINE, A SEROTONIN REUPTAKE INHIBITOR, ON THE SNEEZE-INDUCED CONTINENCE REFLEX IN RATS (2009)

To compare the results of uroflowmetry in the standing and sitting position in men who void only in the sitting position.Two hundred patients were subjected to pelvic ultrasonography while their bladders were full, and then after voiding. Uroflowmetry was done both in sitting and standing positions and compared for all patients. Further comparisons were made according to patients’ age (below and above 50) and Qmax (at or below 15 mL per second versus greater than 15 mL per second). We performed statistical analysis using Wilcoxon matched-pairs signed-ranks test.Comparison of uroflowmetric results in both positions showed no statistical differences except for significantly larger residual urine volume in the standing position (86.1 ± 77) relative to the sitting position (73 ± 80.2) (P = 0.04). On substratifying patients according to age, Qmax was significantly higher in the sitting position (16.6 ± 8.94) relative to the standing position (15.2 ± 7.5) in the young group (P = 0.02). Such a significant difference was not seen in the elder (greater than 50 years) group. In contrary to the low-flow group, cases with high flow showed significantly higher Qmax and Qave and significantly lower voiding and flow times and significantly lower residual urine volume in the sitting position.Voiding in the sitting position showed significantly better flow rates than during standing in patients with higher flow and younger age. Moreover, postvoid residual was significantly less in the sitting position in the previous two groups and in the total groups of patients. On the contrary, the presence of low flow nullifies these uroflowmetric positional differences. Uroflowmetry should be always performed in the preferred position.
From underwater simulation to at-sea testing using the ns-2 network simulator (2011)

Although several network protocols for underwater acoustic wireless sensor networks have been proposed in the past, having a complete and accurate understanding of the performance of these protocols is not an easy task. The unique characteristics of the underwater acoustic communication channel, such as limited capacity, high and variable propagation delays, frequency-dependent attenuation and significant impact of highly variable environmental conditions, motivate the fact it is quite challenging to identify simple but accurate channel models. Such models are instead needed to improve accuracy of simulation results and to be able to derive fundamental results on underwater communications performance. To facilitate the research in underwater sensor networks, it would be really desirable to have a standard platform for simulation, emulation and real-life testing in order to be able to compare and evaluate different network designs, algorithms and protocols in a variety of settings and application scenarios. With this objective in mind, we have developed a framework to seamlessly simulate, emulate and test at sea novel communication protocols, which is based on the open source and well known network simulator ns-2 [1]. Using the proposed framework, anyone willing to implement its solution for simulation experiments using ns-2 can use the same code in emulation mode, adopting real acoustic modem for data transmission. The framework code has also successfully been ported on small portable devices (Gumstix [2]), thus allowing us to embed it inside modem or AUV housings. Therefore, it becomes easy for the research community to write code and evaluate protocols on a real testbed. Different drivers allowing ns-2 to operate with commercial acoustic modems, such as FSK and PSK Micro-Modem [3], Evologics modem [4] and Kongsberg modem [5], have already been implemented.
Prevalence and concentration of Salmonella and Campylobacter in the processing environment of small-scale pastured broiler farms (2013)

A growing niche in the locally grown food movement is the small-scale production of broiler chickens using the pasture-raised poultry production model. Limited research exists that focuses on Salmonella and Campylobacter contamination in the environment associated with on-farm processing of pasture-raised broilers. The objective of this study was to establish data relative to Salmonella and Campylobacter prevalence and concentration in soil and mortality compost resulting from prior processing waste disposal in the small-scale, on-farm broiler processing environment. Salmonella and Campylobacter concentrations were determined in soil (n = 42), compost (n = 39), and processing wastewater (PWW; n = 46) samples from 4 small broiler farms using a 3-tube most probable number (MPN) method for Salmonella and direct plating method for Campylobacter. Salmonella prevalence and concentration (mean log10 MPN per sample weight or volume) in soil [60%, 0.97 (95% CI: 0.66 to 1.27)], compost [64%, 0.95 (95% CI: 0.66 to 1.24)], and wastewater [48%, 1.29 (95% CI: 0.87 to 1.71)] were not significantly different (P > 0.05). Although Campylobacter prevalence was not significantly different by sample type (64.3, 64.3, and 45.7% in soil, compost, and PWW, respectively), the concentration (mean log10 cfu) of this pathogen was significantly lower (P < 0.05) in wastewater [2.19 (95% CI: 0.36 to 3.03)] samples compared with soil [3.08 (95% CI: 2.23 to 3.94)], and compost [3.83 (95% CI: 2.71 to 4.95)]. These data provide insight into small-scale poultry production waste disposal practices and provides a record of data that may serve as a guide for future improvement of these practices. Further research is needed regarding the small-scale broiler production environment in relation to improving disposal of processing waste for optimum control of human pathogens.
Augmenting light coverage for photosynthesis through YFP-enhanced charge separation at the Rhodobacter sphaeroides reaction centre (2017)

Photosynthesis uses a limited range of the solar spectrum, so enhancing spectral coverage could improve the efficiency of light capture. Here, we show that a hybrid reaction centre (RC)/yellow fluorescent protein (YFP) complex accelerates photosynthetic growth in the bacterium Rhodobacter sphaeroides. The structure of the RC/YFP-light-harvesting 1 (LH1) complex shows the position of YFP attachment to the RC-H subunit, on the cytoplasmic side of the RC complex. Fluorescence lifetime microscopy of whole cells and ultrafast transient absorption spectroscopy of purified RC/YFP complexes show that the YFP-RC intermolecular distance and spectral overlap between the emission of YFP and the visible-region (Q<sub>X</sub>) absorption bands of the RC allow energy transfer via a Förster mechanism, with an efficiency of 40±10%. This proof-of-principle study demonstrates the feasibility of increasing spectral coverage for harvesting light using non-native genetically-encoded light-absorbers, thereby augmenting energy transfer and trapping in photosynthesis.
Protective effect of rutin supplementation against cisplatin-induced Nephrotoxicity in rats (2017)

The present study suggested that the anti-oxidant and anti-inflammatory effect of rutin may prevent CP-induced nephrotoxicity via decreasing the oxidative stress, inhibiting the interconnected ROS/JNK/TNF/P38 MAPK signaling pathways, and repairing the histopathological changes against cisplatin administration.
Characterisation of gp34, a GPI-anchored protein expressed by schizonts of Theileria parva and T. annulata (2010)

Using bioinformatics tools, we searched the predicted Theileria annulata and T. parva proteomes for putative schizont surface proteins. This led to the identification of gp34, a GPI-anchored protein that is stage-specifically expressed by schizonts of both Theileria species and is downregulated upon induction of merogony. Transfection experiments in HeLa cells showed that the gp34 signal peptide and GPI anchor signal are also functional in higher eukaryotes. Epitope-tagged Tp-gp34, but not Ta-gp34, expressed in the cytosol of COS-7 cells was found to localise to the central spindle and midbody. Overexpression of Tp-gp34 and Ta-gp34 induced cytokinetic defects and resulted in accumulation of binucleated cells. These findings suggest that gp34 could contribute to important parasite-host interactions during host cell division.
Bonding-pad-oriented on-chip ESD protection structures for ICs (2003)

Several bonding-pad-oriented ESD protection structures, including a ggCMOS, an LVSCR and an all-direction ESD structures are reported, implemented in commercial 0.35 /spl mu/m CMOS and 0.6 /spl mu/m BiCMOS. Measurements agree with simulations well. HBM ESD zapping tests passed 2 kV, 4.4 kV and 14 kV, respectively. The structures are suitable ESD protection solutions for RF, mixed-signal and high-pin-count ICs.
Abstract PR003: Lineage plasticity dictates responsiveness to anti-GD2 therapy in neuroblastoma (2022)

Abstract Epigenetic dysregulation is frequently observed in the disease pathology of pediatric cancers, including neuroblastoma, the most common extracranial solid tumor in pediatric patients. Neuroblastoma tumors co-opt developmentally linked adrenergic or mesenchymal super-enhancer landscapes that rewire their transcriptional programs. Here, we describe that the lineage commitment to a mesenchymal epigenetic state is an important mechanism of resistance to anti-GD2 therapy through loss of GD2 antigen, a ganglioside glycolipid expressed on the cell surface. Low GD2 expression was significantly correlated with the mesenchymal state in a large panel of neuroblastoma cell lines and a forced adrenergic-to-mesenchymal transition conferred downregulation of GD2 and resistance to anti-GD2 antibody. Mechanistically, low-GD2 expressing cell lines demonstrated significantly reduced expression of the ganglioside synthesis enzyme ST8SIA1 (GD3 synthase), resulting in a bottlenecking of GD2 synthesis. Genome-wide CRISPR/Cas9 screening to identify regulators of GD2 in neuroblastoma revealed that the ablation of the polycomb repressive complex 2 (PRC2) significantly upregulates GD2 expression in GD2-low cells. Pharmacologic inhibition of EZH2 resulted in epigenetic rewiring of mesenchymal neuroblastoma cells into an adrenergic-like state, re-expressed ST8SIA1, and restored surface expression of GD2 and sensitivity to anti-GD2 antibody. These data identify developmental lineage as a key determinant of sensitivity to anti-GD2 based immunotherapies and credential PRC2 inhibitors for clinical testing in combination with anti-GD2 antibody to enhance outcomes for children with neuroblastoma. Citation Format: Nathaniel W. Mabe, Min Huang, Daniel A. Schaefer, Guillermo N. Dalton, Giulia Digiovanni, Gabriela Alexe, Anna C. Geraghty, Delan Khalid, Marius M. Mader, Michal Sheffer, Miles H. Linde, Nghi Ly, Maria Caterina Rotiroti, Benjamin A. H. Smith, Marius Wernig, Carolyn R. Bertozzi, Michelle Monje, Constantine Mitsiades, Ravindra Majeti, Ansuman T. Satpathy, Kimberly Stegmaier, Robbie G. Majzner. Lineage plasticity dictates responsiveness to anti-GD2 therapy in neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr PR003.
Correction of the Excitation Coefficients of Ku-band Phased Arrays With a Rotatable Polarization Plane (2021)

This paper presents a method of correcting the excitation coefficients of a Ku-band phased array with a rotatable polarization plane. By optimizing both the amplitudes and phases of the excitation coefficients, the cross-polarization discrimination (XPD) is improved from 8.2 dB to 54.8 dB when controlling the main-beam direction to 30&#x00B0; and the polarization angle to &#x2212;45&#x00B0; at 14.25 GHz.
Inhibition of endothelial cell tube formation by the low molecular weight heparin, tinzaparin, is mediated by tissue factor pathway inhibitor (2004)

Heparin and low molecular weight heparins (LMWHs) have both antithrombotic and anti-angiogenic activities. The anti-angiogenic activity of LMWH may be associated with the release of endothelial tissue factor pathway inhibitor (TFPI), an important endogenous inhibitor of tissue factor/Factor VIIa (TF/fVIIa). To evaluate the effects of LMWH, tinzaparin, and TFPI in a model of angiogenesis-mediated processes, we compared the effects of tinzaparin, and recombinant TFPI in inhibiting either basic fibroblast growth factor-2 (FGF2)- or TF/fVIIa-induced endothelial cell tube formation in human umbilical vein endothelial cells (HUVEC). Our results show that tinzaparin and recombinant TFPI both blocked endothelial tube formation induced by either FGF2 or TF/fVIIa, in a concentration-dependent manner. Endothelial tube formation was only marginally inhibited by a potent and specific anti-Factor Xa, recombinant tick anticoagulant protein (rTAP). A monoclonal anti-TFPI anti-body reversed the inhibitory effects of either tinzaparin or recombinant-TFPI on HUVEC tube formation. Tinzaparin fractions in the range of 8,000 to 12,600 Da were most effective in stimulating the release of TFPI from HUVEC. These results suggest that the inhibitory effect of the LMWH tinzaparin on endothelial tube formation is associated with stimulation of the release of TFPI, but not to anti-Factor Xa activity.
The Immunosuppressive Role of Adenosine A2A Receptors in Ischemia Reperfusion Injury and Islet Transplantation (2012)

Activation of adenosine A2A receptors (A2AR) reduces inflammation by generally inhibiting the activation of pro-inflammatory cells, decreasing endothelial adhesion molecule expression and reducing the release of proinflammatory cytokine mediators. Numerous preclinical studies using selective A2AR agonists, antagonists, A2AR knockout as well as chimeric mice have suggested the therapeutic potential of A2AR agonists for the treatment of ischemia reperfusion injury (IRI) and autoimmune diseases. This review summarizes the immunosuppressive actions of A2AR agonists in murine IRI models of liver, kidney, heart, lung and CNS, and gives details on the cellular effects of A2AR activation in neutrophils, macrophages, dendritic cells, natural killer cells, NKT cells, T effector cells and CD4+CD25+FoxP3+ T regulatory cells. This is discussed in the context of cytokine mediators involved in inflammatory cascades. Whilst the role of adenosine receptor agonists in various models of autoimmune disease has been well-documented, very little information is available regarding the role of A2AR activation in type 1 diabetes mellitus (T1DM). An overview of the pathogenesis of T1DM as well as early islet graft rejection in the immediate peri-transplantation period offers insight regarding the use of A2AR agonists as a beneficial intervention in clinical islet transplantation, promoting islet graft survival, minimizing early islet loss and reducing the number of islets required for successful transplantation, thereby increasing the availability of this procedure to a greater number of recipients. In summary, the use of A2AR agonists as a clinical intervention in IRI and as an adjunct to clinical immunesuppressive regimen in islet transplantation is highlighted.
Extending applications of dielectric elastomer artificial muscle (2007)

Dielectric elastomers have demonstrated high energy density and high strains as well as high electromechanical efficiency and fast speeds of response. These properties, combined with their projected low cost make them attractive for a variety of actuator applications including linear actuators, diaphragm pumps, rotary motors, and haptic displays. Dielectric elastomers have also been shown to offer high energy density, high efficiency, and large strains when operated as generators. Dielectric elastomers have reached a stage of development where standardized products can be applied to new applications. In some cases, dielectric elastomer devices are improvements over existing devices. In other cases, however, dielectric elastomers can enable new types of devices that cannot be made with existing technologies, such as new types of loudspeakers and power generating devices. A new dipole loudspeaker system was developed using a commercially available push-pull diaphragm configuration. This same transducer configuration was used to develop a new power generating system. This generator system enables a power generation of 0.06 to 0.12 W by manually displacing the device by 5 to 6 mm once a second. By introducing a voltage step-down conversion circuit, the device was able to power wireless communications, allowing the control of devices separated by a distance of a few meters. These two devices are examples of the new applications that are enabled as the dielectric elastomer technology commercially emerges. Future improvements to dielectric elastomers could enable new capabilities in clean electrical power generation from ocean waves, for example.
Assessing West Virginia NIPF owner preferred forest management assistance topics and delivery methods (2003)

Four hundred and fourteen non-industrial private forest (NIPF) owners in West Virginia responded to a mail survey questionnaire assessing their forest management assistance topics and delivery methods of interest. Logistic regression was used to analyze 39 independent variables in relation to the dependent variables of wanting a specific topic of forestry assistance or not. Ownership of property for investment, cultivation of wildlife food crops, receiving assistance from the West Virginia State Division of Forestry, and ownership tenure were recurrent significant variables characterizing landowners wanting a specific assistance topic. These results can be used to develop forestry assistance programs that reflect landowner objectives and good forest management.
A novel Syk-dependent mechanism of platelet activation by the C-type lectin receptor CLEC-2 (2005)

The snake venom rhodocytin has been reported to bind to integrin alpha2beta1 and glycoprotein (GP) Ibalpha on platelets, but it is also able to induce activation independent of the 2 receptors and of GPVI. Using rhodocytin affinity chromatography, we have identified a novel C-type lectin receptor, CLEC-2, in platelets that confers signaling responses to rhodocytin when expressed in a cell line. CLEC-2 has a single tyrosine residue in a YXXL motif in its cytosolic tail, which undergoes tyrosine phosphorylation upon platelet activation by rhodocytin or an antibody to CLEC-2, but not to collagen, thrombin receptor agonist peptide (TRAP), or convulxin. Tyrosine phosphorylation of CLEC-2 and other signaling proteins by rhodocytin is inhibited by the Src family kinase inhibitor PP2. Further, activation of murine platelets by rhodocytin is abolished in the absence of Syk and PLCgamma2, and partially reduced in the absence of LAT, SLP-76, and Vav1/Vav3. These findings define a novel signaling pathway in platelets whereby activation of CLEC-2 by rhodocytin leads to tyrosine phosphorylation of its cytosolic tail, binding of Syk and initiation of downstream tyrosine phosphorylation events, and activation of PLCgamma2. CLEC-2 is the first C-type lectin receptor to be found on platelets which signals through this novel pathway.