gebhart/patrepeval huggingface dataset:
Experimental infection of layer hens with a human isolate of Brachyspira pilosicoli (2003)

The anaerobic intestinal spirochaete Brachyspira pilosicoli commonly colonizes the large intestine of a number of species, including chickens and human beings. The purpose of the current study was to determine whether an isolate of B. pilosicoli recovered from an HIV-infected patient with diarrhoea could infect and cause disease in adult chickens. Over a 4-week period following experimental infection, a group of eight inoculated chickens showed a persistent and significant increase in faecal water content ( approximately 6-7 %). The faeces of three of the eight birds became culture-positive, and remained so. At post-mortem examination, no specific pathological changes were found, and no spirochaetal attachment to the caecal epithelium was observed. These findings confirm that B. pilosicoli strains can infect across species barriers and cause chronic mild diarrhoea in intact adult chickens.
Versatile Gas/Liquid Microreactors for Industry (2005)

Abstract The design, fabrication, use and scale‐out of versatile, multi‐channel gas/liquid microreactors, which are suitable for both laboratory and industrial syntheses, are described. Direct fluorination reactions of diethyl malonate and Meldrum's acid using the new microreactor technology were studied to demonstrate the viability of the device for carrying out gas/liquid processes, particularly when using potentially hazardous materials.
MR and cerebrospinal fluid enzymes as sensitive indicators of subclinical cerebral injury after open-heart valve replacement surgery. (1996)

MR imaging is a sensitive measure of subclinical cerebral ischemia after cardiac valve replacement under cardiopulmonary bypass. Cerebrospinal fluid neuron-specific enolase and lactic dehydrogenase are less sensitive than MR imaging for detecting subclinical cerebral ischemia, but these values were elevated after surgery more frequently than was adenylate kinase in our patients.
Tranexamic Acid Alters The Immunophenotype of Phagocytes After Lower Limb Surgery (2021)

Abstract Introduction: Tranexamic acid (TXA) is an antifibrinolytic agent frequently used in elective surgery to reduce blood loss. We recently found it also acts as a potent immune-modulator in patients undergoing cardiac surgery. Methods : Patients undergoing lower limb surgery were enrolled into the “Tranexamic Acid in Lower Limb Arthroplasty” (TALLAS) pilot study. The cellular immune response was characterised longitudinally pre- and post-operatively using full blood examination (FBE) and comprehensive immune cell phenotyping by flowcytometry. Red blood cells and platelets were determined in the FBE and levels of T cell cytokines and the plasmin-antiplasmin complex determined using ELISA. Results : TXA administration increased the proportion of circulating CD141+ conventional dendritic cells (cDC) on post-operative day (POD) 3. It also reduced the expression of CD83 and TNFR2 on classical monocytes and levels of circulating IL-10 at the end of surgery (EOS) time point, whilst increasing the expression of CCR4 on natural killer (NK) cells at EOS, and reducing TNFR2 on POD-3 on NK cells. Red blood cells and platelets were decreased to a lower extent at POD-1 in the TXA group, representing reduced blood loss. Discussion : In this investigation we have extended our examination on the immunomodulatory effects of TXA in surgery by also characterising the end of surgery time point and including B cells and neutrophils in our immune analysis, elucidating new immunophenotypic changes in phagocytes as well as NK cells. This study enhances our understanding of TXA-mediated effects on the haemostatic and immune response in surgery, validating changes in important functional immune cell subsets in orthopaedic patients.
ChemInform Abstract: REACTIONS OF VINYL ETHERS WITH COBALAMINS AND COBALOXIMS (1975)

Abstract Trotz der Argumente anderer Autoren, die die Untersuchungsergebnisse in Frage stellten, wird zum zweiten Mal über die Reaktion von Äthyl‐ bzw. 2‐Hydroxyäthyl‐ vinyläther mit Bromo‐pyridin‐cobaloxim und Hydroxocobalamin in Gegenwart von Alkohol und Basen zu entsprechendem 2,2‐Diäthoxyäthyl‐ bzw. 1,3‐Dioxacyclopentyl‐ (2)‐methyl‐pyridincobaloxim oder ‐cobalamin berichtet.
Colorectal Tumors Require NUAK1 for Protection from Oxidative Stress (2018)

Exploiting oxidative stress has recently emerged as a plausible strategy for treatment of human cancer, and antioxidant defenses are implicated in resistance to chemotherapy and radiotherapy. Targeted suppression of antioxidant defenses could thus broadly improve therapeutic outcomes. Here, we identify the AMPK-related kinase NUAK1 as a key component of the antioxidant stress response pathway and reveal a specific requirement for this role of NUAK1 in colorectal cancer. We show that NUAK1 is activated by oxidative stress and that this activation is required to facilitate nuclear import of the antioxidant master regulator NRF2: Activation of NUAK1 coordinates PP1β inhibition with AKT activation in order to suppress GSK3β-dependent inhibition of NRF2 nuclear import. Deletion of NUAK1 suppresses formation of colorectal tumors, whereas acute depletion of NUAK1 induces regression of preexisting autochthonous tumors. Importantly, elevated expression of NUAK1 in human colorectal cancer is associated with more aggressive disease and reduced overall survival.<b>Significance:</b> This work identifies NUAK1 as a key facilitator of the adaptive antioxidant response that is associated with aggressive disease and worse outcome in human colorectal cancer. Our data suggest that transient NUAK1 inhibition may provide a safe and effective means for treatment of human colorectal cancer via disruption of intrinsic antioxidant defenses. <i>Cancer Discov; 8(5); 632-47. ©2018 AACR.</i><i>This article is highlighted in the In This Issue feature, p. 517</i>.
PO-35 FIRST IN MAN MEASUREMENT OF ARTERIAL STIFFNESS USING A CONNECTED BATHROOM SCALE: CALIBRATION AGAINST SPHYGMOCOR (2016)

Background: Measurement of arterial stiffness (AS) is still considered difficult. We developed a non- invasive technique to assess AS from a connected bathroom scale, based on ballistocardiography (BCG) and impedance plethysmography (IPG). Methods: We included 192 subjects and patients, 106 for calibration study (cal), 86 for validation study (val), 33% hypertensives, mean age 48±17 years, 48% women. The scale pulse transit time (WS- PTT) was calculated as the difference between BCG systolic signals and IPG blood flow in the foot. Distance was estimated from body height and PWV was calculated. Carotid to femoral transit time (CF-PTT) was measured using SphygmoCor. Spearman and robust multivariate regressions were used. Results: The WS-PTT correlated well with CF-PTT with R=0.73 in pooled population (cal 0.79, val 0.66). WS-PWV correlated with CF-PWV with R=0.76 (cal 0.80, val 0.70). The standard deviation of difference was 1.39 m/s with a bias of 0.25 m/s compared with CF-PWV. Correlations of WS-PWV with age and blood pressure were similar (R= 0.72 and 0.59, resp.) to those of CF-PWV (R=0.67 and 0.61, resp.). These good correlations were non-trivial given the differences in wave paths, the fact that measurements are made in orthostatic position and totally investigator-free. Conclusion: We show in two distinct populations that a simple user-oriented instrument such as a connected bathroom scale can estimate arterial stiffness with accuracy close to healthcare-oriented systems. Because these devices will be used by the general population, the availability of arterial stiffness data on very large, non-medicalized populations will change our management of well-being and health.
Robust Workload and Energy Management for Sustainable Data Centers (2016)

A large number of geo-distributed data centers begin to surge in the era of data deluge and information explosion. To meet the growing demand in massive data processing, the infrastructure of future data centers must be energy-efficient and sustainable. Facing this challenge, a systematic framework is put forth in this paper to integrate renewable energy sources (RES), distributed storage units, cooling facilities, as well as dynamic pricing into the workload and energy management tasks of a data center network. To cope with RES uncertainty, the resource allocation task is formulated as a robust optimization problem minimizing the worst-case net cost. Compared with existing stochastic optimization methods, the proposed approach entails a deterministic uncertainty set where generated RES reside, thus can be readily obtained in practice. It is further shown that the problem can be cast as a convex program, and then solved in a distributed fashion using the dual decomposition method. By exploiting the spatio-temporal diversity of local temperature, workload demand, energy prices, and renewable availability, the proposed approach outperforms existing alternatives, as corroborated by extensive numerical tests performed using real data.
Supervised Distance Matrices (2008)

We introduce a novel statistical concept, called a supervised distance matrix, which quantifies pairwise similarity between variables in terms of their association with an outcome. Supervised distance matrices are derived in two stages. First, the observed data is transformed based on particular working models for association. Examples of transformations include residuals or influence curves from regression models. In the second stage, a choice of distance measure is used to compute all pairwise distances between variables in the transformed data. We present consistent estimators of the resulting distance matrix, including an inverse probability of censoring weighted estimator for use with right-censored outcomes. Supervised distance matrices can be used with standard (unsupervised) clustering algorithms to identify groups of similarly predictive variables and to discover subpopulations of related samples. This approach is illustrated using simulations and an analysis of gene expression data with a censored survival outcome. The proposed methods are widely applicable in genomics and other fields where high-dimensional data is collected on each subject.
Centromere defects, chromosome instability, and cGAS-STING activation in systemic sclerosis (2022)

Centromere defects in Systemic Sclerosis (SSc) have remained unexplored despite the fact that many centromere proteins were discovered in patients with SSc. Here we report that lesion skin fibroblasts from SSc patients show marked alterations in centromeric DNA. SSc fibroblasts also show DNA damage, abnormal chromosome segregation, aneuploidy (only in diffuse cutaneous (dcSSc)) and micronuclei (in all types of SSc), some of which lose centromere identity while retaining centromere DNA sequences. Strikingly, we find cytoplasmic "leaking" of centromere proteins in limited cutaneous SSc (lcSSc) fibroblasts. Cytoplasmic centromere proteins co-localize with antigen presenting MHC Class II molecules, which correlate precisely with the presence of anti-centromere antibodies. CENPA expression and micronuclei formation correlate highly with activation of the cGAS-STING/IFN-β pathway as well as markers of reactive oxygen species (ROS) and fibrosis, ultimately suggesting a link between centromere alterations, chromosome instability, SSc autoimmunity, and fibrosis.
Coherently seeded optical parametric amplifier with 500 nJ short-wave infrared signal at 1 MHz (2017)

We introduce an optical parametric amplifier driven by a 3.5 μJ, 130 fs pulse at 1040 nm from a KMLabs Y-Fi HP. The optical parametric amplifier is seeded with white-light generated in a bulk YAG crystal. The net conversion efficiency into the short-wave infrared signal is as high 14%, and we are presently able to cover 1360–1800 nm (signal) and 2.35–4.15 μm (idler).
Peptidyl arginine deiminase 4 deficiency protects against subretinal fibrosis by inhibiting Müller glial hypercitrullination (2022)

Retinal scarring with vision loss continues to be an enigma in individuals with advanced age-related macular degeneration (AMD). Müller glial cells are believed to initiate and perpetuate scarring in retinal degeneration as these glial cells participate in reactive gliosis and undergo hypertrophy. We previously showed in the murine laser-induced model of choroidal neovascularization that models wet-AMD that glial fibrillary acidic protein (GFAP) expression, an early marker of reactive gliosis, increases along with its posttranslational modification citrullination. This was related to increased co-expression of the citrullination enzyme peptidyl arginine deiminase-4 (PAD4), which also colocalizes to GFAP filaments. However, whether such hypercitrullination in Müller glial drives fibrotic pathology has remained understudied. Here, using male and female C57Bl6 mice subjected to laser injury, we investigated in a temporal study how citrullination impacts GFAP and PAD4 dynamics. We found that high molecular weight citrullinated species that accumulate in Müller glia corresponded with dynamic changes in GFAP and PAD4 showing their temporal redistribution from polymeric cytoskeletal to soluble protein fractions using immunostaining and western blot analysis. In conditional glial-specific PAD4 knockout (PAD4cKO) mice subjected to laser injury, there was a stark reduction of citrullination and of polymerized GFAP filaments. These injured PAD4cKO retinas showed improved lesion healing, as well as reduced fibronectin deposition in the subretinal space at 30 days. Taken together, these findings reveal that pathologically overexpressed PAD4 in reactive Müller glia governs GFAP filament dynamics and alters their stability, suggesting chronic PAD4-driven hypercitrullination may be a target for retinal fibrosis.
Production of Highly Aligned Collagen Scaffolds by Freeze-drying of Self-assembled, Fibrillar Collagen Gels (2016)

Matrix and cellular alignment are critical factors in the native function of many tissues, including muscle, nerve, and ligaments. Collagen is frequently a component of these aligned tissues, and collagen biomaterials are widely used in tissue engineering applications. However, the generation of aligned collagen scaffolds that maintain the native architecture of collagen fibrils has not been straightforward, with many methods requiring specialized equipment or technical procedures, extensive incubation times, or denaturing of the collagen. Herein, we present a simple, rapid method for fabrication of highly aligned collagen scaffolds. Collagen was assembled to form a fibrillar hydrogel in a cylindrical conduit with high aspect ratio and then frozen and lyophilized. The resulting collagen scaffolds demonstrated highly aligned topographical features along the scaffold surface. This presence of an initial fibrillar network and the high-aspect ratio vessel were both required to generate alignment. The diameter of fabricated scaffolds was found to vary significantly with both the collagen concentration of the hydrogel suspension and the diameter of conduits used for fabrication. Additionally, the size of individual aligned topographical features was significantly dependent on the conduit diameter and the freezing temperature. When cultured on aligned collagen scaffolds, both rat dermal fibroblasts and axons emerging from chick dorsal root ganglia explants demonstrated elongated, aligned morphology and growth on the aligned topographical features. Overall, this method presents a simple means for generating aligned collagen scaffolds that can be applied to a wide variety of tissue types, particularly those where such alignment is critical to native function.
Optimal investment horizons for the main indices of the Warsaw Stock Exchange (2014)

The investment horizon is the smallest time interval when an asset crosses a fixed value of the return level. For a given return level, the investment horizon distribution is created by putting the investment horizons into a histogram. We fit probability distribution function to the histogram. The maximum of the function is called the optimal investment horizon. We performed the analysis of some indices of the Warsaw Stock Exchange for WIG, WIG20, mWIG40 and shares of KGHM and MBK. For these assets, we found the coefficients of linear proportion between the optimal investment horizons and the logarithm of their return levels.
Cutting Edge: Polycomb Gene Expression Patterns Reflect Distinct B Cell Differentiation Stages in Human Germinal Centers (2000)

Polycomb group (Pc-G) proteins regulate homeotic gene expression in Drosophila, mouse, and humans. Mouse Pc-G proteins are also essential for adult hematopoietic development and contribute to cell cycle regulation. We show that human Pc-G expression patterns correlate with different B cell differentiation stages and that they reflect germinal center (GC) architecture. The transition of resting mantle B cells to rapidly dividing Mib-1(Ki-67)+ follicular centroblasts coincides with loss of BMI-1 and RING1 Pc-G protein detection and appearance of ENX and EED Pc-G protein expression. By contrast, differentiation of centroblasts into centrocytes correlates with reappearance of BMI-1/RING1 and loss of ENX/EED and Mib-1 expression. The mutually exclusive expression of ENX/EED and BMI-1/RING1 reflects the differential composition of two distinct Pc-G complexes. The Pc-G expression profiles in various GC B cell differentiation stages suggest a role for Pc-G proteins in GC development.
Efficient femtosecond mid-infrared generation based on a Cr:ZnS oscillator and step-index fluoride fibers (2019)

Femtosecond light sources in the 3-5 μm region are highly sought after for numerous applications. While they can be generated by using nonlinear effects in optical fibers, the efficiencies and effectiveness of frequency conversion can be significantly enhanced by using ultrashort driving pulses. Here, we report on a few-cycle Cr:ZnS oscillator driving low-order soliton dynamics in soft-glass fibers. By selecting appropriate parameters, sub-two-cycle pulses or broad supercontinua spanning over 1.7 octaves from 1.6 to 5.1 μm can be generated at average power levels exceeding 300 mW. In the same setting, Raman-induced soliton self-frequency shifting has been exploited to generate sub-100-fs pulses continuously tunable from 2.3 to 3.85 μm with a conversion efficiency of ∼50%. These results demonstrate the vast potential of using Cr:ZnS or Cr:ZnSe lasers for powerful mid-infrared generation.
Flexor Carpi Radialis Brevis Resection for Treatment of a Distal Radius Fracture: A Case Report (2021)

The flexor carpi radialis brevis (FCRB) is an anomalous muscle of the forearm that is only present in 3.5 to 8.6% of the population. In the case of volar plating of distal radius fractures, the FCRB inhibits proper fracture exposure and thus hinders proper reduction. A 78-year-old female presented with right distal radius fracture which necessitated internal fixation. Following mobilization and retraction of the flexor carpi radialis tendon, an anomalous muscle belly was identified as the FCRB. With continued difficulty in exposure and fracture site reduction, resection of the FCRB was performed. The patient was able to return to her activities of daily living without pain and demonstrated no appreciable functional deficit. This case report demonstrates a distal radius fracture where FCRB resection was used, resulting in no detrimental clinical outcomes.
Wafer Fusion Technique Applied to GaN/GaN System (2000)

The wafer fusion technique is applied to a GaN/GaN system for the first time. The processing conditions for successful wafer fusion are clarified. The lowest annealing temperature for successful fusion of GaN/GaN is 500°C. It is found that surface smoothness and a large weighting pressure are essential to achieve both a uniform interface and better reproducibility. The electric property of the fused interface is also characterized. Current–voltage ( I – V ) characteristics of the n-GaN/n-GaN and p-GaN/p-GaN fused interface reveal that a pinning effect of the Fermi level exists at the fused interface.
Detecting Hardcoded Login Information from User Input (2022)

Internet of Things (IoT) for smart homes provides high levels of convenience, but it introduces the risk of private data leakage. There were reports in 2020 of some firmware containing hardcoded login information that allows anyone to access the firmware via the Internet. According to OWASP 2018, the most common IoT vulnerability is &#x201C;weak, guessable, or hardcoded passwords. &#x201C; In this paper, we proposed a method for detecting hardcoded login information (username and password) in IoT devices using static analysis with a focus on the user input value. An attacker enters values when attempting to log into IoT devices. As a result, we believe that tracing user input value is an effective method for detecting hardcoded login information. To the best of our knowledge, our method is the first method focusing on user input. This method is also effective to protect from the first vulnerability from the OWASP&#x0027;s ranking. We tested the method&#x0027;s capability by searching six real-world firmware files that contained hardcoded login information. The results showed that the method found the target information within a smaller candidate list than the previous study, implying that our method is more accurate than other searches.
Characterizing a novel scintillating glass for application to megavoltage cone‐beam computed tomography (2018)

Imaging performance of the prototype LKH-5 detector was measured and analyzed for both planar and 3D contexts. Improving noise transfer of the detector results in concurrent improvement of DQE(0). For 3D imaging, temporal characteristics were adequate for artifact-free performance and at relevant doses, the detector retained quantum noise limited performance. Although quantitative MTF measurements suggest poorer resolution, small object representation of the prototype imager is qualitatively improved over the conventional detector due to the measured reduction in noise.