gebhart/patrepeval huggingface dataset:
Supp. Movie 1 from &lt;i&gt;Ex Vivo&lt;/i&gt; Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids (2023)

&lt;p&gt;PDOTS Movie&lt;/p&gt;
ChemInform Abstract: Selective N‐Monomethylation of Primary Amines via N‐Trialkylsilyl‐lithioamines. (1983)

Abstract Durch Silylierung, Metallierung und Alkylierung werden die primären Amine (Ia) und (IX) in die sekundären Amine (VII) und (XI) übergeführt.
ChemInform Abstract: Smart Zeolites: New Forms of Tungsten and Molybdenum Oxides (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
SAFB1 Mediates Repression of Immune Regulators and Apoptotic Genes in Breast Cancer Cells (2009)

The scaffold attachment factors SAFB1 and SAFB2 are paralogs, which are involved in cell cycle regulation, apoptosis, differentiation, and stress response. They have been shown to function as estrogen receptor corepressors, and there is evidence for a role in breast tumorigenesis. To identify their endogenous target genes in MCF-7 breast cancer cells, we utilized a combined approach of chromatin immunoprecipitation (ChIP)-on-chip and gene expression array studies. By performing ChIP-on-chip on microarrays containing 24,000 promoters, we identified 541 SAFB1/SAFB2-binding sites in promoters of known genes, with significant enrichment on chromosomes 1 and 6. Gene expression analysis revealed that the majority of target genes were induced in the absence of SAFB1 or SAFB2 and less were repressed. Interestingly, there was no significant overlap between the genes identified by ChIP-on-chip and gene expression array analysis, suggesting regulation through regions outside the proximal promoters. In contrast to SAFB2, which shared most of its target genes with SAFB1, SAFB1 had many unique target genes, most of them involved in the regulation of the immune system. A subsequent analysis of the estrogen treatment group revealed that 12% of estrogen-regulated genes were dependent on SAFB1, with the majority being estrogen-repressed genes. These were primarily genes involved in apoptosis, such as BBC3, NEDD9, and OPG. Thus, this study confirms the primary role of SAFB1/SAFB2 as corepressors and also uncovers a previously unknown role for SAFB1 in the regulation of immune genes and in estrogen-mediated repression of genes.
Supplementary Data from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER&lt;sup&gt;+&lt;/sup&gt; Metastatic Breast Cancer (2023)

Supplementary Data from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER&lt;sup&gt;+&lt;/sup&gt; Metastatic Breast Cancer
Should pressors be used to augment cerebral blood flow after traumatic brain injury? (2000)

Copyright © by 2000 by the Society of Critical Care Medicine and Wolters Kluwer Health, Inc. All Rights Reserved.
Global carbon emissions from biomass burning in the 20th century (2006)

We used a new, 100‐year, 1 × 1° global fire map and a carbon cycle model (CASA) to provide a yearly gridded estimate of the temporal trend in carbon emissions due to wildfires through the 20th century. 2700–3325 Tg C y −1 burn at the end of the 20th century, compared to 1500–2700 Tg C y −1 at the beginning, with increasing uncertainty moving backward in time. There have been major changes in the regional distribution of emissions from fires, as a consequence of i) increased burning in tropical savannas and ii) a switch of emissions from temperate and boreal forests towards the tropics. The frequently‐used assumption that pre‐industrial emissions were 10% of present biomass burning is clearly inadequate, in terms of both the total amount and the spatial distribution of combustion.
G Protein Coupled Receptor 75 and Its Role in Pulmonary Hypertension (2020)

Pulmonary Hypertension (PH) is a multifactorial disease with poor prognosis and inadequate treatment. Recent studies have shown that the orphan G Protein Coupled Receptor 75 (GPR75) is upregulated in the pulmonary vessels of PH patients, especially in females. Therefore, we hypothesized that GPR75 knock out (GPR75KO) mice will be protected from developing PH. We placed 3‐month‐old female GPR75KO (n=6) and control C57BL/C mice (n=10) in a hypoxic chamber with 10% Oxygen or at atmospheric oxygen for 5 weeks. At the end of 5 weeks, we performed echocardiograms and right heart catheterizations. GPR75KO mice were protected from developing PH (Right Ventricle Systolic Pressure (RVSP) of 26mmHg and Right Ventricle Diastolic Pressure (RVDP) of 2 mmHg), while C57BL/C mice developed PH under hypoxia (RSVP and RDVP of 56mmHg and 12mmHg, respectively). Wire myography was performed on isolated intra‐lobar pulmonary arteries from GPR75KO mice (n=3) and WT mice (n=31). Hypoxic pulmonary vasoconstriction (HPV) was abolished in GPR75KO as compared to WT. HPV response in WT was blocked (P&lt;0.05) by antibody against RANTES (CCL5), a putative GPR75 ligand. These results suggest GPR75 plays a major role in the development of HPV and PH. Support or Funding Information This study was supported by NIH grant 1RO1HL139793 (MLS).
Switchless hybrid analog-digital variable optical delay line for radio frequency signal processing (2009)

The author proposes the design of a novel switchless variable optical delay line (VFODL) for radio frequency (rf) signals that combines an analog mode VFODL with a discrete-state VFODL. This hybrid VFODL proposes the use of a laser with smart, fast (e.g., 1 ns) wavelength tuning in combination with flat-top passband design spatially and temporally dispersive optical elements to simultaneously provide both long and short time delays, thus finely covering a wide nanoseconds delay range. An example design indicates a 9.6-ns time delay range with 6-ps increments, giving 1600 independent delays using a no-moving-parts signal-processing structure. VFODL applications include rf antenna array processing, radar testing, and precision electrical timing systems.
Hierarchic autoepistemic theories for nonmonotonic reasoning (1988)

Nonmonotonic logics are meant to be a formalization of nonmonotonic reasoning. However, for the most part they fail to capture in a perspicuous fashion two of the most important aspects of such reasoning: the explicit computational nature of nonmonotonic inference, and the assignment of preferences among competing inferences. We propose a method of nonmonotonic reasoning in which the notion of inference from specific bodies of evidence plays a fundamental role. The formalization is based on autoepistemic logic, but introduces additional structure, a hierarchy of evidential subtheories. The method offers a natural formalization of many different applications of nonmonotonic reasoning, including reasoning about action, speech acts, belief revision, and various situations involving competing defaults.
Two design of the S4.BEN01 magnet for the CBETA splitter/merger (2017)

The splitter/merger section of the CBETA project [1] consists of 4 beam lines as shown in Fig. 1. Two of the functions of the splitter’s/merger’s lines is to match the beam parameters at the exit of the Energy Recovery Linac (ERL) to the beam parameters at the entrance of the Fixed Field Alternating Gradient (FFAG) arc, and also place the reference particles of the beam bunches at the entrance of the FFAG arc on specified trajectories according to their energies. In this technical note we are presenting results from the 2D and 3D electromagnetic analysis of the S4.BEN01 magnet which is one of the dipole magnets of the 150 MeV line of the splitter/merger. In particular we present results from two designs of the S4.BEN01 magnet, one based on iron dominated current-excited magnet, and the other design based on Halbach-type permanent magnet. An evaluation of the two designs will be given in the section under “conclusion”.
Where Does Debt Fit in the Stress Process Model? (2014)

This paper contrasts two money-related stressors—debt and economic hardship—and clarifies where debt fits into the stress process model. Debt may be a direct or indirect stressor, as something mediated by psychosocial resources, and may be a potential buffer, interacting with economic hardship. The analyses use data from a two-wave panel study of 1,463 adults. One way debt is distinct from economic hardship is that debt is more common among economically advantaged groups. Further, though debt and economic hardship are both associated with negative mental health, the influence of hardship is partly mediated by mastery. This is not true of debt. Finally, debt does not buffer the negative effects of economic hardship, nor does its influence vary by income. We conclude debt is best conceptualized as an unmediated stressor and not as a coping resource. Future research should determine whether different types of debt have distinct mental health consequences.
Key characterization efforts to support the graffiti ink removal and care of Mark Rothko’s painting ‘Black on Maroon’ 1958 (2022)

Abstract Analytical characterization efforts carried out in support of the conservation treatment of Mark Rothko's painting 'Black on Maroon' 1958 (Tate T01170), involving the removal of graffiti (tag) ink, are summarized. The proprietary ink product, of unfamiliar and unknown composition, was investigated using a suite of analytical techniques (IR spectroscopy, GC–MS, ICP-MS, pyrolysis GC–MS, thin layer chromatography, SEC, MALDI-TOF–MS, and UHPLC-MS) to identify key colorants and other components. The ink solubility properties proved vital to informing the solvent selection process for the ink removal procedure, which helped enable the re-display of the painting at Tate Modern in 2014. The possible impact of ink residues remaining within the cotton duck canvas support of the conserved painting was also explored using mockup canvas mechanical strength data, measured before and after ‘soiling’ at two ink levels to assess whether the ink residues had any immediate and possible longer-term effects on canvas properties. These findings, elucidated using a range of complementary analytical techniques, provide information on this hitherto-unknown graffiti product, contribute to a growing body of knowledge in this area, and offer analytical approaches which may be useful for the characterization of similar unknown materials, whether used to damage, augment, or create works of art.
Acid Hydrolysis of κ- and ι-Carrageenan in the Disordered and Ordered Conformations:  Characterization of Partially Hydrolyzed Samples and Single-Stranded Oligomers Released from the Ordered Structures (1998)

κ- and ι-carrageenan that were partially hydrolyzed in dilute acid while being in the ordered conformation (induced by LiI or LiCl, respectively) gave rise to bimodal molecular weight distributions (MWDs) as shown by size-exclusion chromatography (SEC) and gel filtration. Optical rotation measurements showed that the high molecular weight (MW) fraction remained conformationally ordered, whereas the low-MW fraction was in the disordered state. The relative amount of the low-MW fraction increased with degradation time. By inducing the disordered conformation (in 0.01 M LiCl) the weight average molecular weight (Mw) of the partially hydrolyzed samples decreased 1.5−3 times. These results are interpreted in favor of a double-stranded ordered conformation. Partial hydrolysis of this structure yields a metastable, partially double-stranded structure containing chain breaks that are “unexposed” due to partial overlap of the individual chain fragments. When the degree of polymerization (DP) of such fragments decrease below the critical value (DPc) for duplex stabilization the fragments are released and appear as a separate low-MW fraction in the SEC chromatograms. DPc was estimated to be approximately 100 residues in both cases. After induction of the disordered conformation in partially hydrolyzed samples the molecular weight distribution remained bimodal. For κ-carrageenan this is attributed to the higher rate of hydrolysis in the disordered fragments than in the parent ordered chains, which also leads to a rapid accumulation of dialyzable oligomers (DP 1−4). For ι-carrageenan, where the rate of hydrolysis ideally is independent of the conformational state, the bimodality is tentatively attributed to the presence of κ-units (partially formed by desulfation), which are hydrolyzed more rapidly in the disordered state than in the ordered state.
Methods for Evaluating Definite Integrals (2011)

This chapter contains sections titled: Introduction The Rule for Evaluating Definite Integrals Some Rules (Theorems) for Evaluation of Definite Integrals Method of Integration by Parts in Definite Integrals
THORACIC INJURY ASSESSMENT OF BELT RESTRAINT SYSTEMS ON HYBRID III CHEST COMPRESSION (1994)

Measurement of chest compression is vital to properly assessing injury risk for restraint systems. It directly relates chest loading to the risk of serious or fatal compression injury for the vital organs protected by the rib cage. Other measures of loading such as spinal acceleration or total restraint load do not separate how much of the force is applied to the rib cage, shoulders, or lumbar and cervical spines. Hybrid III chest compression is biofidelic for blunt impact of the sternum, but is stiff for belt loading. In this study, an analysis was conducted of two published crash reconstruction studies involving belted occupants. This provides a basis for comparing occupant injury risks with Hybrid III chest compression in similar exposures. Results from both data sources were similar and indicate that belt loading resulting in 40 mm Hybrid III chest compression represents a 20-25% risk of an AIS 3 thoracic injury. For the covering abstract see IRRD 864472.
SLM phase mask optimization for fiber OAM mode excitation (2019)

Fiber orbital angular momentum (OAM) modes can be employed in mode-division multiplexing to increase the channel capacity in optical communication systems. Over the years, several experiments to excite high-purity OAM modes by using one phase-only spatial light modulator (SLM) have been conducted. Since phase-only SLMs are intrinsically imperfect for this purpose due to the impossibility to simultaneously modulate both amplitude and phase in the light source, optimal phase masks need to be generated by iterative algorithms. However, if the state of every pixel in the mask is an unknown of the problem, the computational cost is extremely high. The system circular symmetry can be exploited to overcome this issue. Here, for the fist time, this approach is implemented and a simple machine learning algorithm is developed to calculate optimal phase masks with a low number of unknowns and iterations. Simulated and experimental results show that the developed technique is capable of exciting high-purity OAM modes.
A STATE SPACE REPRESENTATION OF VAR MODELS WITH SPARSE LEARNING FOR DYNAMIC GENE NETWORKS (2010)

We propose a state space representation of vector autoregressive model and its sparse learning based on L1 regularization to achieve efficient estimation of dynamic gene networks based on time course microarray data. The proposed method can overcome drawbacks of the vector autoregressive model and state space model; the assumption of equal time interval and lack of separation ability of observation and systems noises in the former method and the assumption of modularity of network structure in the latter method. However, in a simple implementation the proposed model requires the calculation of large inverse matrices in a large number of times during parameter estimation process based on EM algorithm. This limits the applicability of the proposed method to a relatively small gene set. We thus introduce a new calculation technique for EM algorithm that does not require the calculation of inverse matrices. The proposed method is applied to time course microarray data of lung cells treated by stimulating EGF receptors and dosing an anticancer drug, Gefitinib. By comparing the estimated network with the control network estimated using non-treated lung cells, perturbed genes by the anticancer drug could be found, whose up- and down-stream genes in the estimated networks may be related to side effects of the anticancer drug.
Noncovalent DNA binding of bis(1,10-phenanthroline)copper(I) and related compounds (1991)

The noncovalent DNA binding of the bis(1,10-phenanthroline)copper(I) complex [(Phen)2CuI] was examined under anaerobic conditions by absorption and circular dichroism spectroscopy, and viscometry, as a function of phenanthroline concentration. Analyses according to the McGhee-von Hippel method indicated that binding exhibited both neighbor-exclusion and positive cooperativity effects, with a neighbor-exclusion parameter n approximately 2 and a cooperativity parameter omega approximately 4. The association constant for (Phen)2CuI binding decreased with increasing concentration of phenanthroline in excess over that required to stoichiometrically generate (Phen)2CuI, indicating that free phenanthroline was a weak competitive inhibitor of (Phen)2CuI binding. The maximal association constant for DNA binding of (Phen)2CuI in 0.2 M NaCl and 9.8% ethanol, extrapolated to zero concentration of excess phenanthroline, was 4.7 x 10(4) M-1 (DNA base pairs). The magnitude of the neighbor-exclusion parameter, the changes in spectral properties of (Phen)2CuI induced by DNA binding, and the increase in DNA solution viscosity upon (Phen)2CuI addition are consistent with a model for DNA binding by (Phen)2CuI involving partial intercalation of one phenanthroline ring of the complex between DNA base pairs in the minor groove as suggested previously [Veal & Rill (1989) Biochemistry 28, 3243-3250]. Viscosity measurements indicated that the mono(phenanthroline)copper(I) complex also binds to DNA by intercalation; however, no spectroscopic or viscometric evidence was found for DNA binding of free phenanthroline or the bis(2,9-dimethyl-1,10-phenanthroline)copper(I) complex. DNA binding of free phenanthroline may be cooperative and induced by prior binding of (Phen)2CuI.
Supplementary Table 1 from A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous Recombination–deficient Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Table 1 shows the clinical characteristics of the patients from whom patient-derived xenografts were generated and evaluated in the preclinical trial&lt;/p&gt;
miR-29cb2 promotes angiogenesis and osteogenesis by inhibiting HIF-3α in bone (2021)

Coordination between osteogenesis and angiogenesis is required for bone homeostasis. Here, we show that miR-29cb2 is a bone-specific miRNA and plays critical roles on angiogenesis-osteogenesis coupling during bone remodeling. Mice with deletion of miR-29cb2 exhibit osteopenic phenotypes and osteoblast impairment, accompanied by pronounced decreases in specific H vessels. The decrease in bone miR-29cb2 was associated with pathological ovariectomy stimuli. Mechanistically, hypoxia-inducible factor (HIF)-3α, as a target for miR-29cb2, inhibits HIF-1α activity by competitively bonding with HIF-1β. Notably, miR-29cb2 in peripheral blood (PB) nearly is undetectable in sham and significantly increases in ovariectomy mice. Further evaluation from osteoporosis patients demonstrates similar signatures. ROC analysis shows miR-29cb2 in PB has higher sensitivity and specificity for diagnosing osteoporosis when compared with four clinical biomarkers. Collectively, these findings reveal that miR-29cb2 is essential for bone remodeling by inhibiting HIF-3α and elevated bone-specific miR-29cb2 in PB, which may be a promising biomarker for bone loss.
Insertion procedure, aftercare, and soft-tissue reaction of the 2.5-mm titanium tube system for a transcutaneous air conduction hearing aid system. (2006)

The term transcutaneous air conduction hearing aid system designates a new category of hearing devices established by the U.S Food and Drug Administration in 2002. The only product included in this category is the RetroX device manufactured by Auric Hearing Systems, Rheine, Germany. This device consists of two components: a titanium tube system for sound conduction and a hearing processor. The component implanted in the soft tissue of the outer ear is the titanium tube system, for which the outer diameter of the central part has recently been reduced. Both the implantation tools and the tube system itself have been optimized over the last few years with regard to shape and function, thus effectively reducing the surgery involved to a kind of "functional body piercing" procedure. As a result of this, the time required for implantation has been minimized, as has the duration and severity of postoperative soft-tissue reaction. Complications may be avoided by correct positioning and proper mounting of the tube system in the outer ear, comprehensive patient counseling, and scheduled aftercare. One key objective is to ensure that the soft-tissue channel in which the titanium tube is implanted heals without any inflammatory reaction.
Molecular mechanisms in allergy and clinical immunology (2005)

Lack of adequate macronutrients or selected micronutrients, especially zinc, selenium, iron, and the antioxidant vitamins, can lead to clinically significant immune deficiency and infections in children. Undernutrition in critical periods of gestation and neonatal maturation and during weaning impairs the development and differentiation of a normal immune system. Infections are both more frequent and more often become chronic in the malnourished child. Recent identification of genetic mechanisms is revealing critical pathways in the gastrointestinal immune response. New studies show that the development of tolerance, control of inflammation, and response to normal mucosal flora are interrelated and linked to specific immune mechanisms. Nutrients act as antioxidants and as cofactors at the level of cytokine regulation. Protein calorie malnutrition and zinc deficiency activate the hypothalamicpituitary-adrenal axis. Increased circulating levels of glucocorticoids cause thymic atrophy and affect hematopoiesis. Chronic undernutrition and micronutrient deficiency compromise cytokine response and affect immune cell trafficking. The combination of chronic undernutrition and infection further weakens the immune response, leading to altered immune cell populations and a generalized increase in inflammatory mediators. Obesity caused by excess nutrition or excess storage of fats relative to energy expenditure is a form of malnutrition that is increasingly seen in children. Leptin is emerging as a cytokine-like immune regulator that has complex effects in both overnutrition and in the inflammatory response in malnutrition. Because the immune system is immature at birth, malnutrition in childhood might have long-term effects on health. (J Allergy Clin Immunol 2005;115:1119-28.)
Rainfastness of Poly(vinyl alcohol) Deposits on <i>Vicia faba</i> Leaf Surfaces: From Laboratory-Scale Washing to Simulated Rain (2016)

Rainfastness is the ability of agrochemical deposits to resist wash-off by rain and other related environmental phenomena. This work reports laboratory-scale and raintower studies of the rainfastness of fluorescently labeled poly(vinyl alcohol) (PVA) using fluorescent microscopy combined with image analysis. Samples of hydrolyzed PVA exhibit improved rainfastness over a threshold molecular weight, which correlates with PVA film dissolution, swelling, and crystalline properties. It was also established that the rainfastness of PVA scaled with the molecular weight over this threshold. These PVA samples were further characterized in order to determine the effect of the crystallinity on rainfastness. The quantification of rainfastness is of great interest to the field of agrochemical formulation development in order to improve the efficacy of pesticides and their adjuvants.