gebhart/patrepeval huggingface dataset:
Growth differentiation factor-9 has divergent effects on proliferation and steroidogenesis of bovine granulosa cells (2006)

In addition to gonadotropins, steroidogenesis and proliferation of granulosa cells during follicular development are controlled by a number of intraovarian factors including growth differentiation factor-9 (GDF-9), bone morphogenetic protein-4 (BMP-4), and IGF-I. The objective of this study was to determine the effect of GDF-9 and BMP-4 and their interaction with IGF-I and FSH on ovarian granulosa cell function in cattle. Granulosa cells from small (1-5 mm) and large (8-22 mm) follicles were collected from bovine ovaries and cultured for 48 h in medium containing 10% fetal calf serum and then treated with various hormones in serum-free medium for an additional 48 h. We evaluated the effects of GDF-9 (150-600 ng/ml) and BMP-4 (30 ng/ml) during a 2-day exposure on hormone-induced steroidogenesis and cell proliferation. In FSH plus IGF-I-treated granulosa cells obtained from small follicles, 300 ng/ml GDF-9 reduced (P < 0.05) progesterone production by 15% and 600 ng/ml GDF-9 completely blocked (P < 0.01) the IGF-I-induced increase in progesterone production. In comparison, 300 and 600 ng/ml GDF-9 decreased (P < 0.05) estradiol production by 27% and 71% respectively, whereas 150 ng/ml GDF-9 was without effect (P > 0.10). Treatment with 600 ng/ml GDF-9 increased (P < 0.05) numbers (by 28%) of granulosa cells from small follicles. In the same cells treated with FSH but not IGF-I, co-treatment with 600 ng/ml GDF-9 decreased (P < 0.05) progesterone production (by 28%), increased (P < 0.05) cell numbers (by 60%), and had no effect (P > 0.10) on estradiol production. In FSH plus IGF-I-treated granulosa cells obtained from large follicles, GDF-9 caused a dose-dependent decrease (P<0.05) in IGF-I-induced progesterone (by 13-48%) and estradiol (by 20-51%) production. In contrast, GDF-9 increased basal and IGF-I-induced granulosa cell numbers by over 2-fold. Furthermore, treatment with BMP-4 also inhibited (P < 0.05) steroidogenesis by 27-42% but had no effect on cell numbers. To elucidate downstream signaling pathways, granulosa cells from small follicles were transfected with similar to mothers against decapentaplegics (Smad) binding element (CAGA)- or BMP response element (BRE)-promoter reporter constructs. Treatment with GDF-9 (but not BMP-4) activated the Smad3-induced CAGA promoter activity, whereas BMP-4 (but not GDF-9) activated the Smad1/5/8-induced BRE promoter activity. We have concluded that bovine granulosa cells are targets of both GDF-9 and BMP-4, and that oocyte-derived GDF-9 may simultaneously promote granulosa cell proliferation and prevent premature differentiation of the granulosa cells during growth of follicles, whereas theca-derived BMP-4 may also prevent premature follicular differentiation.
Beyond Availability: Towards a Deeper Understanding of Machine Failure Characteristics in Large Distributed Systems (2004)

Although many previous research efforts have investigated machine failure characteristics in distributed systems, availability research has reached a point where properties beyond these initial findings become important. In this paper, we analyze traces from three large distributed systems to answer several subtle questions regarding machine failure characteristics. Based on our findings, we derive a set of fundamental principles for designing highly available distributed systems. Using several case studies, we further show that our design principles can significantly influence the availability design choices in existing systems.
Precise delay generation using coupled oscillators (1993)

An array oscillator, a series of coupled ring oscillators that achieves a delay resolution equal to a buffer delay divided by the number of rings, is described. Using a 2- mu m n-well CMOS technology, delays as small as 30 ps are achieved at frequencies up to 200 MHz. An array oscillator structured as a two-dimensional array of buffers is shown. The integral linearity and differential nonlinearity versus position in the -22 mode measured from the output ports are shown. The frequency sensitivity to static supply voltage in the -12 mode is investigated. The measured static frequency rejection is less than 0.25% over most of the operating range for each mode. The characteristics and performance of the array oscillator as a voltage-controlled oscillator for each mode are summarized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases (2016)

Microorganisms use a host of enzymes, including processive glycoside hydrolases, to deconstruct recalcitrant polysaccharides to sugars. Processive glycoside hydrolases closely associate with polymer chains and repeatedly cleave glycosidic linkages without dissociating from the crystalline surface after each hydrolytic step; they are typically the most abundant enzymes in both natural secretomes and industrial cocktails by virtue of their significant hydrolytic potential. The ubiquity of aromatic residues lining the enzyme catalytic tunnels and clefts is a notable feature of processive glycoside hydrolases. We hypothesized that these aromatic residues have uniquely defined roles, such as substrate chain acquisition and binding in the catalytic tunnel, that are defined by their local environment and position relative to the substrate and the catalytic center. Here, we investigated this hypothesis with variants of Serratia marcescens family 18 processive chitinases ChiA and ChiB. We applied molecular simulation and free energy calculations to assess active site dynamics and ligand binding free energies. Isothermal titration calorimetry provided further insight into enthalpic and entropic contributions to ligand binding free energy. Thus, the roles of six aromatic residues, Trp-167, Trp-275, and Phe-396 in ChiA, and Trp-97, Trp-220, and Phe-190 in ChiB, have been examined. We observed that point mutation of the tryptophan residues to alanine results in unfavorable changes in the free energy of binding relative to wild-type. The most drastic effects were observed for residues positioned at the "entrances" of the deep substrate-binding clefts and known to be important for processivity. Interestingly, phenylalanine mutations in ChiA and ChiB had little to no effect on chito-oligomer binding, in accordance with the limited effects of their removal on chitinase functionality.
Collaborative annotation-driven adaptation in web portals (2007)

Today's Web Portals suffer from information overload. We try to overcome this drawback by making them more adaptable and adaptive to the user's contexts. Therefore, we focus on the utilization of Web 2.0 techniques, especially semantic annotations, to make use of the portal users' collective intelligence.
Excitonically driven quantum dot light-emitting diodes: exLEDs (2013)

A hybrid platform of colloidal quantum dots integrated into conjugated polymers is reported for excitonically driven light-emitting diodes having pure quantum dot emission in the electroluminescence spectrum with substantially enhanced efficiency.
CSEM as a tool for better exploration decisions: Case studies from the Barents Sea, Norwegian Continental Shelf (2014)

Abstract After more than 30 years of exploration and more than 100 wells drilled in the Barents Sea, only one field is in production and one is under development. However, recent discoveries made over the last three years have heightened the interest for exploration in the region. Nevertheless, the industry is still facing major challenges in finding commercial volumes of hydrocarbons, despite the fact that numerous wells have encountered shows or minor amounts of gas and oil, proving a working hydrocarbon system in large parts of the area. Since 2008, 3D controlled-source electromagnetic (CSEM) data have been acquired in the Barents Sea, providing additional geophysical information in the last three licensing rounds. In this paper, we showed how CSEM data can help the industry make better decisions in various stages of exploration. CSEM data, being sensitive to hydrocarbon saturation and volume, have the potential to reduce the risk of exploration failures of a prospect by influencing the chance of success and the expected size and volume. To illustrate this, we showed three case examples. (1) How CSEM can support certain play models, and hence, give valuable information in a license application phase as well as in drilling decisions. (2) How CSEM can support decisions to apply or not apply for certain blocks in a licensing round. (3) How CSEM can help prospect ranking and drill-or-drop decisions. All these three cases demonstrate the power of using CSEM as a complementary tool together with seismic data and other geologic information. This paper argues that CSEM data could have provided a correct prediction for all of the wells drilled in the Barents Sea where 3D CSEM data are available, provided there are sufficient sensitivity and 3D inversion results. This in turn proves the value of acquiring CSEM data in addition to seismic.
A generic modeling approach for molecule-gated nanowire transistors using VHDL-AMS (2006)

A generic VHDL-AMS model for molecular-gated nanowire FET is presented. This compact modeling aimed at reproducing the specific electrical characteristics of this new class of devices, combining accuracy for circuits' functional analysis with efficient simulation time. Three different devices have been successfully modeled and simulated. Comparison to experimental data shows very good accordance
Abstract LB-134: Analysis of restored FFPE samples on high-density SNP arrays (2010)

Abstract Millions of Formalin Fixed Paraffin Embedded (FFPE) cancer tissue samples currently present in the US and worldwide provide an enormous, invaluable repository to the discovery of biomarkers in cancer research, drug development, diagnosis and treatment of diseases. However, the processes of fixation and storage of FFPE samples lead to degradation and base modification with chemical residues. This degraded FFPE DNA is inefficiently amplified in the Infinium® whole genome amplification (WGA) step leading to poor performance in the Infinium® assay. In this study, FFPE DNA (100 ng input) was restored through a treatment with DNA polymerase, DNA repair enzyme, ligase, and modified Infinium® WGA reaction conditions. Canonical genotype cluster files were generated by creating artificially degraded Coriell DNAs and processing the samples through the restoration process and Infinium® assay. Results of genotyping on high density HumanCytoSNP-12 BeadChip®, featuring approximately 300k SNPs indicated that even highly degraded samples which show initial call rates of 40-70% can be successfully restored to a state that achieved call rates of greater than 90%, at a concordance greater than 99.0%, and associated standard deviation of log intensity less than 0.4. In general, over 80% of FFPE samples, which passed a QC assay metric were successfully restored and genotyped. Infinium® genotyping of restored DNA from a collection of tumor FFPE samples confirmed the presence of genomic aberrations around known cancer genes. Finally, we further demonstrated that paired sample analysis using canonical genotype clusters provide improved precision in CNV and LOH analysis compared to single sample analysis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-134.
Lousy processing increases energy efficiency in massive MIMO systems (2017)

Massive MIMO (MaMIMO) is a key technology for 5G wireless communication, enabling large increase in both spectral and energy efficiency at the same time. Before it can be deployed, it is important to find efficient implementation strategies. Because of the many antennas, an essential part of decreasing complexity, and further improving energy efficiency, is optimization of the digital signal processing (DSP) in the per-antenna functions. Assuming an orthogonal frequency-division multiplexing (OFDM) based MaMIMO system, this paper explores coarse quantization in the per-antenna digital transmit filters and inverse fast Fourier transforms (IFFTs) and evaluates it in terms of performance and complexity savings. Results show that DSP complexity can be greatly reduced per-antenna, and therefore significant power savings can be achieved, with limited performance degradation. More specifically, when going towards MaMIMO and therefore increasing the number of antennas from 8 to 64, it is possible to reduce the complexity in each transmit filter by 55%. Also, when using 6 bits to represent the input signal and 6 bits for the filter coefficients, this results in an SNR degradation of less than 0.5 dB compared to floating-point performance. Consequently, we conclude that the overall system energy greatly benefits from lousy per-antenna processing.
Modeling, synthesis and characterization of zinc containing carbonic anhydrase active site mimics (2011)

Two structurally similar carbonic anhydrase active site mimics are explored computationally and experimentally in order to gain insight into the impact of subtle differences in scaffold structure on CO2 hydration rates.
Estrogen receptor is significantly associated with the epithelioid variants of renal angiomyolipoma: A clinicopathological and immunohistochemical study of 67 cases (2004)

Perivascular epithelioid cells (PEC) in angiomyolipoma (AML) were recently proposed to be its most common progenitor cells. Histologically, triphasic components were present in various proportions, but were overwhelmingly myogenic in epithelioid variants of AML. Despite histological discrimination, the immunophenotypic profiles between triphasic and epithelioid AML have never been compared. The aim of the present study was to clarify the identity of PEC by using immunoreactivity to estrogen receptor (ER), progesterone receptor (PR), bcl-2 and placenta alkaline phosphatase (PLAP), and to use this information to compare triphasic and epithelioid AML. A total of 33 out of 67 cases of renal angiomyolipoma that underwent surgery were reviewed over the period 1998-2003. Two cases were associated with tuberous sclerosis. Ten patients had other malignant tumors, and three patients had a nodal extension. Immunohistochemistry showed that bcl-2 (59.4%), PLAP (46.9%), HMB-45 (100%) was predominantly localized around vessels. The stem cell markers were absolutely negative in all AML types. The estrogen receptors were positive in 14 cases (42.4%) and the progesterone receptors were positive in five cases. Bcl-2 and both female sex hormone receptors were significantly more frequent in the epithelioid variant of AML than in the triphasic type. Perivascular epithelioid cells express bcl-2, ER, PR and PLAP, and ER could be partly associated with myogenic proliferation.
Separation of veins from activated brain tissue in functional magnetic resonance images at 1.5T (1995)

A feasibility study was conducted to segment 1.5T functional magnetic resonance images (fMRIs) into gray matter and veins using individual pixel intensity difference and temporal phase delay as two correlated parameters in 1.5T gradient echo images. The time-course of each pixel in gradient echo images acquired during visual stimulation with a checkerboard flashing at 8 Hz was correlated to the stimulation on-off sequence to identify activated pixels, and the temporal delay of each activated pixel was computed by fitting its time-course to a reference sinusoidal function. A histogram of the product of each pixel's intensity (in the activated image) and corresponding temporal delay could be fitted to a bimodal distribution, which was then used to segment the functional image into veins and activated brain tissue. The results show relatively good demarcation between large veins and activated gray matter using this method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Measurement of the Ratio of Branching Fractions B([bar over B][superscript 0] → D[superscript *+]τ[superscript -][bar over ν][subscript τ])/B([bar over B][superscript 0] → D[superscript *+]μ[superscript -][bar over ν][subscript μ]) (2015)

The branching fraction ratio R(D*) ≡ B([bar over B][superscript 0] → D[superscript *+]τ[superscript -][bar over ν][subscript τ])/B([bar over B][superscript 0] → D[superscript *+]μ[superscript -][bar over ν][subscript μ]) is measured using a sample of proton-proton collision data corresponding to 3.0 fb[superscript -1] of integrated luminosity recorded by the LHCb experiment during 2011 and 2012. The tau lepton is identified in the decay mode τ[superscript -] → μ[superscript -][bar over ν][subscript μ]ν[subscript τ]. The semitauonic decay is sensitive to contributions from non-standard-model particles that preferentially couple to the third generation of fermions, in particular, Higgs-like charged scalars. A multidimensional fit to kinematic distributions of the candidate [bar over B][superscript 0] decays gives R(D*) = 0.336 ± 0.027(stat) ± 0.030(syst). This result, which is the first measurement of this quantity at a hadron collider, is 2.1 standard deviations larger than the value expected from lepton universality in the standard model.
COMPREHENSIVE APPRAISAL KARNA ROGA W.S.R. KARNASHRAVA IN AYURVEDA & CONTEMPORARY SCIENCE (2005)

There is difference of opinions among the Acharya about the total number of karna rogas. In this set of disorders of karna, the diseases belong to Shabdendriya have also been included. Acharya Charaka has described karna rogas in a separate chapter. There is an explanation of these disorders belonging to karna in trimarmiya chikitsa chapter of Charaka Samhita. According to Charaka there are four types of karna rogas based on doshas. They are Vataja, Pittaja, Kaphaja & Sannipataja. In these four types, all the karna rogas are included. Since Charaka belongs to Kayachikitsa School of thoughts, it is natural that a very short description of these disorders of urdhwa jatrugata rogas is found. Charaka has also mentioned a short method of treatment for karna rogas. One, among the treatments is karna purana. Interestingly, there is no mention of disorders of karna pali. (Ch. Chi. 26/71). 1. Vatika Karnaroga 2. Paittika…
Delayed Parkinsonism after CO Intoxication: Evaluation of the Substantia Nigra with Inversion-Recovery MR Imaging (2012)

CO toxicity to the substantia nigra plays a role in pathophysiologic mechanisms of CO-induced parkinsonism. GM-suppressed IR MR imaging is a useful tool in depicting substantia nigra injury following CO intoxication.
Measurements of Iron Compound Content in the Brain Using a Flexible Core Fluxgate Magnetometer at Room Temperature (2018)

It has been observed that patients with neurodegenerative diseases, e.g., Alzheimer's and Parkinson's diseases, accumulate metals and, specifically, iron compounds with a magnetic moment, in specific, anatomic regions of the central nervous systems. In this context, several techniques have been exploited in order to measure increased brain iron levels that, typically, accompany neurodegenerative diseases; these techniques include positron emission tomography (PET), magnetic resonance imaging (MRI) and measurement systems based on magnetic sensors (i.e., HTS or LTS SQUID magnetometers). In particular, the measurement approach based on MRI, unlike PET, does not require the use of radioactive tracers and affords superior spatial resolution. However, MRIs can be expensive and not suitable in patients with implanted devices. SQUID-based measurement techniques usually require a very controlled environment, with good compensation for ambient magnetic noise, and are expensive. In this paper, we investigate the possibility of using a flexible core residence time's difference-fluxgate magnetometer as an alternative low-cost, room temperature solution for carrying out measurements of iron compound contents as observed in neurodegenerative diseases. Our experimental results appear promising enough that one can conclude that it is worth further pursuing this approach, namely, using a very simple sensor to detect ferromagnetic compounds that have accumulated in a localized area in the brain. Our results allow us to state, with good confidence, that monitoring the iron content in (at risk) patients might make it possible to detect the looming onset of some neurodegenerative disorders and could, in fact, be used as a diagnostic tool; all this can be accomplished with an inexpensive, room temperature magnetic field sensor that uses a neuromorphic readout in the time domain.
GaAs Heteroepitaxy on SiGe-on-Insulator Using Ge Condensation and Migration Enhanced Epitaxy (2007)

A novel fabrication technique to grow device quality GaAs on Si substrate is proposed using thin graded SiGe-on-insulator (SGOI) substrate. Combination of low-temperature GaAs molecular beam epitaxy (MBE) growth technique, low-temperature GaAs migration enhanced epitaxy (MEE) technique, and modified two-step Ge condensation technique has demonstrated successful growth of 10-nm GaAs layer grown on a tensile strained 42-nm graded SGOI layer.
Rotational Unit of Memory: A Novel Representation Unit for RNNs with Scalable Applications (2019)

Stacking long short-term memory (LSTM) cells or gated recurrent units (GRUs) as part of a recurrent neural network (RNN) has become a standard approach to solving a number of tasks ranging from language modeling to text summarization. Although LSTMs and GRUs were designed to model long-range dependencies more accurately than conventional RNNs, they nevertheless have problems copying or recalling information from the long distant past. Here, we derive a phase-coded representation of the memory state, Rotational Unit of Memory (RUM), that unifies the concepts of unitary learning and associative memory. We show experimentally that RNNs based on RUMs can solve basic sequential tasks such as memory copying and memory recall much better than LSTMs/GRUs. We further demonstrate that by replacing LSTM/GRU with RUM units we can apply neural networks to real-world problems such as language modeling and text summarization, yielding results comparable to the state of the art.
Dominant-negative IKZF1 mutations cause a T, B, and myeloid cell combined immunodeficiency (2018)

Ikaros/IKZF1 is an essential transcription factor expressed throughout hematopoiesis. IKZF1 is implicated in lymphocyte and myeloid differentiation and negative regulation of cell proliferation. In humans, somatic mutations in IKZF1 have been linked to the development of B cell acute lymphoblastic leukemia (ALL) in children and adults. Recently, heterozygous germline IKZF1 mutations have been identified in patients with a B cell immune deficiency mimicking common variable immunodeficiency. These mutations demonstrated incomplete penetrance and led to haploinsufficiency. Herein, we report 7 unrelated patients with a novel early-onset combined immunodeficiency associated with de novo germline IKZF1 heterozygous mutations affecting amino acid N159 located in the DNA-binding domain of IKZF1. Different bacterial and viral infections were diagnosed, but Pneumocystis jirovecii pneumonia was reported in all patients. One patient developed a T cell ALL. This immunodeficiency was characterized by innate and adaptive immune defects, including low numbers of B cells, neutrophils, eosinophils, and myeloid dendritic cells, as well as T cell and monocyte dysfunctions. Notably, most T cells exhibited a naive phenotype and were unable to evolve into effector memory cells. Functional studies indicated these mutations act as dominant negative. This defect expands the clinical spectrum of human IKZF1-associated diseases from somatic to germline, from haploinsufficient to dominant negative.
Pure single-site robot-assisted pyeloplasty with the da Vinci SP surgical system: Initial experience (2019)

Pure single-site RAP using the da Vinci SP surgical system is feasible and safe.