gebhart/patrepeval huggingface dataset:
Advanced DNA assembly strategies and standards for synthetic biology (2014)

DNA assembly is a fundamental enabling technology for synthetic biology, yet it is also extremely unreliable, expensive and time-consuming. The process usually requires a significant part of total time and effort that can be dedicated to a project, reducing the resources available for the rest of the research, and is also frequently subject to unexpected problems, introducing an undesirable element of unpredictability that might compromise an entire project. This thesis describes the development of three DNA assembly tools that aim to facilitate and speed up synthetic biology research: “MODAL” is a fast and easy to use assembly strategy that brings the advantages of standardisation and modularity to the latest-generation long overlap-based DNA assembly techniques. “Linker” is a software tool that generates DNA sequences specifically optimised to act as high-efficiency homology regions in long overlap-based DNA assembly reactions. Finally with “BASIC” we propose a new DNA assembly standard that incorporates the advances of MODAL and Linker and brings an additional series of improvements in an original assembly workflow. BASIC aims first of all to make DNA assembly significantly more reliable by addressing and/or removing all the unpredictability elements. It also maintains the speed, ease of use and flexibility of MODAL while achieving the same or better efficiency than the best currently available DNA assembly techniques and standards.
Hall effect in Bi-Sr-Ca-Cu-O thin films (1991)

Resistivity and Hall effect are measured in the a-b plane for thin films of Bi2Sr2CaCu2O8 and Bi2Sr2Ca2Cu3O10 superconductors prepared by laser ablation deposition. The Hall coefficient shows a maximum at 150 K for both compounds which could be associated with bipolaron formation.
Status and Safety of Biotech Crops (2000)

Almost 100 million acres of biotech crops, especially corn, soybean, cotton, canola and potatoes, were grown worldwide in 1999. Most were modified to confer agronomic traits such as insect protection, herbicide tolerance or virus resistance. Many benefits are being realized: including less farmer reliance on traditional pesticides, improvements in practices to achieve environmentally sustainable farms, and enhanced food and environmental safety. New nutritional benefits, such as oils enriched in β-carotene or oleic acid, as well as biotech crops which produce valuable pharmaceuticals, are beginning to appear. Food and environmental safety has been assessed according to international risk assessment guidelines, albeit there are distinct procedures in various jurisdictions globally. Risk assessment focuses on the properties of the introduced traits, the genes which confer the traits, and the resulting crop. To date, the genes conferring these traits have been established as safe on the basis of their history (i.e. prior existence in foods and the environment), the well understood function and similarity of the encoded proteins to dietary proteins, and the lack of animal or environmental toxicity of the encoded proteins. Food derived from biotech crops have been assessed to be as safe and nutritious as traditional foods and crops.
Capital Structure and Firm Performance: A New Approach to Testing Agency Theory and an Application to the Banking Industry (2002)

Corporate governance theory predicts that leverage affects agency costs and thereby influences firm performance. We propose a new approach to test this theory using profit efficiency, or how close a firm's profits are to the benchmark of a best-practice firm facing the same exogenous conditions. We are also the first to employ a simultaneous-equations model that accounts for reverse causality from performance to capital structure. We also control for measures of ownership structure in the tests. We find that data on the U.S. banking industry are consistent with the theory, and the results are statistically significant, economically significant, and robust.
A Novel Method for the Production of an Autologous Anti-Inflammatory and Anti-Catabolic Product (Cytorich) from Human Blood: A Prospective Treatment for the COVID-19-Induced Cytokine Storm (2021)

BACKGROUND Autologous blood-derived products can target specific inflammatory molecular pathways and have potentially beneficial therapeutic effects on inflammatory pathologies. The purpose of this study was to assess in vitro the anti-inflammatory and anti-catabolic potential of an autologous blood product as a possible treatment for COVID-19-induced cytokine storm. MATERIAL AND METHODS Blood samples from healthy donors and donors who had recovered from COVID-19 were incubated using different techniques and analyzed for the presence of anti-inflammatory, anti-catabolic, regenerative, pro-inflammatory, and procatabolic molecules. RESULTS The highest concentrations of therapeutic molecules for targeting inflammatory pathways were found in the blood that had been incubated for 24 h at 37°C, whereas a significant increase was observed after 6 h of incubation in blood from COVID-19-recovered donors. Beneficially, the 6-h incubation process did not downregulate anti-COVID-19 immunoglobulin G concentrations. Unfortunately, increases in matrix metalloproteinase 9, tumor necrosis factor alpha, and interleukin-1 were detected in the product after incubation; however, these increases could be blocked by adding citric acid, with no effect on the concentration of the target therapeutic molecules. Our data allow for safer and more effective future treatments. CONCLUSIONS An autologous blood-derived product containing anti-inflammatory and anti-catabolic molecules, which we term Cytorich, has a promising therapeutic role in the treatment of a virus-induced cytokine storm, including that associated with COVID-19.
Anti-SIRT1 autoantibody is elevated in ankylosing spondylitis: a potential disease biomarker (2018)

Our findings indicate that anti-SIRT1 autoantibodies may serve as a marker for diagnosing AS and predicting hip joint involvement at an early stage.
Number of Embryos Transferred and Implantation (2004)

Multiple pregnancies are considered the most frequent and serious complication of assisted reproduction technology. To reduce the frequency of multiple pregnancies, several centers have adopted a policy of reducing the number of embryos transferred in the uterus, suggesting single embryo transfer. Even though a significant number of papers have been published on this issue, no general consensus exists on how many embryos to replace in the uterus and at which cleavage stage. We conducted a retrospective study on cycles performed throughout 2003, analyzing the relation between the number of embryos transferred and the pregnancy and implantation rates, evaluating also the role of the woman's age. No differences were found among the groups except in one-embryo transferred women, which were mostly natural cycles, for estradiol levels, number of mature oocytes retrieved, number of top quality embryos, and pregnancy rate. The implantation rate was significantly higher in the two-embryo transfers versus three-embryo transfers. We found higher pregnancy and implantation rates with similar multiple pregnancy rates in patients where only two embryos were transferred versus three embryos transfer when women were less than 35 years old. In women aged less than 35 years, which in turn have the higher expectancy of successful pregnancy and also the higher risk of multiple pregnancy, the single embryo transfer is a suitable choice for these patients.
Self‐Administered Alcoholism Screening Test: A Comparision of Conventional Versus Computer‐Administered Formats (1991)

The equivalence of paper-and-pencil-administered and computer-administered versions of the Self-Administered Alcoholism Screening Test (SAAST) was investigated with alcoholic inpatients and nonalcoholic psychiatric outpatients. When the two formats were administered in counterbalanced order, total score mean differences were nonsignificant. In addition, mean differences on a short-form version were also nonsignificant. Equivalence was also determined by comparing the two formats in terms of classification agreement (i.e., classification of subjects into alcoholic and nonalcoholic categories). Agreement between the two formats was 95% in both the total score and short-form versions. Implications of these results as well as the advantages and disadvantages of using computer-administered alcoholism screening tests are discussed.
Data from Clinical Proteomics of Metastatic Melanoma Reveals Profiles of Organ Specificity and Treatment Resistance (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Treatment of metastatic melanoma has dramatically improved in recent years, thanks to the development of immunotherapy and BRAF-MEK–targeted therapies. However, these developments revealed marked heterogeneity in patient response, which is yet to be fully understood. In this work, we aimed to associate the proteomic profiles of metastatic melanoma with the patient clinical information, to identify protein correlates with metastatic location and prior treatments.&lt;/p&gt;Experimental Design:&lt;p&gt;We performed mass spectrometry–based proteomic analysis of 185 metastatic melanoma samples and followed with bioinformatics analysis to examine the association of metastatic location, &lt;i&gt;BRAF&lt;/i&gt; status, survival, and immunotherapy response with the tumor molecular profiles.&lt;/p&gt;Results:&lt;p&gt;Bioinformatics analysis showed a high degree of functional heterogeneity associated with the site of metastasis. Lung metastases presented higher immune-related proteins, and higher mitochondrial-related processes, which were shown previously to be associated with better immunotherapy response. In agreement, epidemiological analysis of data from the National Cancer Database showed improved response to anti-programmed death 1, mainly in patients with lung metastasis. Focus on lung metastases revealed prognostic and molecular heterogeneity and highlighted potential tissue-specific biomarkers. Analysis of the &lt;i&gt;BRAF&lt;/i&gt; mutation status and prior treatments with MAPK inhibitors proposed the molecular basis of the effect on immunotherapy response and suggested coordinated combination of immunotherapy and targeted therapy may increase treatment efficacy.&lt;/p&gt;Conclusions:&lt;p&gt;Altogether, the proteomic data provided novel molecular determinants of critical clinical features, including the effects of sequential treatments and metastatic locations. These results can be the basis for development of site-specific treatments toward treatment personalization.&lt;/p&gt;&lt;/div&gt;
CD122 signaling in CD8+ memory T cells drives costimulation-independent rejection (2018)

Interrupting T cell costimulatory signals as a strategy to control undesired immune responses, such as occur in autoimmunity or transplantation, has the potential to alleviate many of the unwanted side effects associated with current immunosuppressive therapies. Belatacept, a high-affinity version of CTLA4-Ig that blocks ligand ligation to CD28, has been approved for use in kidney transplant recipients. Despite the long-term benefits associated with its use, such as improved renal function and lower cardiovascular risk, a subset of patients treated with belatacept experience elevated rates of acute T cell-mediated rejection, tempering enthusiasm for its use. Here we demonstrate that costimulation-independent T cell alloreactivity relies on signaling through CD122, the shared IL-2 and IL-15 receptor β-chain. Combined costimulatory and CD122 blockade improved survival of transplanted tissue in mice and nonhuman primates by controlling proliferation and effector function of CD8+ T cells. The high-affinity IL-2 receptor was dispensable for memory CD8+ T cell responses, whereas signaling through CD122 as a component of the high-affinity IL-15 receptor was critical for costimulation-independent memory CD8+ T cell recall, distinguishing specific roles for IL-2 and IL-15 in T cell activation. These studies outline a novel approach for clinical optimization of costimulatory blockade strategies in transplantation by targeting CD122.
Secretory Acid Sphingomyelinase in the Serum of Medicated Patients Predicts the Prospective Course of Depression (2019)

Major depressive disorder (MDD) is a highly prevalent and devastating psychiatric illness with strong individual and societal burdens. However, biomarkers to improve the limited preventive and therapeutic approaches are scarce. Multilevel evidence suggests that the pathophysiological involvement of sphingolipids particularly increases the levels of ceramides and the ceramide hydrolyzing enzyme, acid sphingomyelinase. The activity of secretory acid sphingomyelinase (S-ASM) and routine blood parameters were determined in the serum of patients with current (unmedicated <i>n</i> = 63, medicated <i>n</i> = 66) and remitted (<i>n</i> = 39) MDD and healthy subjects (<i>n</i> = 61). Depression severity and anxiety and their 3-weeks prospective course of treatment were assessed by psychometric inventories. S-ASM activity was not different between the four groups, did not decrease during treatment, and was not lower in individuals taking medication that functionally inhibited ASM. However, S-ASM correlated positively with depression severity only in remitted patients. High enzyme activity at inclusion predicted milder clinician-evaluated and self-rated depression severity (HAM-D, MADRS, BDI-II) and state anxiety at follow-up, and was related to stronger improvement in these scores in medicated patients. S-ASM was strongly and contrariwise associated with serum lipids in unmedicated and medicated females. These findings contribute to a better understanding of the pathomechanisms underlying depression and the development of clinical strategies and biomarkers.
Porous liquid zeolites: hydrogen bonding-stabilized H-ZSM-5 in branched ionic liquids (2019)

Porous liquids, as a newly emerging type of porous material, have great potential in gas separation and storage. However, the examples and synthetic strategies reported so far likely represent only the tip of the iceberg due to the great difficulty and challenge in engineering permanent porosity in liquid matrices. Here, by taking advantage of the hydrogen bonding interaction between the alkane chains of branched ionic liquids and the Brønsted sites in H-form zeolites, as well as the mechanical bond of the long alkyl chain of the cation penetrated into the zeolite channel at the interface, the H-form zeolites can be uniformly stabilized in branched ionic liquids to form porous liquid zeolites, which not only significantly improve their gas sorption performance, but also change the gas sorption-desorption behavior because of the preserved permanent porosity. Furthermore, such a facile synthetic strategy can be extended to fabricate other types of H-form zeolite-based porous liquids by taking advantage of the tunability of the counter-anion (e.g., NTf2-, BF4-, EtSO4-, etc.) in branched ionic liquids, thus opening up new opportunities for porous liquids for specific applications in energy and environment.
KressArray Xplorer: a new CAD environment to optimize reconfigurable datapath array architectures (2002)

This paper introduces a CAD environment for design-space exploration of coarse grain reconfigurable KressArray architectures and similar platforms, To find an optimal solution to a given application domain this KressArray Xplorer supports experimenting with different architectures. An estimator analyses the input and suggests an architecture onto which then the application is mapped using an heuristic algorithm. A graphic editor supports user interaction. The system generates performance analysis data, which is used by an automatic tool to refine the result iteratively.
Abstraction-based intrusion detection in distributed environments (2001)

Abstraction is an important issue in intrusion detection, since it not only hides the difference between heterogeneous systems, but also allows generic intrusion-detection models. However, abstraction is an error-prone process and is not well supported in current intrusion-detection systems (IDSs). This article presents a hierarchical model to support attack specification and event abstraction in distributed intrusion detection. The model involves three concepts: system view , signature , and view definition . A system view provides an abstract interface of a particular type of information; defined on the instances of system views, a signature specifies certain distributed attacks or events to be monitored; a view definition is then used to derive information from the matches of a signature and presents it through a system view. With the three elements, the model provides a hierarchical framework for maintaining signatures, system views, as well as event abstraction. As a benefit, the model allows generic signatures that can accommodate unknown variants of known attacks. Moreover, abstraction represented by a system view can be updated without changing either its specification or the signatures specified on its basis. This article then presents a decentralized method for autonomous but cooperative component systems to detect distributed attacks specified by signatures. Specifically, a signature is decomposed into finer units, called detection tasks , each of which represents the activity to be monitored on a component system. The component systems (involved in a signature) then perform the detection tasks cooperatively according to the "dependency" relationships among these tasks. An experimental system called CARDS has been implemented to test the feasibility of the proposed approach.
A Case of Severe Congestive Heart Failure with Atrioventricular Valvular Insufficiency in a Young Borzoi Dog (1999)

A2-year-2-month-old female Borzoi dog with fever, cough, pendulous abdomen, and weight loss, was revealed to have systolic and diastolic murmurs and radiographic cardiomegaly. Electrocardiography showed ventricular premature contractions and atrial fibrillation, and echocardiography indicated thickening of the mitral and tricuspid valves, marked enlargement of the left atrium and ventricle, enlargement of the right atrium and ventricle, and smoke-like echo. Color flow Doppler ultrasonography showed severe mitral and tricuspid regurgitation. The case was diagnosed as severe congestive heart failure with atrioventricular valvular insufficiency, treated with the diuretics, cardiac glycosides, angiotensin-converting enzyme inhibitors, β1-blocker, coronary vasodilator. and antibiotics, and survived for 310 days after the first examination.
Phenolic Structure and Colour in Mannich Reaction Products (2007)

Mannich reactions have been carried out with a variety of model alkylphenols and dimethylamine, methylamine, and diethylenetriamine to trace the origin of persistent coloured products occurring in related reactions with pentadeca(e)nylphenol and 4- tert-alkylphenols. It was found to be attributable to the presence of resorcinolic impurities.
NC milling deformation analysis of aluminum alloy thin-walled components based on orthogonal cutting experiments on a vertical machining center (2010)

Because of their poor rigidity, the deformation of thin-walled workpieces caused by cutting force in NC milling is the main factor that decreases machining precision and increases aeronautical product cost. The straight side walls of aluminum LY12CZ workpieces are machined on a vertical machining center THA5656 and their errors are analyzed. Based on orthogonal tests, the deformation characters of the thin-walled workpieces are discussed under different cutting conditions. The research can provide support for machining deformation control and machining simulation model verification.
A formação inicial do professor: os desafios e tensões que a prática pedagógica impõe (2008)

Pretende este trabalho abordar a formacao de professores delimitado a pratica pedagogica na formacao inicial do professor, e o interesse nesta pesquisa releva as questoes da pratica pedagogica e dos saberes sobre a educacao, tendo como embasamento as informacoes sobre os assuntos mais abordados na literatura acerca da formacao de professores: a formacao inicial, modo como sao apreendidas as praticas pedagogicas e as representacoes sobre seus percalcos e desafios.
A Study of the Relationship of the Superior Vena Cava to the Bony Landmarks of the Sternum in the Supine Adult: Implications for Magnetic Guidance Systems (2007)

Abstract This study was a retrospective investigation of computed tomography (CT) images of an Australian adult hospital population. These images were used to evaluate the spatial relationships of the superior vena cava (SVC) to the midsagittal line, the sternal paracoronal plane, and commonly used landmarks of the sternum. Consistent relationships were found between the long axis of the SVC and both the midsagittal line and sternal paracoronal plane. When the sternal paracoronal plane was used as the plane of reference, the angle of Louis was found to approximate the SVC in 99.5% of cases, and the right 2nd intercostal space approximated the SVC in 94% of cases. Constraints on the use of landmarks are discussed with regard to magnetic guidance systems for catheter tracking.
Identification of machine tools linear axes performance using on-machine embedded inertia measurement units | NIST (2017)

The current trend in manufacturing industry is from mass production towards flexible and adaptive manufacturing systems and cloud manufacturing. Self-learning machines and robot systems can play an ...
Application of low scattering antennas to RFID networks (2016)

An established backscattering link between an RFID tag and reader suffers from high interference from other RFID tags in the network. This interference results in low read rates in RFID networks. In this paper, we investigate a new state for an RFID tag in which the tag switches to an invisible (i.e. low scattering) state when a communication link between an RFID reader and another target RFID tag is ongoing. We show both by simulations and measurements that by using this method the interference to the backscattering link is minimized and thus the read rate increases.
GPS and GALILEO Airframe Multipath Error Bounding Method and Test Results (2020)

This paper presents GPS and Galileo airframe multipath statistics derived from more than 50 flight hours on an experimental Boeing 777 airplane using prototype Collins Aerospace Dual-Frequency, Multi-Constellation (DFMC) receivers. These results are an important step toward validation of the integrity and accuracy algorithms that will be used in the first aviation industry standards for use of combined GPS and Galileo for safety of life services such as navigation, landing, and surveillance for aircraft separation. This paper presents the experimental flight test program and equipment setup. Prior work to derive airframe multipath is referenced, then the algorithms and methods used to estimate multipath on GPS L1 and L5, Galileo E1 and E5a, and the ionosphere free combinations of those signals are described in detail. Multiple potential techniques for estimating airframe multipath and deriving integrity bounds appropriate for precision approach and landing are described. Handling of antenna group delay variation with angle of arrival, ionosphere delay, and receiver noise are discussed, and multiple ways to visualize the results are presented to address various trades for consideration in standards bodies. Multipath error statistics are shown to be minimally dependent on the signal direction of arrival for this particular test setup. By aggregating data from all satellite elevation angles, enough samples were available to evaluate the impact of carrier smoothing time with statistical significance. The effect of carrier smoothing on multipath error bounds is explored using 100, 300, and 600 seconds smoothing time constants, showing larger smoothing times as a viable means to reduce multipath errors and increase availability of DFMC position accuracy and integrity bounds.