gebhart/patrepeval huggingface dataset:
Structural Requirements of SLP-76 in Signaling via the High-Affinity Immunoglobulin E Receptor (FcεRI) in Mast Cells (2003)

The adapter SLP-76 plays an essential role in Fc epsilon RI signaling, since SLP-76(-/-) bone marrow-derived mast cells (BMMC) fail to degranulate and release interleukin-6 (IL-6) following Fc epsilon RI ligation. To define the role of SLP-76 domains and motifs in Fc epsilon RI signaling, SLP-76(-/-) BMMC were retrovirally transduced with SLP-76 and SLP-76 mutants. The SLP-76 N-terminal and Gads binding domains, but not the SH2 domain, were critical for Fc epsilon RI-mediated degranulation and IL-6 secretion, whereas all three domains are essential for T-cell proliferation following T-cell receptor (TCR) ligation. Unexpectedly, the three tyrosine residues in SLP-76 critical for TCR signaling, Y112, Y128, and Y145, were not essential for IL-6 secretion, but were required for degranulation and mitogen-activated protein kinase activation. Furthermore, a Y112/128F SLP-76 mutant, but not a Y145F mutant, strongly reconstituted mast cell degranulation, suggesting a critical role for Y145 in Fc epsilon RI-mediated exocytosis. These results point to important differences in the function of SLP-76 between T cells and mast cells.
Characterization and Heterologous Expression of the Genes Encoding Enterocin A Production, Immunity, and Regulation in <i>Enterococcus faecium</i> DPC1146 (1999)

Enterocin A is a small, heat-stable, antilisterial bacteriocin produced by Enterococcus faecium DPC1146. The sequence of a 10, 879-bp chromosomal region containing at least 12 open reading frames (ORFs), 7 of which are predicted to play a role in enterocin biosynthesis, is presented. The genes entA, entI, and entF encode the enterocin A prepeptide, the putative immunity protein, and the induction factor prepeptide, respectively. The deduced proteins EntK and EntR resemble the histidine kinase and response regulator proteins of two-component signal transducing systems of the AgrC-AgrA type. The predicted proteins EntT and EntD are homologous to ABC (ATP-binding cassette) transporters and accessory factors, respectively, of several other bacteriocin systems and to proteins implicated in the signal-sequence-independent export of Escherichia coli hemolysin A. Immediately downstream of the entT and entD genes are two ORFs, the product of one of which, ORF4, is very similar to the product of the yteI gene of Bacillus subtilis and to E. coli protease IV, a signal peptide peptidase known to be involved in outer membrane lipoprotein export. Another potential bacteriocin is encoded in the opposite direction to the other genes in the enterocin cluster. This putative bacteriocin-like peptide is similar to LafX, one of the components of the lactacin F complex. A deletion which included one of two direct repeats upstream of the entA gene abolished enterocin A activity, immunity, and ability to induce bacteriocin production. Transposon insertion upstream of the entF gene also had the same effect, but this mutant could be complemented by exogenously supplied induction factor. The putative EntI peptide was shown to be involved in the immunity to enterocin A. Cloning of a 10.5-kb amplicon comprising all predicted ORFs and regulatory regions resulted in heterologous production of enterocin A and induction factor in Enterococcus faecalis, while a four-gene construct (entAITD) under the control of a constitutive promoter resulted in heterologous enterocin A production in both E. faecalis and Lactococcus lactis.
Genistein Enhances the Cisplatin‐Induced Inhibition of Cell Growth and Apoptosis in Human Malignant Melanoma Cells (2003)

Genistein, a naturally occurring isoflavone found chiefly in soybeans, has been reported to be a potent antitumor agent. Genistein is presumed to exert multiple effects related to the inhibition of cancer growth. Metastatic melanoma is a chemotherapy-refractory neoplasm. The present study was designed to explore the possible activity of genistein to inhibit the aberrant proliferation and to induce apoptosis of human malignant melanoma cells in cooperation with cisplatin treatment. Five human melanoma cell lines were utilized for these experiments. Genistein at physiologic concentrations (20 microM) did not induce apoptosis by itself but did enhance cisplatin-induced apoptosis in all five human melanoma cell lines tested. The enhanced susceptibility among the cell lines was diverse. Changes in the expression of two anti-apoptotic proteins, bcl-2 and bcl-xL, and one pro-apoptotic protein, apoptotic protease activating factor-1 (Apaf-1), were examined. Genistein alone or cisplatin alone generally did not alter bcl-2 expression or bcl-xL expression, but slightly increased Apaf-1 in some cell lines. The combined treatment with genistein and cisplatin significantly reduced bcl-2 and bcl-xL protein and increased Apaf-1 protein expression. These data suggest that genistein therapy may enhance the chemosensitivity of melanoma patients.
Translation between Molecules and Natural Language (2022)

We present $\textbf{MolT5}$ $-$ a self-supervised learning framework for pretraining models on a vast amount of unlabeled natural language text and molecule strings. $\textbf{MolT5}$ allows for new, useful, and challenging analogs of traditional vision-language tasks, such as molecule captioning and text-based de novo molecule generation (altogether: translation between molecules and language), which we explore for the first time. Since $\textbf{MolT5}$ pretrains models on single-modal data, it helps overcome the chemistry domain shortcoming of data scarcity. Furthermore, we consider several metrics, including a new cross-modal embedding-based metric, to evaluate the tasks of molecule captioning and text-based molecule generation. Our results show that $\textbf{MolT5}$-based models are able to generate outputs, both molecules and captions, which in many cases are high quality.
Soft glass microstructured optical fibers: recent progress in fabrication and opportunities for novel optical devices (2009)

This paper reviews recent progress in the fabrication of soft glass microstructured optical fibers with nanowire core sizes, with nanoscale holes in the fiber core itself and with large mode areas. We demonstrate the potential of these fibers for a wide range of applications including high optical nonlinearity, bio/chemical sensing, high-resolution imaging, mid-infrared high power generation and delivery.
Efficient modeling of three-dimensional convection–diffusion problems in stationary flows (2020)

A large number of transport processes in physics, chemistry, and engineering are described by a convection–diffusion equation. This equation is notoriously difficult to solve due to the presence of convection-related first-order gradient differential operators. We describe a new and efficient numerical method for solving the convection–diffusion equation for laminar flows within channels of arbitrary cross section. It is based on reducing the convection–diffusion equation to a set of pure diffusion equations with a complex-valued potential for which fast and numerically stable solvers are readily available. Additionally, we use an eigenvector projection method that allows us to compute snapshots of full concentration distributions over millions of finite elements within a few seconds using a conventional state-of-the-art desktop computer. Our results will be important for all applications where diffusion and convection are both important for correctly describing material transport.
Single incision and reduced port laparoscopic low anterior resection for rectal cancer: initial experience in 96 cases (2014)

The SIL-LAR technique can be applied safely with the optional use of an additional port. One additional port in the right suprapubic area is useful for obtaining a secure distal division and a safe total mesorectal excision, especially in patients with lower lesions or history of neoadjuvant chemoradiation.
Canola oil rich in oleic acid improves diastolic heart function in diet-induced obese rats (2016)

Obesity is a leading cause of cardiovascular disease. It directly affects heart structure and function and contributes to heart failure. Diet is a major factor involved in the development of obesity along with genetic factors. We examined the effects of monounsaturated and polyunsaturated fatty acid-rich oils on cardiac structure and function in the diet-induced rodent model of obesity (DIO). Obese prone (OP) rats were fed a high-fat diet (HF; 55% of kcal) for 12 weeks; Sprague-Dawley rats fed commercial chow served as control. Echocardiography was performed to assess the cardiac structure and function in all rats at 12 weeks. OP rats fed the HF diet showed significant impairment in diastolic function compared to control rats. The HF diet containing high oleic canola oil significantly improved diastolic function of OP rats compared to the HF diet with lard. In conclusion, canola oil rich in oleic acid, when incorporated into an HF diet, prevents the development of diastolic dysfunction in DIO rats.
UO<sub>2</sub><sup>2+</sup>-mediated ring contraction of pyrihexaphyrin: synthesis of a contracted expanded porphyrin-uranyl complex (2019)

A new mixed hexaphyrin, pyrihexaphyrin (0.1.0.0.1.0) (<b>1</b>), was prepared <i>via</i> an acid catalyzed cyclization between 5,5'-(pyridine-2,6-diyl)bis(pyrrole-2-carbaldehyde) (<b>2</b>) and terpyrrole (<b>3</b>). This expanded porphyrin undergoes a ring contraction upon metallation with uranyl silylamide [UO<sub>2</sub>[N(SiMe<sub>3</sub>)<sub>2</sub>]<sub>2</sub>] under anaerobic conditions followed by purification over basic aluminum oxide exposed to air. The uranyl-contracted pyrihexaphyrin (0.0.0.0.1.0) complex (<b>4</b>) produced as a result contains a unique structural architecture and possesses a formally 22 π-electron globally aromatic periphery, as inferred from NMR spectroscopy, single crystal X-ray diffraction, and computational analyses. Support for the proposed contraction mechanism came from experimental data and DFT calculations. Proton NMR and mass spectroscopic analysis provided the first insight into expanded porphyrin-mediated activation of the uranyl dication (UO<sub>2</sub> <sup>2+</sup>).
Review Clinical review: A review and analysis of heart rate variability and the diagnosis and prognosis of infection (2009)

Bacterial infection leading to organ failure is the most common cause of death in critically ill patients. Early diagnosis and expeditious treatment is a cornerstone of therapy. Evaluating the systemic host response to infection as a complex system provides novel insights: however, bedside application with clinical value remains wanting. Providing an integrative measure of an altered host response, the patterns and character of heart rate fluctuations measured over intervals-in-time may be analysed with a panel of mathematical techniques that quantify overall fluctuation, spectral composition, scale-free variation, and degree of irregularity or complexity. Using these techniques, heart rate variability (HRV) has been documented to be both altered in the presence of systemic infection, and correlated with its severity. In this review and analysis, we evaluate the use of HRV monitoring to provide early diagnosis of infection, document the prognostic implications of altered HRV in infection, identify current limitations, highlight future research challenges, and propose improvement strategies. Given existing evidence and potential for further technological advances, we believe that longitudinal, individualized, and comprehensive HRV monitoring in critically ill patients at risk for or with existing infection offers a means to harness the clinical potential of this bedside application of complex systems science.
CA-SVM: Communication-Avoiding Support Vector Machines on Distributed Systems (2015)

We consider the problem of how to design and implement communication-efficient versions of parallel support vector machines, a widely used classifier in statistical machine learning, for distributed memory clusters and supercomputers. The main computational bottleneck is the training phase, in which a statistical model is built from an input data set. Prior to our study, the parallel is efficiency of a state-of-the-art implementation scaled as W = Omega(P <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ), where W is the problem size and P the number of processors, this scaling is worse than even a one-dimensional block row dense matrix vector multiplication, which has W = Omega(P <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ). This study considers a series of algorithmic refinements, leading ultimately to a Communication-Avoiding SVM (CASVM) method that improves the is efficiency to nearly W = Omega(P). We evaluate these methods on 96 to 1536 processors, and show average speedups of 3 - 16× (7× on average) over Dis-SMO, and a 95% weak-scaling efficiency on six real world datasets, with only modest losses in overall classification accuracy. The source code can be downloaded at https://github.com/fastalgo/casvm.
ChemInform Abstract: Microwave‐Assisted Synthesis of Medicinally Relevant Indoles (2011)

Abstract Review: 138 refs.
Generalized Platform for Antibody Detection using the Antibody Catalyzed Water Oxidation Pathway (2014)

Infectious diseases, such as influenza, present a prominent global problem including the constant threat of pandemics that initiate in avian or other species and then pass to humans. We report a new sensor that can be specifically functionalized to detect antibodies associated with a wide range of infectious diseases in multiple species. This biosensor is based on electrochemical detection of hydrogen peroxide generated through the intrinsic catalytic activity of all antibodies: the antibody catalyzed water oxidation pathway (ACWOP). Our platform includes a polymer brush-modified surface where specific antibodies bind to conjugated haptens with high affinity and specificity. Hydrogen peroxide provides an electrochemical signal that is mediated by Resorufin/Amplex Red. We characterize the biosensor platform, using model anti-DNP antibodies, with the ultimate goal of designing a versatile device that is inexpensive, portable, reliable, and fast. We demonstrate detection of antibodies at concentrations that fall well within clinically relevant levels.
Intraoperative Preconditioning of Fixed and Adjustable Loop Suspensory Anterior Cruciate Ligament Reconstruction With Tibial Screw Fixation—An In Vitro Biomechanical Evaluation Using a Porcine Model (2018)

Although the clinical relevance of time-zero graft tension loss is uncertain, the use of an ALD in concert with tibial screw fixation may be favorable to allow for tension optimization.
THC exposure during adolescence increases impulsivity-like behavior in adulthood in a WIN 55,212-2 self-administration mouse model (2023)

These findings suggest that adolescent THC exposure may promote impulsivity-like behavior in adulthood, associated with downregulated <i>drd2</i> and <i>adora2a</i> expression in NAc and HPC.
Developing Concept-Based User Interfaces for Scientific Computing (2006)

Although drawings and graphs can express complex concepts, such methods can't be computationally analyzed. Researchers have developed visual approaches and paradigms that scientists can use to capture and represent scientific models in a computational form that they can link to and integrate with data sets and applications.
Duration of methicillin-resistant Staphylococcus aureus colonization after diagnosis: A four-year experience from southern Sweden (2011)

These results may have implications for the management of patients with MRSA carriage. The study indicates that MRSA carriage can be defined as 'negative' in a follow-up program and shows the importance of performing contact tracing among household members.
Depositing SiO<sub>2</sub> on Al<sub>2</sub>O<sub>3</sub>: a Route to Tunable Brønsted Acid Catalysts (2016)

Strongly Brønsted acidic silica–alumina materials are workhorse catalysts in petroleum processes, including cracking, isomerization, and hydrocarbon synthesis. Here thin, conformal overcoats of SiO2, 2–5 nm by TEM, were synthesized on pre-existing Al2O3 supports by stepwise addition of tetraethyl orthosilicate under basic conditions, and the surfaces were interrogated by N2 physisorption along with NH3 and pyridine chemisorption. SiO2 layers thicker than 5 nm give largely inert surfaces, but adding only 2 nm of SiO2 is shown to quench the underlying Lewis acidity and unexpectedly form Brønsted acid sites strong enough to protonate gas-phase pyridine. Alternately, the use of a molecular template grafted to the alumina surface before SiO2 deposition selectively preserves the most reactive AlOH. In the catalytic cracking of 1,3,5-triisopropylbenzene at 450 °C, Al2O3 overcoated by 2 nm of SiO2 proved to be a highly active catalyst with 10 times higher conversion in comparison to that of Al2O3. Finally, the silica overlayer was deliberately cracked to expose strong interfacial sites, likely between tetrahedral Al and SiO2. In comparison to a material with an intact overlayer, this catalyst had 1.5 times higher conversion and 3 times higher selectivity to deep dealkylation products, including cumene and benzene. This core–shell SiO2@Al2O3 catalyst gives total dealkylation yields, per surface area, similar to those of conventionally prepared SiO2–Al2O3 or zeolite Y catalysts while providing for new synthetic handles for catalyst optimization.
Improving Transitions Between Sophomore Dynamics and Junior Dynamic Systems Courses (2020)

Abstract Improving Transitions Between Sophomore Dynamics and Junior Dynamic Systems CoursesStudents at the South Dakota School of Mines and Technology consider both sophomoredynamics and junior dynamic systems courses “hard”, with both courses routinely havingrelatively high failure / dropout rates. Sophomore-level dynamics tends to cast problems ofmotion as snapshots rather than the continuous evolution of junior-level courses. This paperdescribes two course modifications to sophomore dynamics to improve visualization skills and toimprove knowledge transfer from sophomore to junior courses.The first course modification involves the use of SolidWorks motion simulations to visualize themotion of example problems taught throughout the course. The motion visualization confirmsstudents’ intuition for simple problems and helps to develop it for interconnected rigid bodymotion. It also serves two other purposes: it provides software continuity in the curriculum andprepares students for the continuous nature of junior dynamic systems. This paper discusses twosemesters of implementation; in one, usage was optional, while in the other it was given extracredit. Evaluation was performed using both the Dynamics Concept Inventory and studentsurveys.The second course modification was the introduction of Lagrange’s equations of motion forconservative systems. This formulation of dynamics is typically reserved for courses in which itcan be derived, which students encounter in their senior years at the earliest. However, whiledifficult to derive, Lagrange’s equations are easy to use for conservative systems, even forsophomore students. They perform the functions of uniting energy methods with Newton’ssecond law and introduce students to the concept of equations of motion that will be usedconsistently in junior dynamic systems. Example problems for several projects are presentedalong with student feedback.
OpenFermion: the electronic structure package for quantum computers (2020)

Abstract Quantum simulation of chemistry and materials is predicted to be an important application for both near-term and fault-tolerant quantum devices. However, at present, developing and studying algorithms for these problems can be difficult due to the prohibitive amount of domain knowledge required in both the area of chemistry and quantum algorithms. To help bridge this gap and open the field to more researchers, we have developed the OpenFermion software package ( www.openfermion.org ). OpenFermion is an open-source software library written largely in Python under an Apache 2.0 license, aimed at enabling the simulation of fermionic and bosonic models and quantum chemistry problems on quantum hardware. Beginning with an interface to common electronic structure packages, it simplifies the translation between a molecular specification and a quantum circuit for solving or studying the electronic structure problem on a quantum computer, minimizing the amount of domain expertise required to enter the field. The package is designed to be extensible and robust, maintaining high software standards in documentation and testing. This release paper outlines the key motivations behind design choices in OpenFermion and discusses some basic OpenFermion functionality which we believe will aid the community in the development of better quantum algorithms and tools for this exciting area of research.
Pose Estimation for Objects with Rotational Symmetry (2018)

Pose estimation is a widely explored problem, enabling many robotic tasks such as grasping and manipulation. In this paper, we tackle the problem of pose estimation for objects that exhibit rotational symmetry, which are common in man-made and industrial environments. In particular, our aim is to infer poses for objects not seen at training time, but for which their 3D CAD models are available at test time. Previous work has tackled this problem by learning to compare captured views of real objects with the rendered views of their 3D CAD models, by embedding them in a joint latent space using neural networks. We show that sidestepping the issue of symmetry in this scenario during training leads to poor performance at test time. We propose a model that reasons about rotational symmetry during training by having access to only a small set of symmetry-labeled objects, whereby exploiting a large collection of unlabeled CAD models. We demonstrate that our approach significantly outperforms a naively trained neural network on a new pose dataset containing images of tools and hardware.
Organic Field-Effect Transistors Based on Solution-Processed Single Crystal Films of Alkylphenyl Chrysene Derivatives (2015)

Abstract We synthesized alkyl-substituted phenyl chrysenes as novel solution-processable transistor materials for single crystal organic transistors. All devices displayed typical p-channel characteristics, with the best field-effect mobility of 11.9 cm2 V−1 s−1 belonging to the m-7P-28CR based transistor.