gebhart/patrepeval huggingface dataset:
On Vectorization of Deep Convolutional Neural Networks for Vision Tasks (2015)

We recently have witnessed many ground-breaking results in machine learning and computer vision, generated by using deep convolutional neural networks (CNN). While the success mainly stems from the large volume of training data and the deep network architectures, the vector processing hardware (e.g. GPU) undisputedly plays a vital role in modern CNN implementations to support massive computation. Though much attention was paid in the extent literature to understand the algorithmic side of deep CNN, little research was dedicated to the vectorization for scaling up CNNs. In this paper, we studied the vectorization process of key building blocks in deep CNNs, in order to better understand and facilitate parallel implementation. Key steps in training and testing deep CNNs are abstracted as matrix and vector operators, upon which parallelism can be easily achieved. We developed and compared six implementations with various degrees of vectorization with which we illustrated the impact of vectorization on the speed of model training and testing. Besides, a unified CNN framework for both high-level and low-level vision tasks is provided, along with a vectorized Matlab implementation with state-of-the-art speed performance.
The PIP5K2A and RGS4 genes are differentially associated with deficit and non‐deficit schizophrenia (2006)

Several putative schizophrenia susceptibility genes have recently been reported, but it is not clear whether these genes are associated with schizophrenia in general or with specific disease subtypes. In a previous study, we found an association of the neuregulin 1 (NRG1) gene with non-deficit schizophrenia only. We now report an association study of four schizophrenia candidate genes in patients with and without deficit schizophrenia, which is characterized by severe and enduring negative symptoms. Single-nucleotide polymorphisms (SNPs) were genotyped in the DTNBP1 (dysbindin), G72/G30 and RGS4 genes, and the relatively unknown PIP5K2A gene, which is located in a region of linkage with both schizophrenia and bipolar disorder. The sample consisted of 273 Dutch schizophrenia patients, 146 of whom were diagnosed with deficit schizophrenia and 580 controls. The strongest evidence for association was found for the A-allele of SNP rs10828317 in the PIP5K2A gene, which was associated with both clinical subtypes (P = 0.0004 in the entire group; non-deficit P = 0.016, deficit P = 0.002). Interestingly, this SNP leads to a change in protein composition. In RGS4, the G-allele of the previously reported SNP RGS4-1 (single and as part of haplotypes with SNP RGS4-18) was associated with non-deficit schizophrenia (P = 0.03) but not with deficit schizophrenia (P = 0.79). SNPs in the DTNBP1 and G72/G30 genes were not significantly associated in any group. In conclusion, our data provide further evidence that specific genes may be involved in different schizophrenia subtypes and suggest that the PIP5K2A gene deserves further study as a general susceptibility gene for schizophrenia.
The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4 (2004)

We report the complete genome sequence of Zymomonas mobilis ZM4 (ATCC31821), an ethanologenic microorganism of interest for the production of fuel ethanol. The genome consists of 2,056,416 base pairs forming a circular chromosome with 1,998 open reading frames (ORFs) and three ribosomal RNA transcription units. The genome lacks recognizable genes for 6-phosphofructokinase, an essential enzyme in the Embden-Meyerhof-Parnas pathway, and for two enzymes in the tricarboxylic acid cycle, the 2-oxoglutarate dehydrogenase complex and malate dehydrogenase, so glucose can be metabolized only by the Entner-Doudoroff pathway. Whole genome microarrays were used for genomic comparisons with the Z. mobilis type strain ZM1 (ATCC10988) revealing that 54 ORFs predicted to encode for transport and secretory proteins, transcriptional regulators and oxidoreductase in the ZM4 strain were absent from ZM1. Most of these ORFs were also found to be actively transcribed in association with ethanol production by ZM4.
Papel del receptor de insulina y sus isoformas en el transporte de glucosa y en la supervivencia celular de los hepatocitos neonatales (2008)

La funcion hepatica es crucial para el funcionamiento de los organismos superiores. Dicha funcion hepatica viene determinada, al menos en parte, por el grado de desarrollo alcanzado por el higado en lo que ala masa tisular se refiere. Una masa critica hepatica insuficiente pondria en riesgo la funcionalidad hepatica y un sobre crecimiento del higado podria comprometer la homeostasis energetica de los tejidos extrahepaticos. Dos puntos cruciales seria el consumo basal de glucosa hepatico, insulina-independiente, y la supervivencia celular del hepatocito en relacion con su organogenesis. Por este motivo, nos propusimos investigar el papel del receptor de insulina (IR) y sus isoformas IRA e IRB en la homeostasis glucidica y en el desarrollo de l higado. 
Para ello hemos utilizado lineas celulares de hepatocitos inmortalizados de genotipo salvaje, carentes en IR y reconstituidos con las isoformas IRA e IRB. 
La deleccion del IR en los hepatocitos neonatales inmortalizados lleva asociada una d isminucion en el transporte y/o captacion de glucosa. La expresion de la isoforma IRA del IR en los hepatocitos neonatales inmortalizados restablece el trasporte de glucosa, pero no asi la isoforma IRB. 
Por otro lado, la falta del IR acelera la apoptosis inducida en respuesta a la retirada de factores troficos en los hepatocitos neonatales. La expresion individual de las isoformas A y B del IR en los hepatocitos neonatales carentes del IR recupera la senalizacion anti-apoptotica de la insulina y , como resultado, la insulina recata a dichos hepatocitos de la apoptosis inducida por la retirada de suero. Sin embargo, los hepatocitos neonatales que expresan IRA o IRB experimentan una apoptosis masiva tras la retirada de suero. Esta apoptosis se caracteriza por un aumento muy significativo de la actividad de la caspasa-8 ya que se induce un aumento de complejos proteicos de membrana que incluyen IRA/Fas/FADD o IRB/Fas/FADD, respectivamente. 
Conclusion: el balance de las isoformas del IR e s fundamental en el desarrollo del higado, tanto en el mantenimiento de la homeostasis glucidica tisular como en la organogenesis del propio tejido hepatico. Sin embargo, queda por investigar si la relacion IRA/IRB en los hepatocitos humanos pudiera estar implicada en los mecanismos de proteccion frente a un dano hepatico.
Gradient separation of granulocytic progenitor cells (CFUc) from human blood mononuclear leukocytes. (1985)

Two different density-gradient techniques were compared for separation of human blood-derived granulocyte-macrophage progenitor cells (CFUc) from immunocompetent cells using albumin or Percoll as gradient media. Mean CFUc enrichment by means of discontinuous albumin gradient was twofold, whereas Percoll gradients yielded about 20- to 40-fold enrichment of CFUc in relation to lymphocytes. The pH of gradient media proved to have a major influence on separation quality. Based on these results and the development of a new density-separation technique in a 600-ml plastic bag, replacing customary Ficoll-Hypaque gradients, a method for large-scale purification of CFUc from leukapheresis-derived leukocytes has been constructed, working in a closed, sterile system. About 11 X 10(9) mononuclear cells containing 6 X 10(5) CFUc could be processed within 10 h. Lymphocytes were reduced to less than 1% of their initial number, and an average of about 50% of the original CFUc could be recovered.
Blockade of the MEK/ERK signalling cascade by AS703026, a novel selective MEK1/2 inhibitor, induces pleiotropic anti‐myeloma activity in vitro and in vivo (2010)

This study investigated the cytotoxicity and mechanism of action of AS703026, a novel, selective, orally bioavailable MEK1/2 inhibitor, in human multiple myeloma (MM). AS703026 inhibited growth and survival of MM cells and cytokine-induced osteoclast differentiation more potently (9- to 10-fold) than AZD6244. Inhibition of proliferation induced by AS703026 was mediated by G0-G1 cell cycle arrest and was accompanied by reduction of MAF oncogene expression. AS703026 further induced apoptosis via caspase 3 and Poly ADP ribose polymerase (PARP) cleavage in MM cells, both in the presence or absence of bone marrow stromal cells (BMSCs). Importantly, AS703026 sensitized MM cells to a broad spectrum of conventional (dexamethasone, melphalan), novel or emerging (lenalidomide, perifosine, bortezomib, rapamycin) anti-MM therapies. Significant tumour growth reduction in AS703026- vs. vehicle-treated mice bearing H929 MM xenograft tumours correlated with downregulated pERK1/2, induced PARP cleavage, and decreased microvessels in vivo. Moreover, AS703026 (<200 nmol/l) was cytotoxic against the majority of tumour cells tested from patients with relapsed and refractory MM (84%), regardless of mutational status of RAS and BRAF genes. Importantly, BMSC-induced viability of MM patient cells was similarly blocked within the same dose range. Our results therefore support clinical evaluation of AS703026, alone or in combination with other anti-MM agents, to improve patient outcome.
Increased survival of CFTR knockout mice with an oral osmotic laxative. (1996)

Mouse models of cystic fibrosis that are generated by targeted disruption (knockout) of the cystic fibrosis transmembrane conductance regulator gene, cftr(-/-), typically die shortly after weaning, from intestinal obstruction/rupture caused by an inability to secrete fluid into the bowel lumen. We investigated the use of a commercial osmotic laxative, Colyte, provided continuously in the drinking water, to increase the survival of cftr(-/-) mice. Genotype analysis of 623 offspring surviving at 10 days of age yielded 28.1% cftr(+/+), 59.6% cftr(+/-), and 12.4% cftr(-/-) mice (25% predicted), suggesting that cftr(-/-) mice have a significant perinatal mortality rate. However, of the 77 cftr(-/-) mice alive at 10 days of age, >98% survived weaning and were maintained in apparent health to a minimum of 56 days of age (arbitrary age for experimentation). In intestinal bioelectric studies Colyte-treated drinking water, compared with tap water, had no significant effect on basal short-circuit current, cyclic AMP-stimulated Cl- secretion, Na+-coupled glucose absorption, or electrogenic Na+ absorption across intestinal sections from cftr(+/+ or +/-) mice. Other than a mild dilatation of the distal portion of the colon in the Colyte-treated animals, examination of jejunal and colonic sections revealed no histologic differences between the two treatments. These findings indicate that the chronic use of Colyte osmotic laxative in drinking water is an economical means of greatly increasing the survival of CFTR knockout mice without altering the major electrolyte transport processes or histomorphologic integrity of the intestine.
Precision transfer printing of ultra-thin AlInGaN micron-size light-emitting diodes (2013)

We report the fabrication of a mechanically-flexible 16×16 array of thin-film, micron-size LEDs emitting at 480 nm. Devices were transfer-printed onto a mechanically-flexible ITO backplane using a modified, high-precision (placement accuracy ±25 nm) assembly system.
Lysergic acid diethylamide (LSD) for alcoholism: meta-analysis of randomized controlled trials (2012)

Assessments of lysergic acid diethylamide (LSD) in the treatment of alcoholism have not been based on quantitative meta-analysis. Hence, we performed a meta-analysis of randomized controlled trials in order to evaluate the clinical efficacy of LSD in the treatment of alcoholism. Two reviewers independently extracted the data, pooling the effects using odds ratios (ORs) by a generic inverse variance, random effects model. We identified six eligible trials, including 536 participants. There was evidence for a beneficial effect of LSD on alcohol misuse (OR, 1.96; 95% CI, 1.36-2.84; p = 0.0003). Between-trial heterogeneity for the treatment effects was negligible (I² = 0%). Secondary outcomes, risk of bias and limitations are discussed. A single dose of LSD, in the context of various alcoholism treatment programs, is associated with a decrease in alcohol misuse.
HTRA1 Variant Confers Similar Risks to Geographic Atrophy and Neovascular Age-related Macular Degeneration (2007)

Age-related macular degeneration (AMD) is the most common cause of irreversible visual impairment in the developed world. The two forms of advanced AMD, geographic atrophy (GA) and choroidal neovascularization (wet AMD), represent two types of degenerative processes in the macula that lead to loss of central vision. Soft confluent drusen, characterized by deposits in macula without visual loss are considered a precursor of advanced AMD. A single nucleotide polymorphism, rs11200638, in the promoter of HTRA1 has been shown to increases the risk for wet AMD. However, its impact on soft confluent drusen and GA or the relationship between them is unclear. To better understand the role the HTRA1 polymorphism plays in AMD subtypes, we genotyped an expanded Utah population with 658 patients having advanced AMD or soft confluent drusen and 294 normal controls and found that the rs11200638 was significantly associated with GA. This association remains significant conditional on LOC387715 rs10490924. In addition, rs11200638 was significantly associated with soft confluent drusen, which are strongly immunolabeled with HTRA1 antibody in an AMD eye with GA similar to wet AMD. Two-locus analyses were performed for CFH Y402H variant at 1q31 and the HTRA1 polymorphism. Together CFH and HTRA1 risk variants increase the odds of having AMD by more than 40 times. These findings expand the role of HTRA1 in AMD. Understanding the underlying molecular mechanism will provide an important insight in pathogenesis of AMD.
A Study of Nanophase Tungsten Oxides Thin Films by XPS (2001)

Nanophasic tungsten oxides thin films have been deposited at 500 °C on quartz and glass substrates starting from W(CO)6 using the metal organic chemical vapor deposition technique (MOCVD). Two series of deposition experiments were carried out to make a comparison between the results obtained employing, as reactant gases, O2 mixed with water vapor and a dry mixture of N2 with 25% H2, respectively. The obtained tungsten oxides were analyzed by x-ray diffraction (XRD), x-ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM) in order to investigate their microstructure, chemical composition, and surface morphology. In this work, XPS analyses of two tungsten oxides thin films deposited in different atmospheres are presented. Besides the wide scan spectra, charge corrected binding energies for the W 4f7/2, W 4f5/2, O ls, and C 1s surface photoelectron signals are reported. In particular, the film obtained in H2 atmosphere shows the presence of W in an oxidation state lower than VI.
Development of T-Cell Lines Expressing Functional HIV-1 Envelope Glycoproteins for Evaluation of Immune Responses in HIV-infected Individuals (1996)

The human T-lymphoid cell line, CEM, was transfected with gp 160 cDNA of human immunodeficiency virus type 1 (HIV-1)pm213. Three clones expressing the envelope glycoproteins (env), designated CEM-213env1, -env4, and -env7, were isolated. These clones expressed high levels of surface gp41 and gp120, as demonstrated by flow cytometry with anti-HIV env monoclonal antibodies. Processing and function of env was shown by induction of syncytia with CD4-expressing HeLa cells and by immunoblot analysis. The env expression resulted in specific down-regulation of surface CD4 levels, supporting the role of HIV env in CD4 modulation. Furthermore, serum samples from nine of nine HIV-1-infected individuals bound specifically to the env-expressing transfectants, substantiating the presence of conserved antigenic determinants. These sera also mediated antibody-dependent cellular cytotoxicity (ADCC) of the env-expressing cell lines. The env-expressing cell lines provide a relevant, safe, and practical model for qualitative and quantitative analysis of humoral and cellular immune responses and their role in HIV-1 pathogenesis and therapy.
Comparison of Cu electromigration lifetime in Cu interconnects coated with various caps (2003)

Electromigration in Cu Damascene lines with bamboo-like grain structures, either capped with Ta/TaN, SiNx, SiCxNyHz layers, or without any cap, was investigated. A thin Ta/TaN cap on top of the Cu line surface significantly improves electromigration lifetime when compared with lines without a cap and with lines capped with SiNx or SiCxNyHz. The activation energy for electromigration increased from 0.87 eV for lines without a cap to 1.0–1.1 eV for samples with SiNx or SiCxNyHz caps and to 1.4 eV for Ta/TaN capped samples.
New Approach to the Surgical Treatment of Severe Exophthalmos in Graves Disease (1998)

In the last few years, various surgical techniques to correct orbital decompression in patients with Graves ophthalmopathy have been proposed. In those patients in whom a high degree of exophthalmos is mainly the result of the hypertrophied endorbital muscles with respect to endorbital fat hypertrophy, lipectomy is insufficient to obtain an acceptable increase of endorbital volume. The authors propose a method that provides for the monobloc bilateral quadrantotomy by extracranial access. Despite traditional methods of decompression, the advantage of this technique is better advancement of the orbital margins. The bicoronal and endoral incisions guarantee no facial scars. Compared with the craniotomy, the extracranial access is also less stressful for the patient.
Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two‐dimensional signal intensity map data visualization (2006)

We demonstrate how visualization of liquid chromatography/mass spectrometry data as a two-dimensional signal intensity map can be used to assess the overall quality of the data, for the identification of polymer contaminants and artifacts, as well as for the confirmation of post-translational modifications.
A simplified biochemistry for DNA sequencing. (1990)

A simplified method of DNA sequencing by dideoxy chain termination is developed that approaches a single-step protocol. Utilizing the sequencing advantages contributed by a thermophilic polymerase and a guanine analog, stable sequencing reaction concentrates have been obtained that readily perform the entire sequencing reaction simply by adding prepared DNA to each of the four reaction concentrates required by this method. The mechanics and dynamics of these reactions have been investigated and the capacity of these reactions to withstand normal user variation is demonstrated. This study focuses on one form of this simplified method embodied in the FASTaq DNA sequencing kit.
Sustained transscleral drug delivery (2007)

Transscleral delivery is an emerging, high-potential method for delivering drugs to the posterior eye. If successful, it could offer non-invasiveness comparable to drops and delivery efficiency comparable to intravitreal injection. However, there are numerous challenges to be overcome before transscleral delivery will be a significant treatment option. The resistance of the sclera is extremely well understood, but the other tissues, especially the retinal pigment epithelium, clearly demand more attention and the effect of drug chemistry remains poorly understood. In this review, the major research on transscleral delivery with an emphasis on current understanding of these points and open questions for the field is summarized.
Setting the frequency-tidal volume pattern. (2002)

Alveolar (and thus arterial) P(O2) and P(CO2) clearly depend on minute ventilation. However, we need to balance gas exchange goals against the risk of overstretching, especially of the healthier regions of the lung. The plateau pressure is probably the best easily-obtained marker of the risk of stretch in the lung, and a commonly quoted threshold is 30--35 cm H(2)O, the normal maximum transalveolar pressure at total lung capacity. In establishing the proper balance of stretch versus gas exchange, we need to address what levels of pH and P(aO2) we consider acceptable. There are no good data to guide us on the lowest tolerable pH, but 7.2 is commonly quoted in the literature, and 7.15 was the lower limit of acceptability in the ARDS (acute respiratory distress syndrome) Network trial. P(O2) levels as low as 55 mm Hg may be well tolerated, provided there is reasonable oxygen delivery. In distributing the desired minute volume between respiratory frequency and tidal volume (V(T)), a V(T) of 6 mL/kg ideal body weight has been shown to improve ARDS outcome, compared to 12 mL/kg. Thus, 6 mL/kg should be the "start point." Adjustments upward could be considered the plateau pressure is acceptable, in order to improve gas exchange or comfort. Conversely, downward adjustments should be considered if the plateau pressure is high and the gas exchange is acceptable. Frequency is adjusted for the desired minute ventilation. It must be recognized, however, that as frequency (and minute ventilation) increases, the risk of air trapping and intrinsic positive end-expiratory pressure (PEEP) increases. Just like applied PEEP, intrinsic PEEP increases the baseline pressure and stretch upon which the V(T) is delivered. The end-inspiratory stretch increases accordingly. The shape and duration of the flow pattern may affect gas mixing, recruitment, cardiac function, intrinsic PEEP buildup, and patient comfort. It is also conceivable that certain flow patterns can produce an acceleration injury. Although small clinical trials using physiologic end points espouse certain flow patterns, there are no good outcome data at present supporting any particular approach. Some authors suggest that high-frequency ventilation (HFV) might be considered an "ultimate" lung-protective strategy. HFV creates considerable intrinsic PEEP, which, when coupled with sustained inflation maneuvers, can provide substantial alveolar recruitment. In addition, the small V(T) of HFV prevents excessive end-inspiratory distention. Although considerable clinical data support the use of HFV in pediatric patients at risk for ventilator-induced lung injury, there are few data from adults. Whether HFV will prove valuable in well-designed open lung strategies in the adult population still has to be determined.