gebhart/patrepeval huggingface dataset:
The reaction D(γp)n at intermediate energies (1986)

The study of serotyping of isolates of Candida albicans of clinical material obtained from different geographic areas of Venezuela suggest that serotype A is predominant over type B. These results are in relation with results obtained in other countries. Type A serotype is predominant in 57 to 100% in the areas studied. Only in 2 cities serotype B was isolated. Both serotypes of Candida albicans were observed in intertriginous, mucosal, inguinal and lung forms. These studies have allowed us to have information about the predominance of serotypes in certain areas of the country.
H-induced platelet and crack formation in hydrogenated epitaxial Si∕Si0.98B0.02∕Si structures (2006)

An approach to transfer a high-quality Si layer for the fabrication of silicon-on-insulator wafers has been proposed based on the investigation of platelet and crack formation in hydrogenated epitaxial Si∕Si0.98B0.02∕Si structures grown by molecular-beam epitaxy. H-related defect formation during hydrogenation was found to be very sensitive to the thickness of the buried Si0.98B0.02 layer. For hydrogenated Si containing a 130nm thick Si0.98B0.02 layer, no platelets or cracking were observed in the B-doped region. Upon reducing the thickness of the buried Si0.98B0.02 layer to 3nm, localized continuous cracking was observed along the interface between the Si and the B-doped layers. In the latter case, the strains at the interface are believed to facilitate the (100)-oriented platelet formation and (100)-oriented crack propagation.
An assessment of the RIFLE criteria for acute renal failure in critically ill HIV-infected patients. (2006)

Acute renal failure is common among hospitalized patients with HIV infection, particularly in the intensive care unit (ICU) setting, and increases mortality. Recently, the Acute Dialysis and Quality Initiative (ADQI) group [1] formulated a new classification for acute renal failure -the Risk, Injury, Failure, Loss, and End-stage kidney disease (RIFLE) classificationthat defines three grades of severity -class R (risk), class F (failure), and class I (injury) -and two outcome classes -loss and end-stage kidney disease. Some studies [2,3] have applied the RIFLE criteria in hospitalized patients, particularly in ICU patients, but the clinical ability of these criteria to predict outcome of ICU HIV-infected patients has not yet been assessed. We sought to evaluate retrospectively the ability of the RIFLE criteria (Table Chronic kidney disease patients receiving dialysis were excluded from the analysis. Mortality was assessed at day 60 We evaluated 97 HIV-infected patients (mean age 42.7 12.2 years; 77 male, 69 Caucasian). According to RIFLE, 46 patients (47.4%; mean age 43.2 11.08 years, P = not significant; 39 male, P = not significant; 28 Caucasian, P = not significant) had some degree of acute renal dysfunction. Of these, 12 patients (26%) were class R, 9 patients (19.5%) were class I, and 25 patients (54.3%) were class F; these patients did not differ in terms of age, gender, race, type of HIV, stage of HIV infection, highly active antiretroviral therapy (HAART), comorbidity, and severity of illness. In all cases, maximum RIFLE occurred within the first week of hospitalization.
Prevention and treatment of cancers by tumor antigen-expressing Staphylococcus epidermidis (2023)

In a recent paper in <i>Science,</i> Chen <i>et al</i>. reported the genetic engineering of <i>S. epidermidis</i> expressing tumor cross-reactive antigens that trigger T cell responses and exhibit anticancer effects after topical administration. Here we discuss direct local effects and indirect systemic effects of exposure to engineered <i>S. epidermidis</i> strains.
Design of a 40-nm CMOS integrated on-chip oscilloscope for 5-50 GHz spin wave characterization (2017)

Spin wave (SW) devices are receiving growing attention in research as a strong candidate for low power applications in the beyond-CMOS era. All SW applications would require an efficient, low power, on-chip read-out circuitry. Thus, we provide a concept for an on-chip oscilloscope (OCO) allowing parallel detection of the SWs at different frequencies. The readout system is designed in 40-nm CMOS technology and is capable of SW device characterization. First, the SWs are picked up by near field loop antennas, placed below yttrium iron garnet (YIG) film, and amplified by a low noise amplifier (LNA). Second, a mixer down-converts the radio frequency (RF) signal of 5 − 50 GHz to lower intermediate frequencies (IF) around 10 − 50 MHz. Finally, the IF signal can be digitized and analyzed regarding the frequency, amplitude and phase variation of the SWs. The power consumption and chip area of the whole OCO are estimated to 166.4 mW and 1.31 mm2, respectively.
Discovery of small molecule probe that shows anti-tubercular activity via Mtb bioA (DAPA synthase) enzyme inhibition (2010)

Cofactor biosynthetic pathways are a rich source of potential bacterial drug targets because of their essential nature and lack of corresponding mammalian pathways. The genome sequence of Mycobacterium tuberculosis (Mtb) H37Rv, the model virulent laboratory strain, revealed it has the full metabolic potential to synthesize all vitamins and cofactors. Biotin (vitamin H) is the cofactor responsible for activation of carbon dioxide in acyl-CoA carboxylases involved in fatty acid metabolism and pyruvate carboxylase in gluconeogenesis. Biotin biosynthesis is required for survival of Mtb in vitro and in vivo. Moreover, biotin starvation of an Mtb biotin auxotroph led to cell death, which is unusual as most Mtb auxotrophs enter a nonreplicating phase when starved for their given nutrient in vitro. In a recent study, Schnappinger and co-workers have demonstrated, using a phenotypically well-regulated bioA knockdown Mtb mutant, that silencing of bioA (DAPA synthase) after establishing an infection can defeat a chronic infection in a murine model of TB. These genetic studies provide an unprecedented level of validation for a Mtb target and suggest biotin biosynthesis, BioA in particular, represents an extremely attractive target for the development of new antitubercular agents. We report the discovery of a structurally novel small molecule (CID 1245700) that inhibits bioA and demonstrate antitubercular activity in wild type and Mtb strains that conditionally express bioA.
Stereochemical and Skeletal Diversity Arising from Amino Propargylic Alcohols (2010)

An efficient synthetic pathway to the possible stereoisomers of skeletally diverse heterocyclic small molecules is presented. The change in shape brought about by different intramolecular cyclizations of diastereoisomeric amino propargylic alcohols is quantified using principal moment-of-inertia (PMI) shape analysis.
Propagating patterns of activity across motor cortex facilitate movement initiation (2019)

Abstract Voluntary movement initiation involves the modulation of neurons in the primary motor cortex (M1) around movement onset. Yet, similar modulations of M1 activity occur during movement planning when no movement occurs. Here, we show that a sequential spatio-temporal pattern of excitability based on beta oscillation amplitude attenuation propagates across M1 prior to the initiation of reaching movements in one of two oppositely oriented directions along the rostro-caudal axis. Using spatiotemporal patterns of intracortical microstimulation, we find that reaction time increases significantly when stimulation is delivered against but not with the natural propagation orientation suggesting that movement initiation requires a precise recruitment pattern in M1. Functional connections among M1 units emerge at movement onset that are oriented along the same rostro-caudal axis but not during movement planning. Finally, we show that beta amplitude profiles can more accurately decode muscle activity when these patterns conform to the natural propagating patterns. These findings provide the first causal evidence that large-scale, spatially organized propagating patterns of cortical excitability and activity are behaviorally relevant and may be a necessary component of movement initiation.
Selective Inhibition of the Myeloid Src-Family Kinase Fgr Potently Suppresses AML Cell Growth in Vitro and in Vivo (2018)

Acute myelogenous leukemia (AML) is the most common hematologic malignancy in adults and is often associated with constitutive tyrosine kinase signaling. These pathways involve the nonreceptor tyrosine kinases Fes, Syk, and the three Src-family kinases expressed in myeloid cells (Fgr, Hck, and Lyn). In this study, we report remarkable anti-AML efficacy of an N-phenylbenzamide kinase inhibitor, TL02-59. This compound potently suppressed the proliferation of bone marrow samples from 20 of 26 AML patients, with a striking correlation between inhibitor sensitivity and expression levels of the myeloid Src family kinases Fgr, Hck, and Lyn. No correlation was observed with Flt3 expression or mutational status, with the four most sensitive patient samples being wild-type for Flt3. Kinome-wide target specificity profiling coupled with in vitro kinase assays demonstrated a narrow overall target specificity profile for TL02-59, with picomolar potency against the myeloid Src-family member Fgr. In a mouse xenograft model of AML, oral administration of TL02-59 for 3 weeks at 10 mg/kg completely eliminated leukemic cells from the spleen and peripheral blood while significantly reducing bone marrow engraftment. These results identify Fgr as a previously unrecognized kinase inhibitor target in AML and TL02-59 as a possible lead compound for clinical development in AML cases that overexpress this kinase independent of Flt3 mutations.
Porous Carbon Membrane‐Supported Atomically Dispersed Pyrrole‐Type FeN4 as Active Sites for Electrochemical Hydrazine Oxidation Reaction (2020)

The rational design of catalytically active sites in porous materials is essential in electrocatalysis. Herein, atomically dispersed Fe-N<sub>x</sub> sites supported by hierarchically porous carbon membranes are designed to electrocatalyze the hydrazine oxidation reaction (HzOR), one of the key techniques in electrochemical nitrogen transformation. The high intrinsic catalytic activity of the Fe-N<sub>x</sub> single-atom catalyst together with the uniquely mixed micro-/macroporous membrane support positions such an electrode among the best-known heteroatom-based carbon anodes for hydrazine fuel cells. Combined with advanced characterization techniques, electrochemical probe experiments, and density functional theory calculation, the pyrrole-type FeN<sub>4</sub> structure is identified as the real catalytic site in HzOR.
Supplementary Figure S5 from Predictive Biomarkers for Adjuvant Capecitabine Benefit in Early-Stage Triple-Negative Breast Cancer in the FinXX Clinical Trial (2023)

&lt;p&gt;Supplementary Figure S5 shows a forest plot of the categorical expression of selected genes and metagenes and their association with survival in each treatment arm&lt;/p&gt;
A 32-A, 5-V-Input, 94.2% Peak Efficiency High-Frequency Power Converter Module Featuring Package-Integrated Low-Voltage GaN nMOS Power Transistors (2022)

A buck converter using a low-voltage GaN nMOS power transistor with 5-10x superior switching figure-of-merit over Si laterally-diffused MOS (LDMOS) and stacked CMOS at 5 V has been employed to build a high-frequency (3-20 MHz), high-density (9 A/mm²) buck converter for high-performance-compute applications. The GaN-based converter is co-packaged with a CMOS Companion Die on a 4 mm x 4 mm package and employs on-die gate clamps to minimize the impact of package parasitics for high efficiency. For 5-V input to 1-V output conversion, the converter achieves 94.2% peak efficiency at 3.1-MHz switching frequency with a 40-nH inductor, and >80% peak efficiency at 20 MHz with an air-core inductor.
Designing Ordered Molecular Arrays in Two and Three Dimensions (1992)

Two- and three-dimensional assemblies — self-assembled monolayers (SAMs) and hydrogen-bonded co-crystals, respectively — show substantial changes in their supramolecular structures with seemingly minor changes in the structures of their molecular/atomic constituents. The structure of SAMs obtained by adsorption of alkanethiols onto silver and copper are indistinguishable, although the atomic radii of silver and copper are different. The structure of the SAM on silver is different from that on gold, although the atomic radii of these metals are essentially the same. A macroscopic property of the SAMs, wetting, is not affected by these structural differences. Co-crystals formed from derivatives of barbiturates and melamines form hydrogen-bonded tapes in the solid state. These tapes provide a template for studying the packing forces within crystals. The three-dimensional arrangement of the tapes in the crystals changes markedly in response to subtle differences in the steric and electronic structures of the molecular constituents.
Effect of amorphization on activation and deactivation of boron in source/drain, channel and polygate (2005)

In this work, we investigate the effect of Ge amorphization and low temperature regrowth on the activation and deactivation of boron in the source and drain region, transistor channel and polycrystalline gate. It is concluded that amorphization of silicon offers important advantages for boron activation enhancement and junction depth control. Simultaneously it introduces problems related to the channel deactivation and partially activated poly.
Dependence of network capacity requirements on theallowable flow convergence overloads in ATM backup VP restoration (1997)

Work on capacity design for VP restoration in ATM has to date either been heuristic in nature or has treated the capacity design problem in a 1 for 1 VP replacement manner that is essentially the same as for STM path restorable networks. However, the inherently statistical nature of the traffic in ATM should allow formulation of a backup VP restoration capacity design that permits a controlled maximum of convergent flow overloads on spans during restoration. Results show that significant capacity savings can be obtained relative to STM if ATM restoration is allowed even modest restoration overload factors. We give an integer program formulation permitting controlled exploitation of this intrinsic difference between ATM and STM transport and present results showing the significant capacity benefits motivating this approach.
X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A 2A Adenosine Receptor Antagonists (2020)

Abstract We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A 2A adenosine receptor (AR). Eight A 2A AR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A 2A AR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A 2A AR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A 2A AR, an emerging target in immuno‐oncology.
A Nonperturbing Real-Time In Situ Plasma Diagnosis Technique Using an Optical Emission Spectrometer (OES) (2006)

An optical emission spectrometer (OES) is utilized to measure the sheath thickness (i.e., dark space) of a pulsed glow discharge in a nonperturbing real-time in situ manner. The ion density can be obtained based on the sheath thickness measurements because the ion density is a function of the sheath thickness and applied voltage. Because this method is simple and straightforward, most of the issues involved with a conventional Langmuir probe measurement are eliminated. The ion density measured by this technique was compared with that measured by a time-delayed time-resolved Langmuir probe technique and with measurements simulated by PDP1 plasma simulation code. A good agreement between the measurements taken by the different tools has been demonstrated. Therefore, this method is suitable for a better plasma-based process, which monitors process controllability and repeatability
Ionic Liquids as Green Solvents (2003)

Ionic liquids (ILs) are proving to be increasingly promising as viable media for not only potentially 'green' synthesis and separations operations, but also for novel applications, where the unique property set of the IL materials provides new options based upon different chemical and physical properties. The range and variability in the properties between individual examples within the class of solvents that are known as ILs, however, are both challenges, and opportunities for developing new and improved processes. Some of the challenges in understanding IL behavior and in selecting specific IL media for applications is presented in the context of research from The University of Alabama.
Blind deconvolution and phase retrieval using point zeros (1995)

The Fourier transform of a signal or image of compact support is an entire function of exponential type which can be represented in terms of their zeros by means of a product of factors each encoding a zero of the function. In more than one dimensional problems, an entire function is generally not factorizable into an infinite product of terms, but is irreducible, [1,2] from which it follows that there is a unique phase to be associated with its power spectrum, in principle.
Ultra-Low Voltage Analog Integrated Circuits (2006)

The operation of analog circuits from ultra low supply voltages becomes necessary due to semiconductor technology scaling. Yet traditional design techniques cannot be used. In this paper, we review techniques that allow analog circuits to operate with supply voltages as low as 0.5 V. Biasing considerations are given, and robust bias circuits are discussed. For frequency-tunable circuits, a low-voltage MOS varactor tuning technique is presented. The techniques discussed are applied to two different OTA topologies, as well as to an automatically tuned, fifth-order active RC filter. This material is largely based on the work of the authors as described in [1]-[5].
Supplementary Figure 5 from Complement-Dependent Tumor Cell Lysis Triggered by Combinations of Epidermal Growth Factor Receptor Antibodies (2023)

Supplementary Figure 5 from Complement-Dependent Tumor Cell Lysis Triggered by Combinations of Epidermal Growth Factor Receptor Antibodies
A Homolog of Subtilisin-Like Proprotein Convertase 7 Is Essential to Anterior Neural Development in Xenopus (2012)

SPC7 is required for normal development of the eye and brain, possibly through processing BMPs, though other potential substrates cannot be excluded.
CD3-associated heterodimeric polypeptides on suppressor hybridomas define biologically active inhibitory cells. (1988)

We have investigated the relationship between CD3 expression and the suppressor T-cell function. We have isolated stable clonal cell lines of the F12.23 suppressor T-cell hybridoma that are either CD3+ or CD3-. These lines were subjected to functional assays including inhibition of in vivo hapten-specific delayed-type hypersensitivity responses, in vitro hapten-specific interleukin 2 responses, as well as hapten-specific cytotoxic T-lymphocyte assays. In all assays, the functional suppressor phenotype absolutely correlated with CD3 surface expression. Furthermore, we have immunoprecipitated heterodimeric proteins that share molecular features with some receptor polypeptides previously described. CD3 polypeptides found on the surface of suppressor T cells are phosphorylated after phorbol ester stimulation. Collectively these studies unambiguously define the suppressive supernatant function as a product of CD3+ receptor-bearing T cells.
Towards Mimicking the Fetal Liver Niche: The Influence of Elasticity and Oxygen Tension on Hematopoietic Stem/Progenitor Cells Cultured in 3D Fibrin Hydrogels (2020)

Hematopoietic stem/progenitor cells (HSPCs) are responsible for the generation of blood cells throughout life. It is believed that, in addition to soluble cytokines and niche cells, biophysical cues like elasticity and oxygen tension are responsible for the orchestration of stem cell fate. Although several studies have examined the effects of bone marrow (BM) niche elasticity on HSPC behavior, no study has yet investigated the effects of the elasticity of other niche sites like the fetal liver (FL), where HSPCs expand more extensively. In this study, we evaluated the effect of matrix stiffness values similar to those of the FL on BM-derived HSPC expansion. We first characterized the elastic modulus of murine FL tissue at embryonic day E14.5. Fibrin hydrogels with similar stiffness values as the FL (soft hydrogels) were compared with stiffer fibrin hydrogels (hard hydrogels) and with suspension culture. We evaluated the expansion of total nucleated cells (TNCs), Lin<sup>-</sup>/cKit<sup>+</sup> cells, HSPCs (Lin<sup>-</sup>/Sca<sup>+</sup>/cKit<sup>+</sup> (LSK) cells), and hematopoietic stem cells (HSCs: LSK- Signaling Lymphocyte Activated Molecule (LSK-SLAM) cells) when cultured in 5% O<sub>2</sub> (hypoxia) or in normoxia. After 10 days, there was a significant expansion of TNCs and LSK cells in all culture conditions at both levels of oxygen tension. LSK cells expanded more in suspension culture than in both fibrin hydrogels, whereas TNCs expanded more in suspension culture and in soft hydrogels than in hard hydrogels, particularly in normoxia. The number of LSK-SLAM cells was maintained in suspension culture and in the soft hydrogels but not in the hard hydrogels. Our results indicate that both suspension culture and fibrin hydrogels allow for the expansion of HSPCs and more differentiated progeny whereas stiff environments may compromise LSK-SLAM cell expansion. This suggests that further research using softer hydrogels with stiffness values closer to the FL niche is warranted.
Atypical Metabolism of Deprenyl and Its Enantiomer, (S)-(+)-N,.alpha.-Dimethyl-N-Propynylphenethylamine, by Cytochrome P450 2D6 (1994)

Debrisoquine 4-hydroxylase is a unique cytochrome P450 that effects oxidation of protonated substrates at sites distal from the basic nitrogen. A basic tenet of the several models that have been proposed for the active site of P450 2D6 is that oxidation occurs at distances of approximately 5 or approximately 7 A from the protonated site. In this study, the metabolism of both stereoisomers of deprenyl, a therapeutically valuable monoamine oxidase B inhibitor, was shown to produce N-demethylation and N-depropargylation of the sole basic nitrogen in the molecule by recombinant cytochrome P450 2D6. N-Demethylation of L-(-)-deprenyl leading to nordeprenyl was favored by approximately 13:1 over N-depropargylation which produced methamphetamine. The Km and kcat values for formation of methamphetamine, the minor metabolite, were 56 +/- 5 microM and 0.63 +/- 0.063 nmol of methamphetamine min-1 (nmol of P450)-1, respectively; the kcat for nordeprenyl formation was approximately 8.2 nmol of nordeprenyl min-1 (nmol of P450)-1. Although these pathways would be the anticipated processes for monoamine oxidases and most cytochrome P450s, this mode of biotransformation is not predicted by current active site models and represents a novel pathway for P450 2D6. Statistical analysis indicates that the therapeutically important L-(-)-isomer was preferentially metabolized [kcat/Km (-)/(+) ratio = 2.66]. Competitive inhibition of deprenyl metabolism by both quinidine and quinine with an approximate 10(3) differential confirms that this metabolic pathway is P450 2D6 mediated.(ABSTRACT TRUNCATED AT 250 WORDS)