gebhart/patrepeval huggingface dataset:
Manipulation of <i>OCT4</i> Levels in Human Embryonic Stem Cells Results in Induction of Differential Cell Types (2007)

To fully understand self-renewal and pluripotency and their regulation in human embryonic stem cells (hESCs), it is necessary to generate genetically modified cells and analyze the consequences of elevated and reduced expression of genes. Genes expressed in hESCs using plasmid vectors, however, are subject to silencing. Moreover, hESCs have a low plating efficiency when dissociated to single cells, making creation of subcloned lines inefficient. In addition to overexpression experiments, it is important to perform loss-of-function studies, which can be achieved rapidly using RNA interference (RNAi). We report stable long-term expression of enhanced green fluorescent protein (eGFP) in hESCs using a lentiviral vector, and establishment of an eGFP-expressing subline (RG6) using manual dissection. To demonstrate the efficacy of RNAi in hESCs, an RNAi expression vector was used to achieve reduced expression of eGFP in hESCs. To evaluate the role of OCT4 in the regulation of hESC self-renewal and differentiation, a vector expressing a hairpin RNA targeting endogenous expression of OCT4 was constructed. In a novel experiment in hESCs, the OCT4 cDNA sequence was cloned into an expression vector to allow for the transient upregulation of OCT4 in hESCs. The ability to manipulate levels of OCT4 above and below enodogenous levels allows the determination of OCT4 function in hESCs. Specifically, reduced expression of OCT4 in hESCs promoted upregulation of markers indicative of mesoderm and endoderm differentiation, and elevated levels of OCT4 in hESCs promoted upregulation of markers indicative of endoderm derivatives. Thus, both upregulation and downregulation of Oct4 in hESCs results in differentiation, but with patterns distinct from parallel experiments in mice.
"Answer ka type kya he?" (2015)

Code-Mixing (CM) is defined as the embedding of linguistic units such as phrases, words, and morphemes of one language into an utterance of another language. CM is a natural phenomenon observed in many multilingual societies. It helps in speeding-up communication and allows wider variety of expression due to which it has become a popular mode of communication in social media forums like Facebook and Twitter. However, current Question Answering (QA) research and systems only support expressing a question in a single language which is an unrealistic and hard proposition especially for certain domains like health and technology. In this paper, we take the first step towards the development of a full-fledged QA system in CM language which is building a Question Classification (QC) system. The QC system analyzes the user question and infers the expected Answer Type (AType). The AType helps in locating and verifying the answer as it imposes certain type-specific constraints. In this paper, we present our initial efforts towards building a full-fledged QA system for CM language. We learn a basic Support Vector Machine (SVM) based QC system for English-Hindi CM questions. Due to the inherent complexities involved in processing CM language and also the unavailability of language processing resources such POS taggers, Chunkers, Parsers, we design our current system using only word-level resources such as language identification, transliteration and lexical translation. To reduce data sparsity and leverage resources available in a resource-rich language, in stead of extracting features directly from the original CM words, we translate them commonly into English and then perform featurization. We created an evaluation dataset for this task and our system achieves an accuracy of 63% and 45% in coarse-grained and fine-grained categories of the question taxanomy. The idea of translating features into English indeed helps in improving accuracy over the unigram baseline.
SeeMe in a nutshell – the semi-structured, sociotechnical Modeling Method (2008)

This introduction explains the basis concepts of the modeling notation SeeMe (semi-structured, socio-technical Modeling Method). We assume that most of the readers know other types of diagrammatic modeling languages, and are now interested in a method which is especially designed for representing socio-technical work processes and structures. The following description is mainly focused on the syntactical and semantical aspects of the modeling notation SeeMe. Only the last section provides guidelines about how diagrams can be developed.
Transcatheter closure of very large (≥ 25 mm) atrial septal defects using the Amplatzer septal occluder (2003)

Between June 1999 and September 2002, 45 patients (age, 34 +/- 13 years; mean shunt ratio, 2.6 +/- 0.6) underwent transcatheter atrial septal defect (ASD) closure at our institution with the Amplatzer septal occluder (mean device size, 31.4 +/- 3 mm). Patients were selected by transesophageal echocardiography. The mean ASD dimension was 25.3 +/- 3.7 mm and 33 (73%) patients had deficient anterior rim. Specific procedural details included the use of 13 or 14 Fr introducer sheaths and the right upper pulmonary vein approach if the conventional approach failed. There were two procedural failures, with device embolization in both (surgical retrieval in one, catheter retrieval in one). During follow-up (3-30 months; median, 16 months), one patient (59 years) with previous atrial flutter had pulmonary embolism and was managed with anticoagulation. Two patients developed symptomatic atrial flutter. Fluoroscopy time was 31.6 +/- 19.5 min for the first 22 cases and 19.6 +/- 11.4 min for the rest (P = 0.04). Transcatheter closure of large ASDs is technically feasible but careful long-term follow-up is needed to document its safety.
xin ke cheng li nian xia de kai fang shi shu xue jiao xue (2013)

开放式课堂教学,是对传统教学的“扬弃”.新课程改革期待教师改变这种传统的封闭型教学方式,实行开放式教学,使课堂充满生趣,充满孜孜不倦的探索,变“学知”为“知学”,使学生成为具有初步创新精神和实践能力的人.
(Per)chlorate Reduction by the Thermophilic Bacterium<i>Moorella perchloratireducens</i>sp. nov., Isolated from Underground Gas Storage (2007)

A thermophilic bacterium, strain An10, was isolated from underground gas storage with methanol as a substrate and perchlorate as an electron acceptor. Cells were gram-positive straight rods, 0.4 to 0.6 mum in diameter and 2 to 8 mum in length, growing as single cells or in pairs. Spores were terminal with a bulged sporangium. The temperature range for growth was 40 to 70 degrees C, with an optimum at 55 to 60 degrees C. The pH optimum was around 7. The salinity range for growth was between 0 and 40 g NaCl liter(-1) with an optimum at 10 g liter(-1). Strain An10 was able to grow on CO, methanol, pyruvate, glucose, fructose, cellobiose, mannose, xylose, and pectin. The isolate was able to respire with (per)chlorate, nitrate, thiosulfate, neutralized Fe(III) complexes, and anthraquinone-2,6-disulfonate. The G+C content of the DNA was 57.6 mol%. On the basis of 16S rRNA analysis, strain An10 was most closely related to Moorella thermoacetica and Moorella thermoautotrophica. The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell extracts. Strain An10 is the first thermophilic and gram-positive bacterium with the ability to use (per)chlorate as a terminal electron acceptor.
Stabilization of electro-optic modulator bias voltage drift using a lock-in amplifier and a proportional-integral-derivative controller in a distributed Brillouin sensor system (2007)

In a distributed Brillouin sensor system, it is crucial to keep the pulse energy uniform for a constant signal-to-noise ratio. This means that the variable dc leakage (pulse base) for the electro-optic modulator (EOM) must be locked. We examine two different methods of locking the EOM bias voltage and look at the advantages and disadvantages of each locking method. It is found that the two locking methods, one based on a lock-in amplifier and the other using proportional-integral-derivative control, both have applications in which they excel at locking the pulse base.
Straight and Smooth Etching of GaN (1100) Plane by Combination of Reactive Ion Etching and KOH Wet Etching Techniques (2006)

GaN striped structures along the <11 20 > and <1 100 > directions were fabricated by a combination etching technique, consisting of reactive ion etching followed by KOH wet etching. After wet etching, the sidewalls of the striped structures along the <11 20 > direction became very smooth and straight, compared with normal wet etching and dry etching. From the differences of the etching along the <1 100 > direction, it was found that etching mainly occurs in the (1 100) plane. This phenomenon can be explained by the action of OH- ions, which are repelled by N dangling bonds on the surface and which attack Ga back bonds as well as the mechanism of (000 1) polar GaN etching.
Silencing of Epidermal Growth Factor Receptor Suppresses Hypoxia-Inducible Factor-2–Driven <i>VHL</i> −/− Renal Cancer (2005)

Inactivating mutations in the von Hippel-Lindau (VHL) tumor suppressor gene are associated with clear cell renal cell carcinoma (VHL-/- RCC), the most frequent malignancy of the human kidney. The VHL protein targets the alpha subunits of hypoxia-inducible factor (HIF) transcription factor for ubiquitination and degradation. VHL-/- RCC cells fail to degrade HIF resulting in the constitutive activation of its target genes, a process that is required for tumorigenesis. We recently reported that HIF activates the transforming growth factor-alpha/epidermal growth factor receptor (TGF-alpha/EGFR) pathway in VHL-defective RCC cells. Here, we show that short hairpin RNA (shRNA)-mediated inhibition of EGFR is sufficient to abolish HIF-dependent tumorigenesis in multiple VHL-/- RCC cell lines. The 2alpha form of HIF (HIF-2alpha), but not HIF-1alpha, drives in vitro and in vivo tumorigenesis of VHL-/- RCC cells by specifically activating the TGF-alpha/EGFR pathway. Transient incubation of VHL-/- RCC cell lines with small interfering RNA directed against EGFR prevents autonomous growth in two-dimensional culture as well as the ability of these cells to form dense spheroids in a three-dimensional in vitro tumor assay. Stable expression of shRNA against EGFR does not alter characteristics associated with VHL loss including constitutive production of HIF targets and defects in fibronectin deposition. In spite of this, silencing of EGFR efficiently abolishes in vivo tumor growth of VHL loss RCC cells. These data identify EGFR as a critical determinant of HIF-2alpha-dependent tumorigenesis and show at the molecular level that EGFR remains a credible target for therapeutic strategies against VHL-/- renal carcinoma.
InspIRED by Nature: NADPH‐Dependent Imine Reductases (IREDs) as Catalysts for the Preparation of Chiral Amines (2015)

Imine reductases (IREDs) are NADPH-dependent oxidoreductases that catalyse the asymmetric reduction of cyclic prochiral imines to amines, with excellent stereoselectivity. Since their discovery, stereocomplementary IREDs have been applied to the production of both (S) and (R) cyclic secondary amines, and the expansion in gene sequences recently identified has hinted at new substrate ranges that extend into acyclic imines and even suggest the possibility of asymmetric reductive amination from suitable ketone and amine precursors. Structural studies of various IREDs are beginning to reveal the complexities inherent in determining substrate range, stereoselectivity and mechanism in these enzymes, which represent a valuable emerging addition to the toolbox of available biocatalysts for chiral amine production.
An Ideal Viscous Flow Porometer (1979)

<sec> A new design of viscous flow porometer is described which is based on the pronciple of air suction into a syringe which then measures the volume of air atmosphere pressure. This porometer allows accurate readings to be made on the 0-100 scale on the syringe barrel when the piston has returned following its release. Each reading takes only seconds to make so that data can be collected for statistical analysis before stomata change in aperture and with minimal interference with the leaf envirnionment. Calibiration procedures are described&colon; examples ofthe new porometers and also silicone rubber imprints support the validity of measurements made by the new porometer. </sec>
Nuclear lamin proteins and the structure of the nuclear envelope: Where is the function? (1987)

Abstract The nuclear envelope has recently become the object of intense scrutiny because it is the site of nuclear transport and is possibly involved in the organization of the interphase genome, thereby affecting gene expression. The major structural support for the nuclear envelope is the nuclear lamina, composed of the nuclear lamin proteins. They lie on the surface of the inner nuclear membrane and are in direct contact with the chromatin at the edge of the nucleus. The structure of the nuclear lamin proteins has recently been deduced from their cDNAs and shown to have remarkable homologies to the family of cytoplasmic intermediate filaments. However, the lamin proteins have been found to depolymerize in response to metaphase‐specific phosphorylation events, and reassemble around daughter chromosomes at the completion of cell division. Little is known of the mechanisms of these dynamics, nor of other post‐translational modifications evident in these proteins. In addition, we have as yet no concrete idea of the function of these highly conserved proteins in the cell. This review will summarize our present knowledge of nuclear lamin structure and the new experimental approaches designed to elucidate their function.
Phase retrieval from subdivision of the focal plane with a lenslet array (2004)

A phase retrieval algorithm derived from subdivision of the complex field at the focal plane is proposed. This subdivision is achieved with a lenslet array at the focal plane in a manner similar to the pyramid wave-front sensor. The phase retrieval algorithm significantly improves the wave-front estimate that can be attained as a linear combination of the aperture images. This phase retrieval algorithm also avoids the twin-image stagnation problem inherent in phase retrieval and phase retrieval in conjunction with the Shack-Hartmann sensor.
SCREAMER - A single-line pulsed-power design tool (1985)

SCREAMER is a special purpose circuit code developed as a design tool for single module accelerators. It is fast, accurate, flexible, and user-friendly. Its development was motivated by the excessive costs and long turn-around times incurred when using the SCEPTRE circuit analysis code to perform simulations of circuits with large numbers of nodes and with nonlinear components. Comparable simulations between SCREAMER running on a VAX 11/780 and SCEPTRE running on a CRAY-1S show that turn-around times and costs can be two orders of magnitude lower when using SCREAMER.
Microwave imaging utilizing a soft prior constraint (2009)

Microwave imaging for breast cancer detection is becoming a promising alternative technique to current imaging modalities. The significant contrast between dielectric properties of normal and malignant breast tissues makes microwave imaging a useful technique to provide important functional information for diagnoses. However, one of its limitations is that it intrinsically cannot produce high resolution images as other conventional techniques such as MRI or X-ray CT do. Those modalities are capable of producing high quality anatomical images, but unlike microwave imaging, they often cannot provide the necessary functional information about tissue health. In order to refine the resolution of the microwave images while also preserving the functional information, we have recently developed a new strategy, called soft prior regularization. In this new approach, the prior anatomical information of the tissue from either x-ray, MR or other sources is incorporated into our microwave imaging reconstruction algorithm through the following steps: First, the anatomical information is used to create a reconstruction mesh which defines the boundaries of different internal regions. Second, based on location of each mesh node, an associated weighting matrix is defined, such that all nodes within each region are grouped with each other. Finally, the soft prior matrix is used as a regularizing term for our original Gauss- Newton reconstruction algorithm. Results from initial phantom experiments show a significant improvement in the recovered dielectric properties.
DGAT1 Participates in the Effect of <i>HNF4A</i> on Hepatic Secretion of Triglyceride-Rich Lipoproteins (2010)

This study identified DGAT1 as an important protein that participates in the effect of HNF4A on hepatic secretion of TRLs.
Dose-Response Characteristics for Arginine-Stimulated Insulin Secretion in Man and Influence of Hyperglycemia * (1989)

To test the hypothesis that glucose only affects the responsiveness (maximum velocity) of the beta-cell to arginine without changing the sensitivity (ED50) of the beta-cell to arginine, we investigated the influence of hyperglycemia on the responsiveness and sensitivity of arginine-induced insulin secretion in eight healthy male volunteers. Plasma C-peptide and insulin levels achieved during infusions of five doses of arginine (30 min) with and without a 60-min hyperglycemic clamp (17 mmol/L) were analyzed using a modified Michaelis-Menten equation. At euglycemia, the ED50 (half-maximally stimulating serum arginine concentration) was significantly less for first phase than for second phase plasma C-peptide secretion (0.7 +/- 0.1 vs. 2.7 +/- 0.4 mmol/L; P less than 0.002). Hyperglycemia significantly increased arginine-induced insulin secretion at all arginine infusion rates (P less than 0.01) without significantly altering the ED50 for either phase. We conclude 1) that the regulation of arginine-induced insulin secretion differs between both phases of insulin secretion, and 2) that a 1-h infusion with glucose significantly potentiates arginine-induced insulin secretion without influencing the difference in regulation of both phases of arginine-induced insulin secretion, supporting the validity of the use of arginine as a secretagogue in studies involving hyperglycemia.
The usefulness of determining des-γ-carboxy prothrombin by sensitive enzyme immunoassay in the early diagnosis of patients with hepatocellular carcinoma (1998)

The results of this study indicate that DCP determination by sensitive enzyme immunoassay is useful in the early diagnosis of HCC because a high specificity is maintained.
3D Shape Retrieval Integrated with Classification Information (2007)

3D surface moment invariants are a kind of integral invariants under translation, uniform scaling and rotation, and can be regarded as shape descriptors of 3D unclosed polygonal models. Few of the former literature used prior knowledge from the training set for supervised learning. In this paper, we illustrate how to select the training data and how to feed the feature vectors of the training models to back-propagation neural network for learning. Experimental result shows that the test models are sorted into the correct classes with high accuracy, including two-class classification and multi-class classification. Furthermore, we develop a novel method which uses weighted Manhattan distance to embed classification information into the traditional shape retrieval systems properly. It could determine and refine the retrieval results efficiently.
Alleviation of thermally induced phase mismatch in CsLiB_6O_10 crystal by means of temperature-profile compensation (1998)

A new mechanism was found to alleviate the thermally induced phase mismatch of nonlinear optical crystals. By cooling CsLiB>(6)O(10) at an elevated crystal temperature with gas, we improved laser conversion efficiency from green (532 nm) to UV (266 nm) 2.3 times compared with that without cooling. In situ observation of the temperature profile on the output surface revealed that such cooling initiates a negative temperature profile that compensates for the positive profile generated from laser absorption. A 10.6-W UV output with excellent stability was generated. The optimum crystal length was substantially extended.
The rate of ethylene polymerization initiated by various chelating tertiary diamine : <i>n</i>‐butyllithium complexes (1991)

Abstract The initial rates of ethylene polymerization initiated by 13 chelating tertiary diamine: n‐ butyllithium complexes were determined under a standard set of conditions. Complexes of the cyclic diamines 1,2‐dipyrrolidinoethane, sparteine, and 1,2‐dipiperidinoethane resulted in higher polymerization rates and larger ultimate polymer yields than did complexes of acyclic diamines such as N,N,N′,N′ ‐tetramethylethylenediamine. The rates of polymerization and also the polymer yields were also strongly affected by the length of the chain segment connecting the two amino groups in the diamine. Two carbon segments were superior to three carbon segments which were better than one or four carbon segments. The decomposition rate of n‐ butyllithium was also strongly accelerated by the presence of many of these diamines.
Low resistance Pd/Ge/Au and Ge/Pd/Au ohmic contacts to <i>n</i>-type GaAs (1986)

We have fabricated Pd/Ge/Au and Ge/Pd/Au sintered ohmic contacts on n-type GaAs. These contacts have specific resistances similar to those of conventional Ni/Ge/Au alloyed ohmic contacts, but their surfaces are much smoother and their edges are well defined. The fabrication procedure is compatible with GaAs technology, and the sintered contacts are thermally stable. The properties of these low resistance contacts are insensitive to the sintering temperature and to the thickness of the Pd and Ge layers or their order of deposition.
Effects of Mutant and Antisense RNA of Phospholamban on SR Ca <sup>2+</sup> -ATPase Activity and Cardiac Myocyte Contractility (1999)

K3E/R14E is a dominant negative mutant of PLB that disrupts the structural integrity and function of the endogenous PLB and consequently enhances SERCA2 activity and myocyte contractility. In neonatal myocytes, the decrease in steady-state abundance of PLB by asPLB also leads to increased SERCA2 activity.
Timing-driven Steiner trees are (practically) free (2006)

Traditionally, rectilinear Steiner minimum trees (RSMT) are widely used for routing estimation in design optimizations like floorplanning and physical synthesis. Since it optimizes wirelength, an RSMT may take a non-direct route to a sink, which may give the designer an unnecessarily pessimistic view of the delay to the sink. Previous works have addressed this issue through performance-driven constructions, minimum Steiner arborescence, and critical sink based Steiner constructions. Physical synthesis and routing flows have been reticent to adapt universal timing-driven Steiner constructions out of fear that they are too expensive (in terms of routing resource and capacitance). This paper studies several different performance-driven Steiner tree constructions in order to show which ones have superior performance. A key result is that they add at most 2%-4% extra capacitance, and are thus a promising avenue for today's increasingly aggressive performance-driven P&R flows. We demonstrate using a production P&R flow that timing-driven Steiner topologies can be easily embedded into an incremental routing subflow to obtain significantly improved timing (3.6% and 5.1% improvements in cycle time for two industry testcases) at practically no cost of wirelength or routability.
Micro-rings of Manganese Dioxide Nanocrystals on Mica (1998)

Abstract Circularly ordered self-assembly (micro-ring) of manganese dioxide nanocrystals were formed simply by dewetting a manganese dioxide colloidal aqueous solution on mica. The balance between the repulsive force of the nanocrystals and the compressive force of shrinking droplets plays an important role in forming this peculiar nanosize assembly.