gebhart/patrepeval huggingface dataset:
Ethical and Practical Guidelines for Reporting Genetic Research Results to Study Participants: Updated Guidelines from a National Heart, Lung, and Blood Institute Working Group (2010)

In January 2009, the National Heart, Lung, and Blood Institute convened a 28-member multidisciplinary Working Group to update the recommendations of a 2004 National Heart, Lung, and Blood Institute Working Group focused on Guidelines to the Return of Genetic Research Results. Changes in the genetic and societal landscape over the intervening 5 years raise multiple questions and challenges. The group noted the complex issues arising from the fact that technological and bioinformatic progress has made it possible to obtain considerable information on individuals that would not have been possible a decade ago. Although unable to reach consensus on a number of issues, the working group produced 5 recommendations. The working group offers 2 recommendations addressing the criteria necessary to determine when genetic results should and may be returned to study participants, respectively. In addition, it suggests that a time limit be established to limit the duration of obligation of investigators to return genetic research results. The group recommends the creation of a central body, or bodies, to provide guidance on when genetic research results are associated with sufficient risk and have established clinical utility to justify their return to study participants. The final recommendation urges investigators to engage the broader community when dealing with identifiable communities to advise them on the return of aggregate and individual research results. Creation of an entity charged to provide guidance to institutional review boards, investigators, research institutions, and research sponsors would provide rigorous review of available data, promote standardization of study policies regarding return of genetic research results, and enable investigators and study participants to clarify and share expectations for the handling of this increasingly valuable information with appropriate respect for the rights and needs of participants.
Inverse Kinematic Model of Flexure-Based Microsurgical Manipulator (2005)

This paper presents the development of an inverse kinematic model for a flexure-based micromanipulator using a feedforward neural network. The manipulator is part of an active handheld instrument designed to cancel hand tremor during microsurgery. The manipulator is actuated using three piezoelectric stacks. Preliminary results yield a mean squared error of 5% of the total stack range of motion, and a maximum error of 14% of the total range of motion.
Development of a Compact Digital Reactivity Meter and a Reactor Physics Data Processor (1987)

Reactor physics tests at initial startup and after refuelings are performed to verify the nuclear design and to assure safe operation. Analog computers and instruments are widely used for the acquisition of data, and these data are reduced by hand. These conventional procedures, however, require much time and labor. Since there has been great progress in the development of digital computers and devices, these procedures are digitalized, which successfully reduces the time and labor required for reactor physics tests.
Development of Nanoparticles with Bifunctions of Fluorescence and Magnetic Resonance for Multi Modal Imaging (2010)

CdSe/ZnS quantum dots with core/shell microstructure have been widely used as fl uorescent probes for
The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags (2003)

Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximately 23,500 genes, of which only approximately 1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.
Avaliação das condições de saúde dos moradores do assentamento Monte Alegre 3 do município de Araraquara-SP (2003)

Introdução: O grupo PET- Farmácia vem realizando há alguns anos o Trabalho de Campo com assentados. No período de 21 de janeiro a 5 de fevereiro de 2002, com o apoio da Prefeitura Municipal de Araraquara, realizou-se o Trabalho de Campo no Assentamento Monte Alegre 3, pertencente ao município de Araraquara. O assentamento é composto por 116 famílias, sendo que parte delas vive na agrovila e parte em lotes mais afastados. No local há 2 pessoas que trabalham como agentes de saúde e que auxiliaram o grupo na realização do trabalho. Objetivos: verificar a incidência de parasitoses junto à população de baixa renda, fazer uma análise ampla das condições de saúde e saneamento do meio, orientar os residentes sobre educação sanitária, proporcionar aos alunos o contato direto com a população e a aplicação dos conhecimentos adquiridos em disciplinas envolvidas no trabalho. Métodos: O trabalho constou de visitas domiciliares através das quais realizou-se um questionário sobre os hábitos de saúde da família, uma avaliação das condições sanitárias, principalmente das fossas e fonte de água, distribuição de material para coleta de fezes e também orientações gerais de saúde. O material coletado foi analisado no laboratório de Parasitologia Clínica da Faculdade de Ciências Farmacêuticas. Tendo os resultados em mãos, esses foram levados às respectivas residências orientando os indivíduos a procurarem orientação médica em caso de resultado positivo. Além disso, os laudos foram emitidos ao PSF (Programa de Saúde da Família) local. No sábado de 26 de janeiro a população foi reunida no barracão do assentamento e nesse dia foram realizadas as triagens de anemias e de diabetes, aferições de pressão arterial, palestra sobre Plantas Medicinais e Automedicação e sobre Parasitoses, orientações sobre DST/AIDS e Métodos Contraceptivos com distribuição de preservativos e, ainda, atividade recreativa e cultural com as crianças. Resultados: 293 amostras de fezes foram analisadas pelos métodos Kato modificado, Coprotest e Rugai, das quais 26,62% encontraram-se mono ou poliparasitadas; 19 amostras de água de poços e reservatórios também foram analisadas pela técnica de tubos múltiplos, sendo que 95% encontravam-se impróprias para consumo humano. Realizaram-se 116 medições de taxas de hemoglobina (37,93% encontraram-se anêmicas), 125 de glicemia (8,26% apresentaram taxa de glicose acima do recomendado) e 77 aferições de pressão arterial (19,5% apresentaram-se hipertensas).
A Pilot Trial Targeting the ICOS-ICOS-L Pathway in Nonhuman Primate Kidney Transplantation. (2014)

Novel biologic therapies directed against alternate T cell costimulatory pathways could synergize with currently available CD28/B7 costimulation blockade agents to improve allograft survival after kidney transplantation. One potential target is the ICOS (inducible costimulator)-ICOS-L pathway. ICOS-Ig is a human Fc-fusion protein composed of an ICOS extracellular domain and IgG1 tail that binds ICOS-L, blocking ICOS-ICOS-L interaction. We hypothesized that ICOS-Ig would synergize with CD28/B7 costimulation blockade with belatacept to prolong allograft survival in a nonhuman primate kidney transplant model. Therefore, nine rhesus monkeys underwent MHC-mismatched kidney allotransplantation, with 3 animals receiving ICOS-Ig alone, 3 receiving belatacept alone, and 3 receiving ICOS-Ig and belatacept. Belatacept (20 mg/kg) was given on days 0, 3, 7, and 14, then every 2 weeks until day 180, and monthly thereafter. ICOS-Ig (10 mg/kg) was given on day 0, and 5 mg/kg on days 3, 7, 14, 21, and 28. Rejection-free survivals were 6, 6, and 6 days with ICOS-Ig alone; 44, 71, and >385 days with belatacept alone; and 36, 44, and 45 days with ICOS-Ig and belatacept. ICOS-Ig, with or without belatacept, did not prolong rejection-free survival compared to belatacept alone or untreated animals, respectively. Acute rejections were graded Banff 2a to 3. Lymphocytes from peripheral blood, lymph node, spleen and the kidney allograft were isolated at the time of rejection and analyzed for CD28, ICOS, and PD-1 expression by flow cytometry. In the ICOS-Ig alone group, a large percentage of CD8 (60-76%) and CD4 (58-73%) graft infiltrating T cells co-expressed high levels of ICOS and PD-1. The addition of belatacept significantly decreased the proportion of CD8 and CD4 ICOS+PD-1+ T cells (26-54% and 10-16%, respectively). Similar patterns were observed in peripheral blood. The proportions of CD8 CD28- memory T cells were notably higher in the animals receiving belatacept, both in the kidney and peripheral blood. However, T cells that were ICOS+PD-1+ were overwhelmingly CD28+ (80-99%). We concluded that ICOS-Ig, with or without belatacept, did not effectively prolong renal allograft survival in nonhuman primates in this study. DISCLOSURES:Chapin, S.: Employee, Perseid Therapeutics. Devens, B.: Employee, Perseid Therapeutics. Karrer, E.: Employee, Perseid Therapeutics.
Histogram-based template matching for object detection in images with varying contrast (2007)

Our challenge was to develop a semi-automatic target detection algorithm to aid human operators in locating potential targets within images. In contrast to currently available methods, our approach is relatively insensitive to image brightness, image contrast and object orientation. Working on overlapping image blocks, we used a sliding difference method of histogram matching. Incrementally sliding the histograms of the known object template and the image region of interest (ROI) together, the sum of absolute histogram differences was calculated. The minimum of the resultant array was stored in the corresponding spatial position of response surface matrix. Local minima of the response surface suggest possible target locations. Because the template contrast will rarely perfectly match the contrast of the actual image contrast, which can be compromised by illumination conditions, background features, cloud cover, etc., we perform a random contrast manipulation, which we term 'wobble', on the template histogram. Our results have shown increased object detection with the combination of the sliding histogram difference and wobble.
Disruption of the L‐arabitol dehydrogenase encoding gene in Aspergillus tubingensis results in increased xylanase production (2013)

Abstract Fungal xylanases are of major importance to many industrial sectors, such as food and feed, paper and pulp, and biofuels. Improving their production is therefore highly relevant. We determined the molecular basis of an improved xylanase‐producing strain of Aspergillus tubingensis that was generated by UV mutagenesis in an industrial strain improvement program. Using enzyme assays, gene expression, sequencing of the ladA locus in the parent and mutant, and complementation of the mutation, we were able to show that improved xylanase production was mainly caused by a chromosomal translocation that occurred between a subtilisin‐like protease pepD gene and the L ‐arabitol dehydrogenase encoding gene ( ladA ), which is part of the L ‐arabinose catabolic pathway. This genomic rearrangement resulted in disruption of both genes and, as a consequence, the inability of the mutant to use L ‐arabinose as a carbon source, while growth on D ‐xylose was unaffected. Complementation with constitutively expressed ladA confirmed that the xylanase overproducing phenotype was mainly caused by loss of ladA function, while a knockout of xlnR in the UV mutant demonstrated that improved xylanase production was mediated by XlnR. This study demonstrates the potential of metabolic manipulation for increased production of fungal enzymes.
Multipole Plasmon Resonances in Gold Nanorods (2006)

The optical properties of gold rods electrochemically deposited in anodic aluminum oxide templates have been investigated. Homogeneous suspensions of rods with an average diameter of 85 nm and varying lengths of 96, 186, 321, 465, 495, 578, 641, 735, and 1175 nm were fabricated. The purity and dimensions of these rod nanostructures allowed us to observe higher-order multipole resonances for the first time in a colloidal suspension. The experimental optical spectra agree with discrete dipole approximation calculations that have been modeled from the dimensions of the gold nanorods.
Characterization of the retention motif in the C-terminal part of the long splice form of platelet-derived growth factor A-chain. (1994)

Platelet-derived growth factor (PDGF) A-chain is found in two different splice variants; the long A-chain variant differs from the short one in that it contains a stretch of basic amino acid residues in the C-terminal part that mediates retention of the growth factor inside the producer cell and to the cell matrix. By analyzing mutants in which different amino acid residues in the retention motif had been changed to alanine residues, we found that the total positive charge of the sequence is of importance for the function of the retention motif. Moreover, we showed that retention also occurs if only one of the polypeptides in the PDGF dimer carries the retention motif. Surface iodination and competition with a peptide having the sequence of the retention motif revealed that the long A-chain variant, in contrast to the short A-chain variant, is localized on the outside of the cells and is also associated to the cell matrix. The association is likely to be mediated partially through heparan sulfate proteoglycans since treatment of matrix with heparitinase released the long A-chain variant.
Feasibility study of underground energy storage using high-pressure, high-temperature water. Final report (1977)

A technical, operational and economic feasibility study on the storage of energy as heated high pressure water in underground cavities that utilize the rock overburden for containment is presented. Handling peak load requirements of electric utility power networks is examined in some detail. The cavity is charged by heating water with surplus steaming capacity during periods of low power requirement. Later this hot water supplies steam to peaking turbines when high load demands must be met. This system can be applied to either new or existing power plants of nuclear or fossil fuel type. The round trip efficiency (into storage and back) is higher than any other system - over 90%. Capital costs are competitive and the environmental impact is quite benign. Detailed installation and design problems are studied and costs are estimated. The continental United States is examined for the most applicable geology. Formations favorable for these large cavities exist in widespread areas.
Domains with transcriptional regulatory activity within the ALL1 and AF4 proteins involved in acute leukemia. (1995)

The ALLI gene, located at chromosome band 11q23, is involved in acute leukemia through a series of chromosome translocations and fusion to a variety of genes, most frequently to A4 and AF9. The fused genes encode chimeric proteins proteins. Because the Drosophila homologue of ALL1, trithorax, is a positive regulator of homeotic genes and acts at the level of transcription, it is conceivable that alterations in ALL1 transcriptional activity may underlie its action in malignant transformation. To begin studying this, we examined the All1, AF4, AF9, and AF17 proteins for the presence of potential transcriptional regulatory domains. This was done by fusing regions of the proteins to the yeast GAL4 DNA binding domain and assaying their effect on transcription of a reporter gene. A domain of 55 residues positioned at amino acids 2829-2883 of ALL1 was identified as a very strong activator. Further analysis of this domain by in vitro mutagenesis pointed to a core of hydrophobic and acidic residues as critical for the activity. An ALL1 domain that repressed transcription of the reporter gene coincided with the sequence homologous to a segment of DNA methyltransferase. An AF4 polypeptide containing residues 480-560 showed strong activation potential. The C-terminal segment of AF9 spanning amino acids 478-568 transactivated transcription of the reporter gene in HeLa but not in NIH 3T3 cells. These results suggest that ALL1, AF4, and probably AF9 interact with the transcriptional machinery of the cell.
Dynamics of cell and tissue growth acquired by means of 25 mm2to 10 cm2lens-free imaging (2015)

In this paper, we discuss a new methodology based on lens-free imaging to perform wound healing assay with unprecedented statistics. Our video lens-free microscopy setup is a simple optical system featuring only a CMOS sensor and a semi coherent illumination system. Yet it is a powerful means for the real-time monitoring of cultivated cells. It presents several key advantages, e.g., integration into standard incubator, compatibility with standard cell culture protocol, simplicity and ease of use. It can perform the follow-up in a large field of view (25 mm<sup>2</sup>) of several crucial parameters during the culture of cells i.e. their motility, their proliferation rate or their death. Consequently the setup can gather large statistics both in space and time. But in the case of tissue growth experiments, the field of view of 25 mm<sup>2</sup> remains not sufficient and results can be biased depending on the position of the device with respect to the recipient of the cell culture. Hence, to conduct exhaustive wound healing assay, here we propose to enlarge the field of view up to 10 cm<sup>2</sup> through two different approaches. The first method consists in performing a scan of the cell culture by moving the source/sensor couple and then stitch the stack of images. The second is to make an acquisition by scanning with a line scan camera. The two approaches are compared in term of resolution, complexity and acquisition time. Next we have performed acquisitions of wound healing assay (keratinocytes HaCaT) both in real-time (25 mm<sup>2</sup>) and in final point (10 cm<sup>2</sup>) to assess the combination of these two complementary modalities. In the future, we aim at combining directly super wide field of view acquisitions (&gt;10 cm<sup>2</sup>) with real time ability inside the incubator.
Non-contact removal of 60-nm latex particles from silicon wafers with laser-induced plasma (2004)

In micro- and nano-manufacturing particles are created and circulated as by-products of the processes utilized. The removal of micro- and nano-particles during manufacturing processes is of great importance in many industries, including semiconductors, optics, photonics and microelectromechanical systems (MEMS). One specific application is in the cleaning of silicon wafers. According to the 2002 update of the International Technology Roadmap for Semiconductors, by the year 2006, techniques for the removal of polystyrene latex (PSL)-equivalent particles with size less than 35 nm will be required and currently, according to the roadmap update, there is no known method to remove PSL-equivalent particles smaller than diameter D = 40 nm. The current study reports and demonstrates a non-contact laser-induced plasma method for removal of particles with D = 60 nm. Non-contact techniques are desired to reduce the risk of substrate damage. Chemical usage in traditional cleaning methods is also a serious concern for process cost, workplace safety and environmental conservation. The development of dry, rapid, non-contact and non-damaging nanoparticle removal methods is, therefore, a critical need for various applications. Using a scanning mechanism, the process discussed can be automated for rapid cleaning of large silicon wafers.
Semi-supervised Variational Autoencoder for Regression: Application on Soft Sensors (2022)

We present the development of a semi-supervised regression method using variational autoencoders (VAE), which is customized for use in soft sensing applications. We motivate the use of semi-supervised learning considering the fact that process quality variables are not collected at the same frequency as other process variables leading to many unlabelled records in operational datasets. These unlabelled records are not possible to use for training quality variable predictions based on supervised learning methods. Use of VAEs for unsupervised learning is well established and recently they were used for regression applications based on variational inference procedures. We extend this approach of supervised VAEs for regression (SVAER) to make it learn from unlabelled data leading to semi-supervised VAEs for regression (SSVAER), then we make further modifications to their architecture using additional regularization components to make SSVAER well suited for learning from both labelled and unlabelled process data. The probabilistic regressor resulting from the variational approach makes it possible to estimate the variance of the predictions simultaneously, which provides an uncertainty quantification along with the generated predictions. We provide an extensive comparative study of SSVAER with other publicly available semi-supervised and supervised learning methods on two benchmark problems using fixed-size datasets, where we vary the percentage of labelled data available for training. In these experiments, SSVAER achieves the lowest test errors in 11 of the 20 studied cases, compared to other methods where the second best gets 4 lowest test errors out of the 20.
Bone and Soft Tissue Trauma Research at the USAISR (2004)

Since its establishment in 1943, the United States Army Institute of Surgical Research (USAISR) has conducted research focused on improving the surgical care given to soldiers. Just as our predecessors addressed the unacceptably high impact of thermal injury on combat casualties, the Bone and Soft Tissue Research Team focuses research on combat casualties by examining the epidemiology of combat wounds to identify needed improvements in combat casualty care. This paper provides an overview of the bone and soft tissue trauma research currently being conducted at the USAISR and introduces the available combat casualty data from recent conflicts that were used to identify areas where research can achieve maximum impact on reducing the morbidity and mortality rates of combat casualties. 1.0 COMBAT CASUALTY STATISTICS Because the Vietnam War ended over a quarter century ago, we sought data from more recent conflicts on which to base our research efforts. While we have been fortunate to have suffered relatively few combat casualties at the end of the 20th century, Operation Just Cause (Panama), Operation Desert Storm (Kuwait and Iraq) and the Battle of the Black Sea (Somalia) offered the opportunity to investigate more recent patterns of combat injury. Fortunately, the patterns of injury were documented both during and after each of these