gebhart/patrepeval huggingface dataset:
Replication, Repair, and Translesion Polymerase Bypass of N6-Oxopropenyl-2′-deoxyadenosine (2013)

The oxidative stress products malondialdehyde and base propenal react with DNA bases forming the adduction products 3-(2'-deoxy-β-D-erythro-pentofuranosyl)pyrimido[1,2-a]purin-10(3H)-one (M1dG) and N(6)-(oxypropenyl)-2'-deoxyadenosine (OPdA). M1dG is mutagenic in vivo and miscodes in vitro, but little work has been done on OPdA. To improve our understanding of the effect of OPdA on polymerase activity and mutagenicity, we evaluated the ability of the translesion DNA polymerases hPols η, κ, and ι to bypass OPdA in vitro. hPols η and κ inserted dNTPs opposite the lesion and extended the OPdA-modified primer to the terminus. hPol ι inserted dNTPs opposite OPdA but failed to fully extend the primer. Steady-state kinetic analysis indicated that these polymerases preferentially insert dTTP opposite OPdA, although less efficiently than opposite dA. Minimal incorrect base insertion was observed for all polymerases, and dCTP was the primary mis-insertion event. Examining replicative and repair polymerases revealed little effect of OPdA on the Sulfolobus solfataricus polymerase Dpo1 or the Klenow fragment of Escherichia coli DNA polymerase I. Bacteriophage T7 DNA polymerase displayed a reduced level of OPdA bypass compared to unmodified DNA, and OPdA nearly completely blocked the activity of base excision repair polymerase hPol β. This work demonstrates that bypass of OPdA is generally error-free, modestly decreases the catalytic activity of most polymerases, and blocks hPol β polymerase activity. Although mis-insertion opposite OPdA is relatively weak, the efficiency of bypass may introduce A → G transitions observed in vivo.
Supplementary Table 11 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia (2023)

&lt;p&gt;Super-Enhancer-Type Analysis of STAT5 ChIP-Seq Peaks (24 Hours After Drug Treatment).&lt;/p&gt;
Calcification of Human Vascular Cells In Vitro Is Correlated With High Levels of Matrix Gla Protein and Low Levels of Osteopontin Expression (1998)

The cellular and molecular events leading to calcification in atherosclerotic lesions are unknown. We and others have shown that bone-associated proteins, particularly matrix Gla protein (MGP) and osteopontin (OP), can be detected in atherosclerotic lesions, thus suggesting an active calcification process. In the present study, we aimed to determine whether human vascular smooth muscle cells (VSMCs) could calcify in vitro and to determine whether MGP and OP have a role in vascular calcification. We established that human aortic VSMCs and placental microvascular pericytes spontaneously form nodules in cell culture and induce calcification, as detected by von Kossa's method, Alizarin red S staining, and electron microscopy. The cells in calcifying nodules differed from those in monolayer cultures by expressing higher levels of the SMC markers alpha-SM actin, SM22alpha, and calponin. In addition, Northern blot analysis revealed that in human VSMCs, calcification was associated with increased levels of MGP mRNA. In contrast, OP mRNA was barely detectable in calcified human VSMCs and pericyte nodules, nor was OP protein detected, suggesting that OP was not necessary for calcification to occur. These studies reveal that human VSMCs are capable of inducing calcification and that MGP may have a role in human vascular calcification.
Continuous Software Bug Prediction (2021)

Background: Many software bug prediction models have been proposed and evaluated on a set of well-known benchmark datasets. We conducted pilot studies on the widely used benchmark datasets and observed common issues among them. Specifically, most of existing benchmark datasets consist of randomly selected historical versions of software projects, which poses non-trivial threats to the validity of existing bug prediction studies since the real-world software projects often evolve continuously. Yet how to conduct software bug prediction in the real-world continuous software development scenarios is not well studied.
Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure (2012)

Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.
THE PREPARATION AND PROPERTIES OF A DOUBLE SERIES OF ALIPHATIC MERCAPTANS1,2,3 (1932)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE PREPARATION AND PROPERTIES OF A DOUBLE SERIES OF ALIPHATIC MERCAPTANS1,2,3L. M. Ellis Jr. and E. Emmet ReidCite this: J. Am. Chem. Soc. 1932, 54, 4, 1674–1687Publication Date (Print):April 1, 1932Publication History Published online1 May 2002Published inissue 1 April 1932https://pubs.acs.org/doi/10.1021/ja01343a067https://doi.org/10.1021/ja01343a067research-articleACS PublicationsRequest reuse permissionsArticle Views540Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Hypervolemic therapy prevents volume contraction but not hyponatremia following subarachnoid hemorrhage (1992)

Hyponatremia is common following subarachnoid hemorrhage and has alternatively been attributed to either the inappropriate secretion of antidiuretic hormone or natriuresis causing intravascular volume contraction. We prospectively studied body sodium and intravascular volume regulation in 19 patients, beginning within 3 days after acute aneurysmal subarachnoid hemorrhage occurred, in order to determine the impact of hypervolemic therapy on both hyponatremia and volume contraction and to ascertain whether humoral factors account for hyponatremia. Serial measurements of plasma arginine vasopressin, atrial natriuretic factor, renin activity, aldosterone, and catecholamines were correlated with body sodium and fluid balance, change in blood volume, serum sodium concentration, and osmolality. Six patients (32%) developed hyponatremia, but only 2 had a negative sodium balance. In most patients, levels of atrial natriuretic factor were elevated, while plasma renin activity and aldosterone concentrations were generally suppressed. Plasma arginine vasopressin levels were not suppressed during hypo-osmolality and did not correlate with serum osmolality in hyponatremic patients. Only 1 patient had a decrease in blood volume, which was associated with marked rises in aldosterone and plasma renin activity, but normal serum sodium and plasma atrial natriuretic factor levels. We conclude that following subarachnoid hemorrhage: (1) Hypervolemic therapy prevents volume contraction but not hyponatremia, (2) humoral factors may favor both sodium loss and water retention, and (3) arginine vasopressin regulation is disturbed and may contribute to hyponatremia.
Addressing problem gambling: South Africa's National Responsible Gambling Programme. (2011)

In the English-speaking world and some parts of Europe, problem and pathological gambling are treated as a significant public health problem. At the same time, these jurisdictions recognise that for most of those who engage in it, gambling is a harmless leisure activity that may yield public benefits by contributing more in taxation than other leisure industries and/or contributing to out-of-town tourism. Strategies that combine minimising the harm caused with maximising the benefits of gambling are therefore crucial for good public policy. Such lessons may also be relevant to other legal and illegal industries, such as those involving the production and sales of alcohol, where analogous harms and benefits exist.
Response to Proning in Moderate to Severe Acute Respiratory Distress Syndrome: A New Talking Point in an Ongoing Conversation* (2020)

Division of Critical Care Medicine, Departments of Medicine and Emergency Medicine, Cooper University Healthcare, Cooper Medical School of Rowan University, Camden, NJ Department of Anesthesia, Intensive Care and Emergency Medicine, University Medical Center Göttingen, Göttingen, Germany *See also p. 1729. The authors have disclosed that they do not have any potential conflicts of interest.
ChemInform Abstract: HYDROZIRCONATION OF NITRILES: DETECTION OF A LINEAR HETEROALLENE STRUCTURE IN (BENZYLIDENAMIDO)ZIRCONOCENE CHLORIDE (1984)

Abstract Die C ‐substituierten Methylenamido‐zirconocenchloride (III) entstehen als feuchtigkeitsempfindliche Festkörper durch Hydrozirconierung der Nitrile (II).
The adaptive equalizer (2006)

This paper relates the author's experience in inventing the adaptive equalizer including how he addressed intersymbol interference and how he designed the adjustable filter.
Postural Orthostatic Tachycardia Syndrome (POTS): Assess, Diagnose, and Evaluate for POTS Treatment (ADEPT) (2017)

&lt;b&gt;&lt;i&gt;Background/Aims:&lt;/i&gt;&lt;/b&gt; Postural orthostatic tachycardia syndrome (POTS) is often identified as being clinically underdiagnosed and undertreated, resulting in unnecessary costs and poorer patient outcomes. &lt;b&gt;&lt;i&gt;Method:&lt;/i&gt;&lt;/b&gt; Through a literature search, the information has been synthesized, supporting the creation of a POTS diagnostic screening tool that can be implemented within the psychiatric outpatient clinic. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; POTS patients are often referred to psychiatry for the treatment of chronic fatigue and anxiety disorders. Psychiatric professionals are in a position to prescreen for POTS in patients with orthostatic intolerance. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; A diagnostic prescreening tool helps to identify patients with POTS so they can be referred for proper treatment, improving their functionality and quality of life, and decreasing the healthcare burden.
Noise-tolerant Audio-visual Online Person Verification Using an Attention-based Neural Network Fusion (2019)

In this paper, we present a multi-modal online person verification system using both speech and visual signals. Inspired by neuroscientific findings on the association of voice and face, we propose an attention-based end-to-end neural network that learns multi-sensory association for the task of person verification. The attention mechanism in our proposed network learns to conditionally select a salient modality between speech and facial representations that provides a balance between complementary inputs. By virtue of this capability, the network is robust to missing or corrupted data from either modality. In the VoxCeleb2 dataset, we show that our method performs favorably against competing multi-modal methods. Even for extreme cases of large corruption or missing data on either modality, our method demonstrates robustness over other unimodal methods.
Iterative Algorithms for Large Scale Wave Front Reconstruction (2001)

We present preliminary results on large scale iterative wave front reconstruction algorithms for use with multiple deformable mirrors and wave front sensors for rectangular apertures. We describe a class of reconstructors based on circulant preconditioners for Toeplitz block matrices.
Accounting for High Stress Gradient by a Modified Weibull Failure Theory (2007)

A high stress gradient occurs in a component when the stress, due to external loading, rises asymptotically. The Weibull failure theory overestimates the probability of failure for components with high stress gradients generated due to the geometric irregularities, material mismatch, thermal mismatch, and contact loading. A modified Weibull failure theory is proposed in this paper. The method is based on the weight function method. The modified Weibull failure theory was applied to two specimens, and the results showed the ability of the proposed theory to handle high stress gradients. The theory considers variable equivalent stress intensity factors along the faces of cracks; hence, it considers the strength of a specimen to be dependent on the stress field.
Supporting sub-document updates and queries in an inverted index (2008)

Inverted indexes have become the standard indexing method for supporting search queries in a variety of content-based applications. Examples of such applications include enterprise document management, e-mail, web search, and social networks. One shortcoming in current inverted index designs is that they support only document-level updates, forcing a full document to be reindexed even if just part of it changes. This paper describes a new inverted index design that enables applications to break a document into semantically meaningful sub-documents or "sections". Each section of a document can be updated separately, but search queries can still work seamlessly across sections. Our index design is motivated by applications where there is metadata associated with each document that tends to be smaller and more frequently updated than the document's content, but at the same time, it is desireable to search the metadata and content with the same index structure. A novel self-optimizing query execution algorithm is described to efficiently join the sections of a document in the inverted index. Experimental results on TREC and patent data are provided, showing that sections can dramatically improve overall system throughput on a mixed workload of updates and queries.
Impact of power-supply noise on timing in high-frequency microprocessors (2003)

This paper analyses the impact of power-supply noise on the performance of high-frequency microprocessors. First, a delay model that takes this noise into account is proposed for device-dominated and interconnect-dominated timing paths. Then, realistic values for the model parameters are measured on a 2.53 GHz Pentium/sup /spl reg// 4 microprocessor. These values imply that the power-supply noise present on the system board currently reduces clock frequency by 6.5%. The model suggests that the frequency penalty associated with this power-supply noise will reach 8.0% for the 90-nm technology generation.
A model to estimate the cost effectiveness of the indoor environment improvements in office work (2004)

Deteriorated indoor climate is commonly related to increases in sick building syndrome symptoms, respiratory illnesses, sick leave, reduced comfort and losses in productivity. The cost of deteriorated indoor climate for the society is high. Some calculations show that the cost is higher than the heating energy costs of the same buildings. Also building-level calculations have shown that many measures taken to improve indoor air quality and climate are cost-effective when the potential monetary savings resulting from an improved indoor climate are included as benefits gained. As an initial step towards systemizing these building level calculations we have developed a conceptual model to estimate the cost-effectiveness of various measures. The model shows the links between the improvements in the indoor environment and the following potential financial benefits: reduced medical care cost, reduced sick leave, better performance of work, lower turn over of employees, and lower cost of building maintenance due to fewer complaints about indoor air quality and climate. The pathways to these potential benefits from changes in building technology and practices go via several human responses to the indoor environment such as infectious diseases, allergies and asthma, sick building syndrome symptoms, perceived air quality, and thermal environment. The model also includes the annual cost of investments, operation costs, and cost savings of improved indoor climate. The conceptual model illustrates how various factors are linked to each other. SBS symptoms are probably the most commonly assessed health responses in IEQ studies and have been linked to several characteristics of buildings and IEQ. While the available evidence indicates that SBS symptoms can affect these outcomes and suspects that such a linkage exists, at present we can not quantify the relationships sufficiently for cost-benefit modeling. New research and analyses of existing data to quantify the financial importance of SBS symptoms would enable more widespread consideration of the effects of IEQ in cost benefit calculations.
Clinical Correlates of Herpes Simplex Virus Viremia among Hospitalized Adults (2009)

HSV viremia may be associated with a variety of signs and symptoms of morbidity in immunocompetent and immunocompromised hospitalized adults and is associated with high rates of mortality, although causality can be determined only by additional studies.
<title>Application of artificial neural networks to gaming</title> (1995)

Recently, neural network technology has been applied to various actual problems. It has succeeded in producing a large number of intelligent systems. In this article, we suggest that it could be applied to the field of gaming. In particular, we suggest that the neural network model could be used to mimic players' characters. Several computer simulation results using a computer gaming system which is a modified version of the COMMONS GAME confirm our idea.
PD-L1 expression in non-clear cell renal cell carcinoma. (2014)

424 Background: Programmed death-1 (PD-1) receptor negatively regulates T cell-mediated responses.PD-1 ligand (PD-L1) is aberrantly expressed in clear cell renal cell carcinoma (ccRCC) and is associated with worse prognosis. Levels of PD-L1 expressions in non-ccRCC and its association with clinicopathological features and survival are unknown. Methods: Formalin-fixed paraffin-embedded (FFPE) specimens were obtained from 97 patients with chromophobe (CHR), papillary (PAP), translocation Xp11.2 (TrL) RCC and oncoytoma (ONC) and were included in the analysis. PD-L1 expression was evaluated by immunohistochemistry using a mouse monoclonal anti-PD-L1 antibody (405.9A11). The assay was validated using FFPE cell line controls known to be positive or negative for PD-L1 expression by flow cytometry. PD-L1 tumor positivity (PD-L1+) was defined as ≥5% tumor cell membrane staining. For PD-L1 expression in immune cells, a combined score based on the intensity of infiltrate and percentage of positive cells was used. Baseline characteristics including stage/grade, and survival data were collected. Comparisons between PD-L1 expression and clinicopathological features were evaluated using chisq or wilcoxon rank sum tests. Cox model tests for association of PD-L1 expression with OS in univariate and multivariable analysis. Results: Among 97 patients, 12 (12.4%) were considered PD-L1+ in tumor cells: 2/36 (5%) of CHR RCC, 5/50 (10%) of PAP RCC, 3/7 (43%) of TrL RCC, and 2/4 (50%) of ONC. PD-L1 positivity in tumor cells was significantly associated with higher stage (p=0.026) and grade (p=0.046), as well as lower OS on univariate (p=0.02) but not multivariate analysis (p=0.29). On the other hand, PD-L1 positivity by immune cells was observed in 50 (51.5%) patients: 13/36 (36%) of CHR RCC, 30/50 (60%) of PAP RCC, 6/7 (86%) of TrL RCC, and 1/4 (25%) of ONC. PD-L1 positivity in immune cells did not correlate with stage (p=0.7), grade (p=0.1) or OS (p=0.8). Conclusions: PD-L1 expression is variable in non-ccRCC and depends on histology and tumor vs. immune cells scoring. Only PD-L1 positivity in tumors cells was associated with aggressive features. Patients with non-ccRCC should not be automatically excluded from trials of agents that target the PD-1/PD-L1 pathway.
Key Performance Indicators of the Reference 6TiSCH Implementation in Internet-of-Things Scenarios (2020)

Tens of thousands of wireless industrial monitoring deployments exist today, logging more than 18 billion operating hours. These solutions have been around for over a decade and are based on standards such as WirelessHART and ISA100.11a to provide performance guarantees to the applications. The new trend in industry deployments is the convergence of operational and information technologies happening through the Industrial Internet of Things (IIoT) paradigm. The challenge is to bridge the performance of these well-proven industrial standards with the interoperability of IP-based systems. The Internet Engineering Task Force (IETF), the organization behind most of the technical solutions of the Internet, has produced a set of specifications with this requirement in mind. The output of this effort is the 6TiSCH protocol stack based on open standards, such as those that have played a key role in the Internet's ubiquitous adoption. The standardization of 6TiSCH is done. The state-of-the-art research work focus is on important, but niche, optimizations and performance evaluations of the 6TiSCH stack. This paper takes a different approach - it evaluates the performance of the standards-compliant 6TiSCH solution from the end user point of view. It does so on two experimental testbeds, in typical IoT test scenarios based on a well-defined experimentation methodology. We provide a set of Key Performance Indicators (KPIs) useful for the end user to decide whether the 6TiSCH technology is a good fit performance-wise for a particular use case. We demonstrate reliability of a vanilla open-source implementation of 6TiSCH above 99.99%, upstream latency on the order of a second and radio duty cycle well below 1%.
<title>Oxide-defined VCSEL-based smart pixels for the optical database filter</title> (1997)

This paper presents the construction of the smart pixel arrays which perform AND and XOR functions with three-input and one-output optical signals for the application of an optical database filter. The device is based on oxide confined VCSELs bump bonded to GaAs MESFET pixels. The MSM photodetectors are monolithically integrated with MESFETs.