gebhart/patrepeval huggingface dataset:
DEPENDÊNCIA QUÍMICA E O CENÁRIO DOS USUÁRIOS DE DROGAS ATENDIDOS NOS CENTROS DE ATENÇÃO PSICOSSOCIAL ÁLCOOL E DROGAS: A POLÍTICA DE SAÚDE NA ATENÇÃO INTEGRAL AOS IDOSOS (2021)

O uso de drogas lícitas e ilícitas, se constitui em enorme desafio para a saúde pública, no entanto, com o aumento da expectativa de vida da população brasileira, essa realidade também se faz presente em idosos. Investigou-se o uso de drogas lícitas e ilícitas, o tempo de uso, as associações destas drogas com transtornos mentais, e o perfil sociodemográfico dos idosos frequentadores dos Caps-AD, Município do Rio de Janeiro, que nasceram até 31 de dezembro de 1958 e que procuraram atendimento no período de 2001 a dezembro de 2019. Trata-se de um estudo com delineamento descritivo, analítico observacional de temporalidade retrospectiva, baseado em dados secundários. Foi feita inicialmente uma análise descritiva da população estudada a partir do cálculo de medidas de tendência central e dispersão para variáveis contínuas e de frequência para variáveis categóricas. A associação das variáveis dependentes com as variáveis explicativas foi investigada através da estimativa das odds ratio (OR) simples e ajustadas. A significância estatística foi avaliada através do teste de Tukey (ANOVA). Verificaram-se maiores percentuais de homens (76,62%), com idade entre 60 e 73 anos (87,4%), sem companheiro(a) (64,35%), com ensino fundamental (67,59%), desempregados (32,87%) e em tratamento entre 1 e 5 anos (69,21%). As drogas de maior uso foram: o álcool, a maconha, o crack e a cocaína. Evidencia-se necessidade de maior conhecimento sobre dependência química na terceira idade e uso de estratégias e aplicação de instrumentos que facilitem a identificação precoce desses usuários.DOI: http://dx.doi.org/10.16891/2317-434X.v9.e2.a2021.pp1147-1157a
Optimization of turn-back primers in isothermal amplification (2011)

The application of isothermal amplification technologies is rapidly expanding and currently covers different areas such as pathogen detection and SNP genotyping. Meanwhile, many of such technologies have complex reaction processes and often require a fine-tuned primer set where existing primer design tools are not sufficient. We have developed a primer selection system for one important primer, the turn-back primer (TP), which is commonly used in loop-mediated amplification (LAMP) and smart amplification process (SmartAmp). We chose 78 parameters related to the primer and target sequence, and explored their relationship to amplification speed using experimental data for 1344 primer combinations. We employed the least absolute shrinkage and selection operator (LASSO) method for parameter selection and estimation of their numerical coefficients. The evaluation showed that our approach yields a superior primer design in isothermal amplification and is robust against variations in the experimental setup. Our computer script is freely available at: http://gerg.gsc.riken.jp/TP_optimization/.
Support for context-aware intelligibility and control (2009)

Intelligibility and control are important user concerns in context-aware applications. They allow a user to understand why an application is behaving a certain way, and to change its behavior. Because of their importance to end users, they must be addressed at an interface level. However, often the sensors or machine learning systems that users need to understand and control are created long before a specific application is built, or created separately from the application interface. Thus, supporting interface designers in building intelligibility and control into interfaces requires application logic and underlying infrastructure to be exposed in some structured fashion. As context-aware infrastructures do not provide generalized support for this, we extended one such infrastructure with Situations, components that appropriately exposes application logic, and supports debugging and simple intelligibility and control interfaces, while making it easier for an application developer to build context-aware applications and facilitating designer access to application state and behavior. We developed support for interface designers in Visual Basic and Flash. We demonstrate the usefulness of this support through an evaluation of programmers, an evaluation of the usability of the new infrastructure with interface designers, and the augmentation of three common context-aware applications.
Applying HTM to an OLTP System (2015)

Transactional memory is a promising way for implementing efficient synchronization mechanisms for multicore processors. Intel's introduction of hardware transactional memory (HTM) into their Haswell line of processors marks an important step toward mainstream availability of transactional memory. Transaction processing systems require execution of dozens of critical sections to insure isolation among threads, which makes them one of the target applications for exploiting HTM.
ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure (2004)

http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/consseq/, http://trantor.bioc.columbia.edu/SMS/STINGm/consseq/, http://mirrors.rcsb.org//SMS/STINGm/consseq/, http://www.es.embnet.org/SMS/STINGm/consseq/ and http://www.ar.embnet.org/SMS/STINGm/consseq/
Bi-stability of contact angle and its role in tuning the morphology of self-assisted GaAs nanowires (2018)

We demonstrate the existence of two stable contact angles for the gallium droplet on top of self-assisted GaAs nanowires grown by MBE on patterned silicon substrates. Contact angle around 130 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ο </sup> features a continuous increase in the nanowire radius, while 90 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ο</sup> allows for the nanowire thinning, followed by the stable growth of ultra-thin tops. We develop a model that explains the observed morphological evolution under the two different scenarios.
Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation (2018)

X-chromosome inactivation (XCI), i.e., the inactivation of one of the female X chromosomes, restores equal expression of X-chromosomal genes between females and males. However, ~10% of genes show variable degrees of escape from XCI between females, although little is known about the causes of variable XCI. Using a discovery data-set of 1867 females and 1398 males and a replication sample of 3351 females, we show that genetic variation at three autosomal loci is associated with female-specific changes in X-chromosome methylation. Through cis-eQTL expression analysis, we map these loci to the genes SMCHD1/METTL4, TRIM6/HBG2, and ZSCAN9. Low-expression alleles of the loci are predominantly associated with mild hypomethylation of CpG islands near genes known to variably escape XCI, implicating the autosomal genes in variable XCI. Together, these results suggest a genetic basis for variable escape from XCI and highlight the potential of a population genomics approach to identify genes involved in XCI.
Measurement of the Thermal Performance of a Custom-Build Single-Phase Immersion Cooled Server at Various High and Low Temperatures for Prolonged Time (2019)

Abstract The next radical change in the thermal management of data centers is to shift from conventional cooling methods like air-cooling to direct liquid cooling to enable high thermal mass and corresponding superior cooling. There has been in the past few years a limited adoption of direct liquid cooling in data centers because of its simplicity and high heat dissipation capacity. Single-phase engineered fluid immersion cooling has several other benefits like better server performance, even temperature profile, and higher rack densities and the ability to cool all components in a server without the need for electrical isolation. The reliability aspect of such cooling technology has not been well addressed in the open literature. This paper presents the performance of a fully single-phase dielectric fluid immersed server over wide temperature ranges in an environmental chamber. The server was placed in an environmental chamber and applied extreme temperatures ranging from −20 °C to 10 °C at 100% relative humidity and from 20 to 55 °C at constant 50% relative humidity for extended durations. This work is a first attempt of measuring the performance of a server and other components like pump including flow rate drop, starting trouble, and other potential issues under extreme climatic conditions for a completely liquid-submerged system. Pumping power consumption is directly proportional to the operating cost of a data center. The experiment was carried out until the core temperature reached the maximum junction temperature. This experiment helps to determine the threshold capacity and the robustness of the server for its applications in extreme climatic conditions.
Manipulation of Magnetic Skyrmion Density in Continuous Ir/Co/Pt Multilayers (2022)

We show that magnetic skyrmions can be stabilised at room temperature in continuous [Ir/Co/Pt]<sub>5</sub> multilayers on SiO<sub>2</sub>/Si substrates without the prior application of electric current or magnetic field. While decreasing the Co thickness, a transition of the magnetic domain patterns from worm-like state to separated stripes is observed. The skyrmions are clearly imaged in both states using magnetic force microscopy. The density of skyrmions can be significantly enhanced after applying the "in-plane field procedure". Our results provide means to manipulate magnetic skyrmion density, further allowing for the optimised engineering of skyrmion-based devices.
Modeling Procedures for Estimation of Extensional Stiffness of Knitted Fabric Reinforced Composites (1997)

This paper presents effective extensional stiffness of plain-weft knitted fabric reinforced composites obtained from finite element analysis and analytical calculations. For micro-mechanical analyses, a unit cell, enclosing the characteristic periodic repeat pattern in the knitted fabric, is isolated and modeled. Psuedo three-dimensional finite element model is constructed using laminated shell elements. Composite extensional stiffness is estimated for plane-stress and plane-strain conditions. Further, stiffness and compliance averaging methods have been used to determine the upper and lower limits of composite stiffness. The models are explicitly based on the properties of fiber and matrix materials and orientation of yarns. Results obtained from the models are compared with experimental values.
Enabling one-sided communication semantics on ARM (2017)

In this paper, we present our work to enable optimized one-sided communication operations on the ARM v8 architecture using a high-performance InfiniBand network interconnect, as well as an evaluation of our implementation. For this study, we started with an OpenSHMEM implementation based on Open MPI/SHMEM, and combined it with the UCX framework and the XPMEM kernel extension for shared memory communication. UCX is a unified communication abstraction that provides high-performance communication services over a variety of network interconnects and shared memory technologies. The UCX, XPMEM, and OpenSHMEM components were specially ported for this work in order to enable efficient access to shared memory and RDMA network capabilities on ARM. To the best of our knowledge, this is the first investigation of one-sided communication semantics and OpenSHMEM on the ARM architecture combined with a high-performance InfiniBand network and XPMEM shared memory transport.
Tyrosine phosphorylation regulates the adhesions of ras-transformed breast epithelia (2020)

Transformed epithelial cells often are characterized by a fibroblastic or mesenchymal morphology. These cells exhibit altered cell-cell and cell-substrate interactions. Here we have identified changes in the adhesions and cytoskeletal interactions of transformed epithelial cells that contribute to their altered morphology. Using MCF-10A human breast epithelial cells as a model system, we have found that transformation by an activated form of ras is characterized by less developed adherens- type junctions between cells but increased focal adhesions. Contributing to the modified adherens junctions of the transformed cells are decreased interactions among beta-catenin, E-cadherin, and the actin cytoskeleton. The ras-transformed cells reveal elevated phosphotyrosine in many proteins, including beta-catenin and p120 Cas. Whereas in the normal cells beta-catenin is found in association with E- cadherin, p120 Cas is not. In the ras-transformed cells, the situation is reversed; tyrosine-phosphorylated p120 Cas, but not tyrosine- phosphorylated beta-catenin, now is detected in E-cadherin complexes. The tyrosine-phosphorylated beta-catenin also shows increased detergent solubility, suggesting a decreased association with the actin cytoskeleton. p120 Cas, whether tyrosine phosphorylated or not, partitions into the detergent soluble fraction, suggesting that it is not tightly bound to the actin cytoskeleton in either the normal or ras- transformed cells. Inhibitors of tyrosine kinases decrease the level of tyrosine phosphorylation and restore a normal epithelial morphology to the ras-transformed cells. In particular, decreased tyrosine phosphorylation of beta-catenin is accompanied by increased interaction with both E-cadherin and the detergent insoluble cytoskeletal fraction. These results suggest that elevated tyrosine phosphorylation of proteins such as beta-catenin and p120 Cas contribute to the altered adherens junctions of ras-transformed epithelia.
Parameter Identification on Flexible Multibody Models Using the Adjoint Variable Method and Flexible Natural Coordinate Formulation (2020)

Abstract This work proposes a methodology for in situ parameter identification using system-level measurements of (flexible) multibody systems, opposed to dedicated component-level identification. The sensitivity information employed for the optimization is obtained using the adjoint variable method (AVM). This method has the advantage of obtaining sensitivity information at a computational cost independent of the amount of model parameters. The underlying flexible multibody formulation employed is a novel approach called the flexible natural coordinates formulation (FNCF). This formulation combines the advantageous properties of the floating frame of reference formulation (FFRF) and the generalized component mode synthesis (GCMS) methods and results in a constant mass and stiffness matrix with quadratic constraint equations. This work shows how the specific structure of equations obtained through FNCF drastically reduces the complexity of the AVM as the simulation derivatives can be readily obtained and are of limited order. The proposed approach has been implemented in an in-house object-oriented matlab multibody code. The methodology is illustrated by identifying 13 model parameters of a MacPherson suspension model, in situ and using system-level measurements.
Spectrum of spontaneous HPRT mutations in TK6 human lymphoblasts (1993)

The occurrence of deletions, coding sequence alterations, and intronic changes leading to aberrant splicing has been characterized among 33 spontaneous HPRT- mutants in TK6 human lymphoblasts. Deletions detectable by multiplex PCR amplification accounted for 45% (15/33) of the mutant collection. Base substitutions represented 30% (10/33) of the total, and were predominated by changes at G:C base pairs. The remaining mutants were distributed among frameshifts (9%, 3/33), small deletions (6%, 2/33), and compound alterations (9%, 3/33). Five mutants (15%) demonstrated aberrant splicing of the hprt transcript. A cluster of 4 deletion/insertion events was identified in hprt exon 6. A nearly perfect 13 bp duplication differed from the original sequence only by an A:T to G:C transition, which was observed as a unique alteration in another HPRT- mutant. A model involving correction of a mismatch in a secondary structure formed by the duplicated sequence may account for these results.
ChemInform Abstract: NaIO<sub>4</sub>—NaN<sub>3</sub>‐Mediated Diazidation of Styrenes, Alkenes, Benzylic Alcohols, and Aryl Ketones. (2012)

Abstract Various substrates can be successfully transformed to diazides as precursors of synthetically important diamines.
Projection-Based Iterative Learning Control for Wafer Scanner Systems (2009)

In this paper, an iterative learning controller (ILC) that uses partial but most pertinent information in the error signal from previous cycles is employed for precision control of a wafer stage. Typically, ILC schemes use the error signal from the previous cycle for updating the control input. This error contains both repetitive and nonrepetitive components. The nonrepetitive components of the error cause degradation of performance of the ILC scheme. Based on structural information about the plant and the disturbances, we can determine some basis functions along which the repetitive error is concentrated. This information is extracted by projecting the error signal onto the subspace spanned by these basis functions. The projected error signal is then used in the ILC update law. Stability and convergence conditions are presented for this projection-based ILC update law. The proposed idea is motivated by precision control of a wafer stage. For a constant velocity scan by the wafer stage, the major sources of repetitive error are found to be phase-mismatch and force ripple. These effects are mathematically modeled to obtain the subspace spanned by them. The projection-based ILC scheme using this subspace is then implemented on a prototype one DOF stage and its performance is compared to the standard ILC scheme that uses a frequency-domain filtering to remove nonrepetitive components of the error.
Clinical and Cellular Roles for TDP1 and TOP1 in Modulating Colorectal Cancer Response to Irinotecan (2014)

Colorectal cancer is the third most common cancer in the world. Despite surgery, up to 50% of patients relapse with incurable disease. First-line chemotherapy uses the topoisomerase 1 (TOP1) poison irinotecan, which triggers cell death by trapping TOP1 on DNA. The removal of TOP1 peptide from TOP1-DNA breaks is conducted by tyrosyl-DNA phosphodiesterase 1 (TDP1). Despite putative roles for TDP1 and TOP1 in colorectal cancer, their role in cellular and clinical responses to TOP1-targeting therapies remains unclear. Here, we show varying expression levels of TOP1 and TDP1 polypeptides in multiple colorectal cancer cell lines and in clinical colorectal cancer samples. TDP1 overexpression or TOP1 depletion is protective. Conversely, TDP1 depletion increases DNA-strand breakage and hypersensitivity to irinotecan in a TOP1-dependent manner, presenting a potential therapeutic opportunity in colorectal cancer. TDP1 protein levels correlate well with mRNA and with TDP1 catalytic activity. However, no correlation is observed between inherent TDP1 or TOP1 levels alone and irinotecan sensitivity, pointing at their limited utility as predictive biomarkers in colorectal cancer. These findings establish TDP1 as a potential therapeutic target for the treatment of colorectal cancer and question the validity of TOP1 or TDP1 on their own as predictive biomarkers for irinotecan response.
Ramipril reduces incidence and prolongates latency time of radiation-induced rat myelopathy after photon and carbon ion irradiation (2020)

To test the hypothesis that the use of an angiotensin-converting enzyme inhibitor (ACEi) during radiotherapy may be ameliorative for treatment-related normal tissue damage, a pilot study was conducted with the clinically approved (ACE) inhibitor ramipril on the outcome of radiation-induced myelopathy in the rat cervical spinal cord model. Female Sprague Dawley rats were irradiated with single doses of either carbon ions (LET 45 keV/μm) at the center of a 6 cm spread-out Bragg peak (SOBP) or 6 MeV photons. The rats were randomly distributed into 4 experimental arms: (i) photons; (ii) photons + ramipril; (iii) carbon ions and (iv) carbon ions + ramipril. Ramipril administration (2 mg/kg/day) started directly after irradiation and was maintained during the entire follow-up. Complete dose-response curves were generated for the biological endpoint radiation-induced myelopathy (paresis grade II) within an observation time of 300 days. Administration of ramipril reduced the rate of paralysis at high dose levels for photons and for the first time a similar finding for high-LET particles was demonstrated, which indicates that the effect of ramipril is independent from radiation quality. The reduced rate of myelopathy is accompanied by a general prolongation of latency time for photons and for carbon ions. Although the already clinical approved drug ramipril can be considered as a mitigator of radiation-induced normal tissue toxicity in the central nervous system, further examinations of the underlying pathological mechanisms leading to radiation-induced myelopathy are necessary to increase and sustain its mitigative effectiveness.
Total Synthesis of Trapoxin A, a Fungal HDAC Inhibitor from <i>Helicoma ambiens</i> (2018)

Peptide modification reactions, e.g., via palladium-catalyzed allylic alkylations, are useful tools for the synthesis of peptides containing interesting nonproteinogenic amino acids, which are often essential for the biological activity of natural products and drugs. Herein we report the utilization of such modification reactions in the first total synthesis of trapoxin A, a naturally occurring tetrapeptidic histone deacetylase (HDAC) inhibitor.
THE PATH OF SCREW INSERTION FOR STABILIZATION OF THE SCAPHOLUNATE JOINT: A CADAVERIC STUDY (2014)

The aim of this study was to determine the path of screw placement to avoid breaching the articular surface of both lunate and scaphoid bones at the radiocarpal and midcarpal joints. An Acutrak screw was inserted into the right scapholunate joint of ten cadavers starting immediately distal to the tip of the radial styloid and aiming for the tip of the ulnar styloid. The articular surfaces of the scaphoid and lunate bones in all ten cadavers were exposed and examined. A computed tomography (CT) scan of four wrists was performed. Eight of the ten cadavers had no perforation or destruction of the articular surfaces. Screw stabilization of the scapholunate joint can be performed without perforation or destruction of the lunate or scaphoid surfaces. We recommend that if this form of fixation is being used then the screw should be inserted commencing at the radial styloid tip and aiming for ulnar styloid tip, under radiological guidance.