gebhart/patrepeval huggingface dataset:
Enhanced electrostatic force generation capabilityof angled comb finger design used in electrostatic comb-drive actuators (1998)

A new comb finger design which enhances the operational performance of the commonly used electrostatic comb-drive actuator is presented. The angled comb finger design is discussed and shown experimentally to produce a greater actuating force than conventional rectangular comb fingers. Displacements up to twice as large as that achieved using rectangular comb fingers are shown for the same applied voltage.
Hydrogen peroxide disproportionation with manganese macrocyclic complexes of cyclen and pyclen (2020)

The catalase family of enzymes, which include a variety with a binuclear manganese active site, mitigate the risk from reactive oxygen species by facilitating the disproportionation of hydrogen peroxide into molecular oxygen and water. In this work, hydrogen peroxide disproportionation using complexes formed between manganese and cyclen or pyclen were investigated due to the spectroscopic similarities with the native MnCAT enzyme. Potentiometric titrations were used to construct speciation diagrams that identify the manganese complex compositions at different pH values. Each complex behaves as a functional mimic of catalase enzymes. UV-visible spectroscopic investigations of the H<sub>2</sub>O<sub>2</sub> decomposition reaction yielded information about the structure of the initial catalyst and intermediates that include monomeric and dimeric species. The results indicate that rigidity imparted by the pyridine ring of pyclen is a key factor in increased TON and TOF values measured compared to cyclen.
Horovod: fast and easy distributed deep learning in TensorFlow (2018)

Training modern deep learning models requires large amounts of computation, often provided by GPUs. Scaling computation from one GPU to many can enable much faster training and research progress but entails two complications. First, the training library must support inter-GPU communication. Depending on the particular methods employed, this communication may entail anywhere from negligible to significant overhead. Second, the user must modify his or her training code to take advantage of inter-GPU communication. Depending on the training library's API, the modification required may be either significant or minimal. Existing methods for enabling multi-GPU training under the TensorFlow library entail non-negligible communication overhead and require users to heavily modify their model-building code, leading many researchers to avoid the whole mess and stick with slower single-GPU training. In this paper we introduce Horovod, an open source library that improves on both obstructions to scaling: it employs efficient inter-GPU communication via ring reduction and requires only a few lines of modification to user code, enabling faster, easier distributed training in TensorFlow. Horovod is available under the Apache 2.0 license at https://github.com/uber/horovod
A Phase Transformation Model for the Austenitisation of Martensite in Dual-Phase Steel (2007)

This work presents a unique approach for the modelling of the austenitisation of martensite in dual-phase steels within the phase-field method. Driving forces for nucleation and growth are derived from thermodynamic databases. Routines for nucleation are based on a discretisation of the classical nucleation theory. Validation is given via dilatometric experiments.
“DISTANT PARTS OF MYSELF”: THE TOPOGRAPHY OF ALICE MUNRO'S FICTION (1988)

(1988). “DISTANT PARTS OF MYSELF”: THE TOPOGRAPHY OF ALICE MUNRO'S FICTION. American Review of Canadian Studies: Vol. 18, No. 1, pp. 33-38.
A Biological OR(XNOR) Logic Gate Couples Carbon Source and Transgene Expression Switching in a Komagataella phaffii (Pichia pastoris) Strain Co-producing Process-Enhancing Lipase and a Virus-like Particle (VLP) Vaccine (2023)

We constructed a three-input biological logic gate: S OR (G XNOR M), where S is sorbitol, G is glycerol, and M is methanol, to optimize co-expression of two transgenes in <i>Komagataella phaffii</i> using batch-mode carbon source switching (CSS). <i>K. phaffii</i> was engineered to harbor transgenes encoding a <i>Candida rugosa</i> triacylglycerol lipase, which can enhance downstream processing by removing host cell lipids from homogenates, and the hepatitis B virus surface antigen (HBsAg), a protein that self-assembles into a virus-like particle (VLP) vaccine. Using the native alcohol oxidase 1 (P<sub>AOX1</sub>) and enolase 1 (P<sub>ENO1</sub>) promoters to direct VLP vaccine and lipase expression, respectively, successfully provided an OR(XNOR) gate function with double-repression as the output. This logic gate functionality enabled use of CSS to ensure that approximately 80% of total VLP yield was accumulated before cells were burdened with lipase expression in 250 mL DasGip bioreactor cultivation.
Voltage-gated sodium channels were differentially expressed in human normal prostate, benign prostatic hyperplasia and prostate cancer cells (2014)

Voltage-gated sodium channels (VGSCs) are expressed not only in excitable cells but also in numerous metastatic cells, particularly in certain types of cancer cells. In some types of cancer, including prostate cancer, the expression of VGSCs is associated with cancer migration, invasion and metastasis <i>in vivo</i>. However, the detailed expression profiles of VGSC α subunits in normal human prostate, in prostatic hyperplasia and prostatic cancer remain controversial. In the present study, quantitative polymerase chain reaction was used to systematically detect all subtypes of VGSC α subunits in normal human prostate, benign prostatic hyperplasia (BPH) and prostate cancer cells. The expression profile of VGSC α subunits was observed to differ between these cell types. Nav1.5 was the major isoform expressed in normal human prostate tissue, while Nav1.5 and Nav1.2 were the predominant isoforms in BPH tissue. However, in PC-3 and LNCaP cells, two typical prostate cancer cell lines, Nav1.6 and Nav1.7 were abundantly expressed. By comparing the relative expression levels of Nav1.5, Nav1.6 and Nav1.7 in these cells, the mRNA levels of Nav1.6 and Nav1.7 were identified to be 6- to 27-fold higher in PC-3 and LNCaP cells than in either normal or BPH samples (P<0.05); however, Nav1.5 mRNA levels were relatively lower compared with those of Nav1.6 or Nav1.7 in all cells analyzed. To confirm whether Nav1.6 and Nav1.7 expression in cancer cells was functional, a patch-clamp technique was used to record whole-cell currents. A tetrodotoxin-sensitive sodium current was successfully recorded in PC-3 cells, but not in LNCaP cells. It was concluded that although all types of VGSC α subunits exhibited low expression levels in normal prostate and BPH cells, both Nav1.6 and Nav1.7 were significantly upregulated in the prostate cancer cell lines, suggesting these subtypes may be potential diagnostic markers and therapeutic targets for certain types of prostate cancer in humans.
Clinical evaluation of a developed paper-based Dengue NS1 rapid diagnostic test for febrile illness patients (2021)

DEN-NS1-PAD is a valuable tool for diagnosing DENV infections, especially for diagnosed patients with early acute phase samples with high viral load. DEN-NS1-PAD has better sensitivity than SD-NS1 but less specificity.
Parameter Selection Methods in Inverse Problem Formulation (2020)

We discuss methods for {\em a priori} selection of parameters to be estimated in inverse problem formulations (such as Maximum Likelihood, Ordinary and Generalized Least Squares) for dynamical systems with numerous state variables and an even larger number of parameters. We illustrate the ideas with an in-host model for HIV dynamics which has been successfully validated with clinical data and used for prediction.
Introduction (1993)

Vico’s fundamental importance in the history of European ideas lies in his strong anti-Cartesian, anti-French and anti-Enlightenment views. In an age in which intellectuals congratulated themselves on their modern (which was to say, rational) approach to life, Giambattista Vico (1668–1744) stressed the nonrational elements in man — in particular, imagination — as well as social and civic relationships, none of them easily reducible to the scientific theories so popular in his time. It is well known that the chief reason Vico gave for his anti-Cartesian stance was that man could not fully know the natural world (science) as it was made by God, but that human history was largely, if not entirely, comprehensible precisely because it was man-made. Yet it is important to note that although Vico turned his back on Cartesian rationalism, he nevertheless applied rational methods to the subject René Descartes (1596–1650) despised — history.
Do Lactic Acid Bacteria in Fermented Foods Persist in the Gastrointestinal Tract: An In Vitro Investigation (2020)

It is now well established that the composition of the gastrointestinal (GI) microbiota has a profound influence on intestinal and overall health. Many contemporary diseases such as type two diabetes, IBS and obesity are associated with a dysbiotic microbiota. Therefore, researchers are interested in how diet and specific dietary components can modulate the gastrointestinal microbiota and possibly repair a dysbiotic state. One approach to improve gastrointestinal health is by consuming probiotics and prebiotics or a diet rich in fermented foods containing live microbes. Fermented foods are popular because of their enhanced preservation, safety, organoleptic, functionality, and nutritional properties. These fermented foods can also contain live microorganisms that may play a role in improving gastrointestinal health. One of the challenges, however, is that the GI environment is very stable and resistant to change. This is mainly due to barriers along the GI tract (pH, bile, enzymes). Persistence of allochthonous microorganisms within the GI tract is also limited by host response such as absence of ecological niches and colonization resistance. In addition, the microbiota composition varies in every individual, making it difficult to formulate a single therapeutic solution. It may be possible to overcome these barriers and regulate a dysbiotic system through a diet rich in fermented foods and supplemented with prebiotics.
Microbial Dynamics of Commercial Makgeolli Depending on the Storage Temperature (2012)

Market fresh makgeolli was stored at different temperatures of 4°C and 25°C to assess the change of the microbial diversity according to the storage temperature and period. Yeast counts increased until day 3 of storage and decreased thereafter. General and lactic acid bacterial counts continuously increased during storage. The data indicated that the control of growth of microorganisms, particularly general bacteria and lactic acid bacteria (LAB), is essential. Total acid levels started to decrease in the makgeolli stored at 4°C, and increased from day 6 of storage in the makgeolli stored at 25°C. The increase of total acid in the non-refrigerated condition greatly affected the quality of makgeolli. In both the fresh makgeolli samples stored at 4°C and 25°C, yeast (Saccharomyces cerevisiae) and molds (Aspergillus tubingensis, Candida glaebosa, and Aspergillus niger) were noted. Denaturing gradient gel electrophoresis (DGGE) band patterns were almost constant regardless of the storage period. As for bacteria, Lactobacillus crustorum, L. brevis, and Microlaena stipoides were found in the makgeolli stored at 4°C, and L. crustorum, Lactobacillus sp., L. plantarum, L. brevis, L. rhamnosus, and L. similis were found in the makgeolli stored at 25°C. In particular, in the makgeolli stored at 25°C, L. crustorum and L. plantarum presented dark bands and were identified as the primary microorganisms that affected spoilage of fresh makgeolli.
IM2 removal in direct conversion receivers (2002)

DC offsets cause interference in homodyne receivers. They are caused by non-linearity and imbalances in the receiving amplifier and mixing circuits as well as local oscillator (LO) leakage into the RF input port and RF leakage into the LO port. The latter causes a squaring action (hence second order intermodulation distortion, IM2) in the mixer which generates a DC offset (low frequency) that varies with the amplitude of any high power RF interfering (jamming) signal, whatever its applied frequency. A method for removing this DC offset is described The signal immediately after the mixer is squared to obtain a distortion estimate of the jamming signal, and then subtracted from the main signal path to remove the interference from the desired signal. The experimental results indicate a 11.5 dB improvement in jamming margin for systems with 30 kHz RF bandwidth.
The Purinergic Receptor P2X7 Triggers α-Secretase-dependent Processing of the Amyloid Precursor Protein (2010)

The amyloid precursor protein (APP) is cleaved by β- and γ-secretases to generate the β-amyloid (Aβ) peptides, which are present in large amounts in the amyloid plaques of Alzheimer disease (AD) patient brains. Non-amyloidogenic processing of APP by α-secretases leads to proteolytic cleavage within the Aβ peptide sequence and shedding of the soluble APP ectodomain (sAPPα), which has been reported to be endowed with neuroprotective properties. In this work, we have shown that activation of the purinergic receptor P2X7 (P2X7R) stimulates sAPPα release from mouse neuroblastoma cells expressing human APP, from human neuroblastoma cells and from mouse primary astrocytes or neural progenitor cells. sAPPα shedding is inhibited by P2X7R antagonists or knockdown of P2X7R with specific small interfering RNA (siRNA) and is not observed in neural cells from P2X7R-deficient mice. P2X7R-dependent APP-cleavage is independent of extracellular calcium and strongly inhibited by hydroxamate-based metalloprotease inhibitors, TAPI-2 and GM6001. However, knockdown of a disintegrin and metalloproteinase-9 (ADAM9), ADAM10 and ADAM17 by specific siRNA, known to have α-secretase activity, does not block the P2X7R-dependent non-amyloidogenic pathway. Using several specific pharmacological inhibitors, we demonstrate that the mitogen-activated protein kinase modules Erk1/2 and JNK are involved in P2X7R-dependent α-secretase activity. Our study suggests that P2X7R, which is expressed in hippocampal neurons and glial cells, is a potential therapeutic target in AD.
A Piecewise Monotone Subgradient Algorithm for Accurate <formula formulatype="inline"><tex Notation="TeX">${\rm L}^{1}$</tex></formula>-TV Based Registration of Physical Slices With Discontinuities in Microscopy (2013)

Image registration tasks are often formulated in terms of minimization of a functional consisting of a data fidelity term penalizing the mismatch between the reference and the target image, and a term enforcing smoothness of shift between neighboring pairs of pixels (a min-sum problem). Most methods for deformable image registration use some form of interpolation between matching control points. The interpolation makes it impossible to account for isolated discontinuities in the deformation field that may appear, e.g., when a physical slice of a microscopy specimen is ruptured by the cutting tool. For registration of neighboring physical slices of microscopy specimens with discontinuities, Janácek proposed an L¹-distance data fidelity term and a total variation (TV) smoothness term, and used a graph-cut (GC) based iterative steepest descent algorithm for minimization. The L¹-TV functional is nonconvex; hence a steepest descent algorithm is not guaranteed to converge to the global minimum. Schlesinger presented transformation of max-sum problems to minimization of a dual quantity called problem power, which is--contrary to the original max-sum functional--convex. Based on Schlesinger's solution to max-sum problems we developed an algorithm for L¹-TV minimization by iterative multi-label steepest descent minimization of the convex dual problem. For Schlesinger's subgradient algorithm we proposed a novel step control heuristics that considerably enhances both speed and accuracy compared with standard step size strategies for subgradient methods. It is shown experimentally that our subgradient scheme achieves consistently better image registration than GC in terms of lower values both of the composite L¹-TV functional, and of its components, i.e., the L¹ distance of the images and the transformation smoothness TV, and yields visually acceptable results even in cases where the GC based algorithm fails. The new algorithm allows easy parallelization and can thus be sped up by running on multi-core graphic processing units.
The Applicability of a Keratin 7 Monoclonal Antibody in Routinely Papanicolaou-stained Cytologic Specimens for the Differential Diagnosis of Carcinomas (1994)

The monoclonal antibody OV-TL 12/30, which detects keratin 7, was tested for its usefulness in cytologic diagnosis by reincubating previously Papanicolaou-stained slides. For this purpose malignant effusions of 73 patients with histologically confirmed cancers of the colon, ovary, mesothelium, breast, lung, esophagus, pancreas, urinary bladder, stomach, kidney, and prostate were used. All malignant cells from ovarian adenocarcinomas were positive, whereas malignant cells from colonic adenocarcinomas and malignant mesotheliomas were negative. Adenocarcinomas of gastric, renal, pancreatic, esophageal, and mammary origin demonstrated variable staining. Transitional cell carcinomas were positive, whereas squamous and small cell lung carcinomas were negative. Because OV-TL 12/30 does not react with normal and atypical mesothelial cells in these preparations, this reagent is a valuable tool in distinguishing benign mesothelial cells and adenocarcinoma cells. The authors' results demonstrate that this antibody is an excellent tool in the differential diagnosis of malignant cells in effusions and can be used in routinely stained cytologic specimens to determine primary tumor localization. In addition to its ability to distinguish between ovarian and colonic adenocarcinomas, its negativity in mesotheliomas may prove helpful in several diagnostic considerations.
Abstract B25: “TargetDBR”—A DNA repair drug and target discovery collaboration: Exploiting synthetic lethal, high content, and functional cellular reporter assays to accelerate DNA repair targeted drug discovery (2017)

Abstract Most cancer therapies involve a component of treatment that inflicts DNA damage in tumor cells, such as double-strand breaks (DSBs), which are considered the most serious threat to genomic integrity. Inhibition of DSB repair sensitizes cells to these therapies. Mutations have been reported in nearly every DNA repair pathway and these pathways often exhibit redundancy. Inhibition of functional repair factors can induce synthetic lethality in repair-deficient tumors even in the absence of exogenous DNA damage and whilst sparing healthy tissue. We demonstrate a compound and target discovery platform comprising the integration of isogenic cell line screening, high content repair foci assays and relative DSB repair pathway reporting cells, along with chemical biology and medicinal chemistry. Two diverse drug-like compound library screens have been conducted. Screening for synthetic lethality with deficiency in FANCD2 and BRCA2 led to a hit series broadly active against a range of homologous recombination (HR) repair deficiencies, which is now undergoing medicinal chemistry optimization and target deconvolution studies. Outcome of these initial chemoproteomic target pulldown experiments will be presented. A second cellular screen, (50k compounds) for inhibition of BRCA1 and Rad51 foci formation following radiomimetic drug induced DNA damage, has led to identification of compounds that inhibit damage response after ionizing radiation and selectively inhibit HR repair. Focusing on therapeutic targeting of proliferating tumor cells, our research platform has enabled novel hit compound identification, mechanistic profiling, hit-to-lead optimization chemistry and proof of concept efficacy in in vitro tumor models. Effects on tumor cell clonogenic survival and sensitization towards chemotherapeutics and ionizing radiation will be presented, along with comparisons to known DNA repair inhibitors that demonstrate these compounds' differentiated mechanisms of action. TargetDBR has created a technology platform focused on DNA repair inhibitor discovery and has identified differentiated hits and lead series with potential for development and opportunity to meet the need for new druggable targets in oncology. Citation Format: Jonathan J. Hollick, Laura Abriola, Francoise Bono, Denise Hegan, Pamela Klingbeil, Yanfeng Liu, Ranjini Sundaram, Yulia V. Surovtseva, Mark Whittaker, Ranjit S. Bindra, Peter M. Glazer. “TargetDBR”—A DNA repair drug and target discovery collaboration: Exploiting synthetic lethal, high content, and functional cellular reporter assays to accelerate DNA repair targeted drug discovery [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr B25.
Theoretical analysis of driven magnetic reconnection experiments (1995)

In this paper the authors develop a theoretical framework for the Magnetic Reconnection Experiment (MRX) in order to understand the basic physics of the experiment, including the effect of the external driving force, and the difference between co and counterhelicity cases of the experiment. In order to simplify the problem they reduce it to a 1-D resistive MHD model. Also, they define a special class of holonomic boundary conditions under which a unique sequence of global equilibria can be obtained, independent of the rate of reconnection. This enables them to break the whole problem into two parts: a global problem for the ideal region, and a local problem for the resistive reconnection layer. The authors carry out the calculations and obtain the global solution for the ideal region in one particular case of holonomic constraints, the so called `constant force`` regime, for both the co and counterhelicity cases. After the sequence of equilibria in the ideal region is found, they tackle the problem of the rate of reconnection in the resistive reconnection region. This rate tells how fast they proceed through the sequence of global equilibria but does not affects the sequence itself. Assuming the Sweet-Parker model for the reconnection layer, they calculate the reconnection rate, and demonstrate the difference between the co and counterhelicity cases, as well as the role of the external forces. The authors find their results to be in reasonable agreement with the experiment. Magnetic reconnection is important both in laboratory experiments and in astrophysics.
Engraftment of circulating cells during partial skin regeneration (2008)

Saja Scherer, Sandra MD; Pietramaggiori, Giorgio MD, PhD; Chin, Bin MD; Song, GuoDong MD; Ioannis, Yannas PhD; Murphy, George F. MD, PhD; Wagers, Amy PhD; Orgill, Dennis P. MD, PhD, FACS Author Information
Shprintzen-Goldberg syndrome with osteopenia and progressive hydrocephalus (1997)

We report on a boy with Shprintzen-Goldberg syndrome, the 12th patient described to date. In addition to the commonly described anomalies of individuals with SGS, this patient also had cranial asymmetry, hypotonia, osteopenia, and hydrocephalus. These manifestations should be included in the diagnosis and anticipatory guidance of children with SGS. Am. J. Med. Genet. 70:450–453, 1997. © 1997 Wiley-Liss, Inc.