gebhart/patrepeval huggingface dataset:
Genetic Associations and Differential mRNA Expression Levels of Host Genes Suggest a Viral Trigger for Endemic Pemphigus Foliaceus (2022)

The long search for the environmental trigger of the endemic pemphigus foliaceus (EPF, fogo selvagem) has not yet resulted in any tangible findings. Here, we searched for genetic associations and the differential expression of host genes involved in early viral infections and innate antiviral defense. Genetic variants could alter the structure, expression sites, or levels of the gene products, impacting their functions. By analyzing 3063 variants of 166 candidate genes in 227 EPF patients and 194 controls, we found 12 variants within 11 genes associated with differential susceptibility (p < 0.005) to EPF. The products of genes TRIM5, TPCN2, EIF4E, EIF4E3, NUP37, NUP50, NUP88, TPR, USP15, IRF8, and JAK1 are involved in different mechanisms of viral control, for example, the regulation of viral entry into the host cell or recognition of viral nucleic acids and proteins. Only two of nine variants were also associated in an independent German cohort of sporadic PF (75 patients, 150 controls), aligning with our hypothesis that antiviral host genes play a major role in EPF due to a specific virus−human interaction in the endemic region. Moreover, CCL5, P4HB, and APOBEC3G mRNA levels were increased (p < 0.001) in CD4+ T lymphocytes of EPF patients. Because there is limited or no evidence that these genes are involved in autoimmunity, their crucial role in antiviral responses and the associations that we observed support the hypothesis of a viral trigger for EPF, presumably a still unnoticed flavivirus. This work opens new frontiers in searching for the trigger of EPF, with the potential to advance translational research that aims for disease prevention and treatment.
DNA double-strand breaks with 5′ adducts are efficiently channeled to the DNA2-mediated resection pathway (2015)

DNA double-strand breaks (DSBs) with 5' adducts are frequently formed from many nucleic acid processing enzymes, in particular DNA topoisomerase 2 (TOP2). The key intermediate of TOP2 catalysis is the covalent complex (TOP2cc), consisting of two TOP2 subunits covalently linked to the 5' ends of the nicked DNA. In cells, TOP2ccs can be trapped by cancer drugs such as etoposide and then converted into DNA double-strand breaks (DSBs) that carry adducts at the 5' end. The repair of such DSBs is critical to the survival of cells, but the underlying mechanism is still not well understood. We found that etoposide-induced DSBs are efficiently resected into 3' single-stranded DNA in cells and the major nuclease for resection is the DNA2 protein. DNA substrates carrying model 5' adducts were efficiently resected in Xenopus egg extracts and immunodepletion of Xenopus DNA2 also strongly inhibited resection. These results suggest that DNA2-mediated resection is a major mechanism for the repair of DSBs with 5' adducts.
Multimodal detection of sleep apnoea using electrocardiogram and oximetry signals (2008)

A method for the detection of sleep apnoea, suitable for use in the home environment, is presented. The method automatically analyses night-time electrocardiogram (ECG) and oximetry recordings and identifies periods of normal and sleep-disordered breathing (SDB). The SDB is classified into one of six classes: obstructive, mixed and central apnoeas, and obstructive, mixed and central hypopnoeas. It also provides an estimated apnoea, hypopnoea and apnoea-hypopnoea index. The basis of the method is a pattern recognition system that identifies episodes of apnoea by analysing the heart variability, an ECG-derived respiration signal and blood oximetry values. The method has been tested on 183 subjects with a range of apnoea severities who have undergone a full overnight polysomnogram study. The results show that the method separates control subjects from subjects with clinically significant sleep apnoea with a specificity of 83 per cent and sensitivity of 95 per cent. These results demonstrate that home-based screening for sleep apnoea is a viable alternative to hospital-based tests with the added benefit of low cost and minimal waiting times.
Tiaspirone in Schizophrenia (1987)

It was predicted that tiaspirone, a novel compound, would benefit schizophrenic patients since in animal experiments it is a potent dopamine blocker. Following a placebo washout period of 1 to 2 weeks, 14 patients were treated for 28 days with the drug in a single-blind, dose ranging trial. GAS, NOSIE, and BPRS scores all showed significant improvement. No serious adverse effects were found. The absence of extrapyramidal symptoms was particularly encouraging since 10 of the 14 subjects had previously had them on other neuroleptics. Tiaspirone may represent a step forward in the search for a safer antipsychotic.
Molecular Design of Zwitterionic Polymer Interfaces: Searching for the Difference (2018)

The widespread occurrence of zwitterionic compounds in nature has incited their frequent use in designing biomimetic materials. Therefore, zwitterionic polymers are a thriving field. A particular interest for this particular polymer class has currently focused on their use in establishing neutral, low-fouling surfaces. After highlighting strategies to prepare model zwitterionic surfaces as well as those that are more suitable for practical purposes relying strongly on radical polymerization methods, we present recent efforts to diversify the structure of the hitherto quite limited variety of zwitterionic monomers and of the derived polymers. We identify key structural variables, consider their influence on essential properties such as overall hydrophilicity and long-term stability, and discuss promising targets for the synthesis of new variants.
Prognostic Impact of Acute Myeloid Leukemia Classification: Importance of Detection of Recurring Cytogenetic Abnormalities and Multilineage Dysplasia on Survival (2003)

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system. We compared the diagnostic performance of isoelectric focusing (IEF) combined with IgG immunoblotting to high-resolution agarose gel electrophoresis for the detection of intrathecal synthesis of IgG due to the MS disease process. In 20 patients with definite MS, IEF and high-resolution agarose gel electrophoresis had sensitivities of 90% and 60%, respectively. In the 51 patients with no evidence of MS, the methods had specificities of 94% and 96%, respectively. With a prevalence of 15% in this test population, IEF and high-resolution agarose gel electrophoresis had positive predictive values of 73% and 73% and negative predictive values of 98% and 93%, respectively. The IEF method improves the sensitivity and the negative predictive value of the oligoclonal-banding assay, the IEF gels are easier to interpret, and the IEF assay requires a smaller cerebrospinal fluid volume.
Selective atomic layer etching of HfO2 over silicon by precursor and substrate-dependent selective deposition (2020)

The early work of John Coburn and Harold Winters revealed a synergistic effect in ion-enhanced Si etching by the concurrent irradiation of Ar+ and XeF2. This finding provided an important foundation for the development of plasma dry etching processes. The experimental results of Coburn and Winters also found effects that are useful for the development of atomic layer etching (ALE) processes characterized by a self-limited etch rate. ALE approaches are widely established and can be utilized in either directional or isotropic etching by employing proper surface modification and product removal steps. Nevertheless, the development of material selective ALE processes is still limited. An approach that combines substrate-selective deposition with etching opens a new processing window for selective ALE. The authors studied the deposition behavior of mixtures of methane (CH4) with trifluoromethane (CHF3) and mixtures of methane with octafluorocyclobutane (C4F8) on HfO2 and Si surfaces. The experimental results show that a CH4/C4F8 mixture produces a comparable fluorocarbon (FC) deposition thickness on both HfO2 and Si during the deposition step. In contrast, a CH4/CHF3 mixture deposits an FC film on Si, whereas it fluorinates the HfO2 surface with negligible FC deposition. Utilizing these behaviors allows for an ALE process based on CH4/CHF3 for selective removal of HfO2 over Si. Surface characterization data that provide mechanistic insights into these processes are also provided and discussed.
Anesthesia for Cesarean Section and Acid Aspiration Prophylaxis (1999)

In Response: We greatly appreciate the interest of Dr. Goudsouzian, who was among the first investigators to recommend H2 blockers in pediatric anesthesia. Concerning the first paragraph of his letter, however, he obviously misread our summary, which states, "more widespread use in obstetric anesthesia and [instead of than] in other patients at risk." Moreover, we clearly stated that the number of more than one fatality per year relies on death from acid aspiration in Germany in the context of cesarean section only. We have no data allowing even for a guess on fatalities in other surgical fields. With an incidence of acid aspiration of approximately 1:1500-3000 and a mortality as low as 5%, no ethically conducted study will ever prove the benefit of prophylactic measures in humans, be it drugs, positioning, esophageal compression, or even nil per os. We are as uncomfortable as Dr. Goudsouzian seems to be with what is generally called critical gastric volume or critical acidity, because both have been arbitrarily set after a single, not too elaborate, experiment in one almost suffocated monkey [1]. A later well designed study in primates clearly showed that aspirating gastric juice of pH 1.0 was deleterious only if high volumes were administered [2]. In other species, however, acidity of the aspirate proved crucial for outcome [3,4]. We fully agree with Dr. Goudsouzian that there are no data to scientifically prove the benefit of any prophylactic measure to avoid acid aspiration or to alleviate its consequences once it occurs. However, with the data from animal studies and clinical observations in mind, we still believe that lowering gastric volume (e.g., by fasting), decreasing the probability of regurgitation (e.g., by positioning, cricoid pressure, or fast induction), and reducing the acidity of an occasionally aspirated aliquot is worth the small effort. We believe this even more because, in most circumstances, a sensible head-up position, an expertly performed Sellick's maneuver, newer H2 blockers, and sodium citrate are easily applied, without real side effects, and inexpensive. In the worst case, all recommended measures may be unnecessary. This, however, cannot be proven, either. Because all measures are not really harmful, we would prefer taking the risk of applying useless measures instead of missing a potential benefit. Hajo Schneck, MD Michaela Scheller, MD Eberhard Kochs, MD Institut fur Anaesthesiologie der Technischen; Universitat Munchen; Klinikum Rechts der Isar; 81675 Munchen, Germany
Biochemical Markers for Monitoring Response to Therapy: Evidence for Higher Bone Specificity by a Novel Marker Compared with Routine Markers (2008)

The aim of the present study was to compare a novel marker for high bone turnover with two routine markers for screening in prostate cancer patients. The markers were evaluated in two studies: (a) a cross-sectional study of 170 prostate cancer patients with local disease stratified by +/-lymph node metastases (N 0, N1) compared with controls and (b) a longitudinal study of 40 hormone refractory prostate cancer patients stratified by skeletal involvement and followed during docetaxel (+/-BM) and zoledronate (+BM) treatment. Presence or absence of bone metastases (BM) was assessed by imaging techniques (magnetic resonance imaging or X-ray) and technetium-99m scintigraphy. The serum or urinary levels of alpha C-telopeptide of collagen type I (alphaalphaCTX), prostate-specific antigen (PSA), and total alkaline phosphatase (tALP) were assessed. PSA was elevated in both N 0 and N1 patients compared with controls, whereas alphaalphaCTX was elevated only in N1 patients. tALP exhibited no difference in any of the groups. In the treatment study, PSA decreased with treatment in both the -BM and +BM groups compared with baseline values, showing similar effect of docetaxel or docetaxel/zoledronate treatment on this marker. On the contrary, alphaalphaCTX and tALP did not decrease with docetaxel treatment in the -BM group compared with baseline, whereas it decreased significantly with docetaxel/zoledronate treatment in the +BM group, already after 1 month of treatment for alphaalphaCTX. Results suggest that alphaalphaCTX is superior to PSA and tALP for identifying patients having a high risk of metastatic disease and for monitoring skeletal progression in +BM prostate cancer patients during treatment.
Improving Translation Models for Predicting the Energy Yield of Photovoltaic Power Systems. Cooperative Research and Development Final Report, CRADA Number CRD-13-526 (2015)

The project under this CRADA will analyze field data of various flat-plate and concentrator module technologies and cell measurements at the laboratory level. The field data will consist of current versus voltage data collected over many years on a latitude tilt test bed for Si, CdTe, amorphous silicon, and CIGS technologies. The concentrator data will be for mirror- and lens-based module designs using multijunction cells. The laboratory data will come from new measurements of cell performance with systematic variation of irradiance, temperature and spectral composition. These measurements will be labor-intensive and the aim will be to cover the widest possible parameter space for as many different PV samples as possible. The data analysis will require software tools to be developed. These tools will be customized for use with the specific NREL datasets and will be unsuitable for commercial release. The tools will be used to evaluate different translation equations against NREL outdoor datasets.
Handling of Non-Periodic Contra Rotating Open Rotor Data (2012)

In this contribution, we present two different concepts to handle the non-periodic nature of Contra Rotating Open Rotor (CROR) if the front and the aft rotor rotate with a slightly different rotational speed. The first procedure that is presented consists of a correction matrix applied to the source data used in the DLR FWH-code APSIM+. For periodic data the correction matrix reduces to the identity matrix, thereby recovering the standard Fourier transformation. The second method is based on the Vanicek approximation, and consists of a successive least-square approximation of non-periodic data. The developed methods are tested with artificially generated data, illustrating the ability to accurately representing non-periodic data. A comparison between the two methods shows that the first method is more accurate than the Vanicek approximation. Preliminary results on actual non-periodic CROR data reveals the influence of the non-periodic correction as compared to uncorrected data, i.e., differences ranging up to 10 dB are seen for the considered cases.
Performance debugging in the large via mining millions of stack traces (2012)

Given limited resource and time before software release, development-site testing and debugging become more and more insufficient to ensure satisfactory software performance. As a counterpart for debugging in the large pioneered by the Microsoft Windows Error Reporting (WER) system focusing on crashing/hanging bugs, performance debugging in the large has emerged thanks to available infrastructure support to collect execution traces with performance issues from a huge number of users at the deployment sites. However, performance debugging against these numerous and complex traces remains a significant challenge for performance analysts. In this paper, to enable performance debugging in the large in practice, we propose a novel approach, called StackMine, that mines callstack traces to help performance analysts effectively discover highly impactful performance bugs (e.g., bugs impacting many users with long response delay). As a successful technology-transfer effort, since December 2010, StackMine has been applied in performance-debugging activities at a Microsoft team for performance analysis, especially for a large number of execution traces. Based on real-adoption experiences of StackMine in practice, we conducted an evaluation of StackMine on performance debugging in the large for Microsoft Windows 7. We also conducted another evaluation on a third-party application. The results highlight substantial benefits offered by StackMine in performance debugging in the large for large-scale software systems.
New Impossible Differential Cryptanalysis of ARIA. (2008)

Abstract. This paper studies the security of ARIA against impossible differential cryptanalysis. Firstly an algorithm is given to find many new 4-round impossible differentials of ARIA. Followed by such impossible differentials, we improve the previous impossible differential attack on 5/6-round ARIA. We also point out that the existence of such impossible differentials are due to the bad properties of the binary matrix employed in the diffusion layer. Key Words: Block Cipher, Impossible Differential, ARIA 1
Adaptive Predictive Control of ATM Networks with Multiple Nodes (2006)

There may be in great oscillation and degradation in ATM networks due to higher-priori traffic, such as CBR/VBR, multiple-loop delays, measured disturbance and dynamical variants. An adaptive predictive congestion control is presented for multi-node ATM networks, in which real-time rate control is realized by online estimation of networks parameters, and closed-loop stability is guaranteed, and the extent and duration of congestion has been greatly reduced, and the utilization is maximized and packet loss rate is decreased. The effectiveness of the proposed methods is demonstrated by the simulation results
Cost-analysis model of colonoscopy preparation using split-dose reduced-volume oral sulfate solution (OSS) and polyethylene glycol with electrolytes solution (PEG-ELS) (2015)

From a payer's perspective, the model showed that the use of OSS as the cleansing agent resulted in potential cost savings compared with PEG-ELS. Cost savings under OSS remained under various sensitivity analyses.
Applications of lossless MD structures for the filtering of digital image sequences (1991)

It is pointed out that multidimensional (MD) recursive digital filters may be designed from passive s-domain prototype LCR filters. Unrealizable delay-free loops are avoided by applying a predistortion technique to the reactance branches of the prototype filter, prior to bilinear transformation. Recursive differentiators are used to implement the multidimensional discrete reactance branches in a Type II ladder signal flow graph. The resultant filters exhibit a high level of concurrency and therefore the potential for high-speed processing. The 3D recursive filters that are designed are well suited for the enhancement of linear trajectory signals in dynamic images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Practical aspects of model predictive control implementation on an industrial lime kiln (1997)

Rotary lime kilns are significant energy consumers. In the past, little attention has been paid to kilns resulting in poor efficiency and lime quality. With the adoption of stringent environmental regulations and increased competitiveness, the need for improved lime kiln control has become significant. Lime quality and granular size are primarily determined by the temperature profile along the kiln and the solids residence time. Total reduced sulphur (TRS) and energy consumption can be minimized by maintaining the excess oxygen between constraints. A constrained model predictive control algorithm was implemented on an industrial lime kiln to improve lime quality, decrease energy consumption, reduce maintenance cost and eliminate TRS emissions. The control strategy is very successful in controlling the temperature profile along the kiln while respecting the constraints in excess oxygen and in the manipulated variables. The strategy is also successful in controlling the temperatures during recurrent upset conditions caused by regular washing of the lime mud filter.
Size Exclusion Chromatography of Copolymers (1983)

Size exclusion chromatography (SEC) of copolymers has two basic requirements: the capability to detect selectively the concentration of the copolymer components in the eluting solution, and to obtain suitable calibration and interpretation for both size and composition fractionation. To calibrate and interpret copolymer fractionation results by using the existing theory, it is necessary to determine the experimental conditions that guarantee either size or composition fractionation. Sufficient knowledge of the hydrodynamic properties of the copolymer molecules in solution is also required to relate copolymer size to molecular weight. This chapter reviews the SEC fractionation of copolymers and outlines techniques used to ensure size separation for styrene—acrylonitrile copolymers. To test the separation mechanism, a number of solvents and column configurations were investigated. Conditions that give mainly size or mainly composition fractionation are discussed, as well as guidelines for the selection of solvent and column configuration. Extensive characterization of styrene—acrylonitrile copolymers, based on size fractionation and careful selection of the detection system, is reported.
Suppressive myeloid cells are expanded by biliary tract cancer-derived cytokines in vitro and associate with aggressive disease (2020)

BTC-derived factors promote suppressive myeloid cell expansion, and higher numbers of CD33<sup>+</sup>S100a9<sup>+</sup> cells in resectable BTC tumours correlates with more aggressive disease.
Promoter Architecture of the Porphyromonas gingivalis Fimbrillin Gene (1999)

Porphyromonas gingivalis fimbriae can mediate adherence to many of the available substrates in the oral cavity. Expression of P. gingivalis fimbriae is regulated at the transcriptional level by environmental signals, such as temperature and hemin concentration. The arrangement of the upstream promoter and regulatory sequences required for transcription and control of the fimbrial structural gene (fimA) was investigated. Primer extension analysis demonstrated that the transcriptional start site of the fimA gene is located 41 bp upstream from the translational start codon. A region (upf) spanning 648 bp upstream of the start codon to 44 bp downstream of the translational start site was cloned upstream of a promoterless lacZ reporter gene. A series of deletion and base substitution mutations were then generated in the upf region. The constructs were introduced into the chromosome of P. gingivalis, and promoter activity measured by assaying levels of beta-galactosidase. The results showed that fimA contains sequences resembling sigma70 promoter consensus sequences, consisting of a -10 region (TATGAC) located at -18 to -23 and a -35 region (TTGTTG) located at -41 to -46 from the transcriptional start point. The AT-rich upstream sequences spanning bases -48 to -85 and bases -90 to -240 were required for full expression of the fimA gene, indicating the existence of positive regulation regions. Moreover, the -48 to -64 region may constitute an UP element, contributing to promoter activity in P. gingivalis. Thus, our data suggest that the P. gingivalis fimA gene has a transcription complex consisting of -10 and -35 sequences, an UP element, and additional AT-rich upstream regulatory sequences.
ChemInform Abstract: Some Reactions of N‐Ethylisatin with Methyl Ketones. (1990)

Abstract In the presence of NEt 3 , N‐ethylisatin (I) adds to the methyl ketones (II) to afford the products (III) some conversions of which are investigated.