gebhart/patrepeval huggingface dataset:
Supplemental Material from Identification of Tumoricidal TCRs from Tumor-Infiltrating Lymphocytes by Single-Cell Analysis (2023)

&lt;p&gt;S1. The expression of CD137 on splenic CD8+ T cells and the expression of PD1 and CD137 on CD8+ TILs of tumor bearing mice. S2. Analysis of TILs. (A) CD137 expression of TILs and RLN cells. S3. Transfection of TCR cDNA into splenic T cells. S4. IFN-γ-induced expression of MHC class I molecules on the surface of B16F10 cells. S5. The IFN-γ-secretion of TIL-derived TCR-transduced spleen T cells. S6. The cytotoxicity of TIL-derived TCR-expressing T cells against unstimulated B16F10 cells. S7. A correlation between the INF-γ production and the cytotoxicity. S8. Transfection efficiency of TCR gene into splenic T cellsforin vivoexperiment. S9. MHC-restriction of TIL-derived TCR. (A) Expression of H-2Kband H-2Dbmolecules on H-2Kbor H-2DbcDNA-transfected B16F10 cells. S10. IFN-γ-induced expression of MHC class I molecules on the surface of cells. Supplementary Table 1. Clonally expanded populations in human cancer TILs&lt;/p&gt;
Myofascial Trigger Points and Sensitization: An Updated Pain Model for Tension-Type Headache (2007)

Present pain models for tension-type headache suggest that nociceptive inputs from peripheral tender muscles can lead to central sensitization and chronic tension-type headache (CTTH) conditions. Such models support that possible peripheral mechanisms leading to pericranial tenderness include activation or sensitization of nociceptive nerve endings by liberation of chemical mediators (bradikinin, serotonin, substance P). However, a study has found that non-specific tender points in CTTH subjects were not responsible for liberation of algogenic substances in the periphery. Assuming that liberation of algogenic substances is important, the question arising is: if tender muscle points are not the primary sites of on-going neurogenic inflammation, which structure can be responsible for liberation of chemical mediators in the periphery? A recent study has found higher levels of algogenic substances, and lower pH levels, in active myofascial trigger point (TrPs) compared with control tender points. Clinical studies have demonstrated that referred pain elicited by head and neck muscles contribute to head pain patterns in CTTH. Based on available data, an updated pain model for CTTH is proposed in which headache can at least partly be explained by referred pain from TrPs in the posterior cervical, head and shoulder muscles. In this updated pain model, TrPs would be the primary hyperalgesic zones responsible for the development of central sensitization in CTTH.
Anthracycline-related cardiotoxicity: risk factors and therapeutic options in childhood cancers (2008)

Anthracyclines play an important role in chemotherapeutic regimens for a wide spectrum of childhood tumors, but they can cause cytotoxic damage to cardiac cells, especially in combination with radiotherapy. Furthermore, cardiotoxicity increases with the cumulative dose and may lead to congestive heart failure and cardiomyopathy. Other factors, including age, pre-existing cardiac disease, length of follow-up, gender, route of administration, concomitant exposure to some chemotherapeutic drugs, trisomy 21 and black race, play a role in increasing the risk of cardiac dysfunction. The prevention of anthracycline-induced cardiotoxicity is mandatory as children are expected to survive for decades after being cured of their cancer. The purpose of this work is to point out the major risk factors of cardiotoxicity in children and to summarize some strategies to limit or prevent this complication and to treat the development of acute heart failure.&nbsp;
3D stereoscopic image pairs by depth-map generation (2004)

This work presents a new unsupervised technique aimed to generate stereoscopic views estimating depth information from a single input image. Using a single input image, vanishing lines/points are extracted using a few heuristics to generate an approximated depth map. The depth map is then used to generate stereo pairs. The overall method is well suited for real time application and works also on CFA (colour filtering array) data acquired by consumer imaging devices. Experimental results on a large dataset are reported.
Automatic recording of individual voluntary feed intake in group housed pigs (1990)

Genetic improvement of pigs relies heavily on improving feed conversion and controlling feed intake capacity. For this purpose it is vital to measure feed intake of individual pigs. Traditionally this has been achieved by keeping pigs singly or in sib-pairs in small pens. Such facilities are expensive to build and are difficult to design to cater adequately for pigs over a wide range of weights and at low stocking density. Keeping animals in small pens is less than satisfactory from a welfare aspect.
Sunlight UV-Induced Skin Cancer Relies upon Activation of the p38α Signaling Pathway (2013)

The activation of cellular signal transduction pathways by solar ultraviolet (SUV) irradiation plays a vital role in skin tumorigenesis. Although many pathways have been studied using pure ultraviolet A (UVA) or ultraviolet B (UVB) irradiation, the signaling pathways induced by SUV (i.e., sunlight) are not understood well enough to permit improvements for prevention, prognosis, and treatment. Here, we report parallel protein kinase array studies aimed at determining the dominant signaling pathway involved in SUV irradiation. Our results indicated that the p38-related signal transduction pathway was dramatically affected by SUV irradiation. SUV (60 kJ UVA/m(2)/3.6 kJ UVB/m(2)) irradiation stimulates phosphorylation of p38α (MAPK14) by 5.78-fold, MSK2 (RPS6KA4) by 6.38-fold, and HSP27 (HSPB1) by 34.56-fold compared with untreated controls. By investigating the tumorigenic role of SUV-induced signal transduction in wild-type and p38 dominant-negative (p38 DN) mice, we found that p38 blockade yielded fewer and smaller tumors. These results establish that p38 signaling is critical for SUV-induced skin carcinogenesis.
Fibrinolysis in chronic renal failure, dialysis and renal transplantation. (2002)

The best known function of the fibrinolytic system is its ability to dissolve blood clots. The key enzyme of fibrinolysis, plasmin, is formed by conversion from plasminogen through the action of activators, the most important of which is tissue type plasminogen activator (tPA). Low levels of tPA or excessive levels of plasminogen activator inhibitor-I (PAI-I) cause hypofibrinolysis, causally related to the development of atherosclerosis and associated thrombotic complications, as well as with the development of venous and arterial thrombosis. A chronic decrease in renal function leads to hypofibrinolysis due primarily to low levels of tPA. Hypofibrinolysis is present both in patients treated by long-term hemodialysis and by peritoneal dialysis. The hemodialysis procedure acutely raises the plasma levels of tPA, primarily as a result of the bioincompatibility of materials in the extracorporeal circuit. In peritoneal dialysis, dialysis solution dwell time is associated with an increase in PAI-I levels in the abdominal cavity. Fibrinolysis defects occur also in renal transplant recipients. In transplant patients, the main abnormality is also hypofibrinolysis which, however, unlike the situation with the other methods of renal replacement therapy, is secondary to a rise in PAI-I. A role in the increase of the plasma levels of PAI-I in transplant patients is played by steroid- and cyclosporine-based immunosuppression, most likely by metabolic disorders such as insulin resistance or dyslipoproteinemia, and by genetic factors. Animal experiments with chronic rejection have shown abnormalities in local fibrinolysis in the graft, particularly increased PAI-I expression. Fibrinolysis defects may contribute to an early and frequent development of atherosclerosis in patients with chronic renal failure, to chronic dysfunction of the renal transplant, or to peritoneal fibrosis and peritoneal catheter obstruction in patients on peritoneal dialysis. The exact role of hypofibrinolysis in the development of these complications, and the potential for modulating it, warrant further research.
The Advanced Life Support Human-Rated Test Facility: Testbed Development and Testing to Understand Evolution to Regenerative Life Support (1996)

&lt;div class="htmlview paragraph"&gt;As part of its integrated system test bed capability, NASA's Advanced Life Support Program has undertaken the development of a large-scale advanced life support facility capable of supporting long-duration testing of integrated, regenerative biological and physicochemical life support systems. This facility--the Advanced Life Support Human-Rated Test Facility (HRTF) is currently being built at the Johnson Space Center. The HRTF is comprised of a series of interconnected chambers with a sealed internal environment capable of supporting a test crew of four for periods exceeding one year. The life support system will consist of both biological and physicochemical components and will perform air revitalization, water recovery, food production, solid waste processing, thermal management, and integrated command and control functions. Currently, a portion of this multichamber facility has been constructed and is being outfitted with basic utilities and infrastructure. This paper summarizes the recent progress in development of the HRTF and discusses how the facility will be used to help understand the evolution of regenerative life support systems from physicochemically based systems to predominantly biologically based systems.&lt;/div&gt;
TARDBP Mutation Analysis in TDP-43 Proteinopathies and Deciphering the Toxicity of Mutant TDP-43 (2012)

The identification of TAR DNA-binding protein 43 (TDP-43) as the major disease protein in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin inclusions has defined a new class of neurodegenerative conditions: the TDP-43 proteinopathies. This breakthrough was quickly followed by mutation analysis of TARDBP, the gene encoding TDP-43. Herein, we provide a review of our previously published efforts that led to the identification of 3 TARDBP mutations (p.M337V, p.N345K, and p.I383V) in familial ALS patients, two of which were novel. With over 40 TARDBP mutations now discovered, there exists conclusive evidence that TDP-43 plays a direct role in neurodegeneration. The onus is now on researchers to elucidate the mechanisms by which mutant TDP-43 confers toxicity, and to exploit these findings to gain a better understanding of how TDP-43 contributes to the pathogenesis of disease. Our biochemical analysis of TDP-43 in ALS patient lymphoblastoid cell lines revealed a substantial increase in TDP-43 truncation products, including a ≈ 25 kDa fragment, compared to control lymphoblastoid cell lines. We discuss the putative harmful consequence of abnormal TDP-43 fragmentation, as well as highlight additional mechanisms of toxicity associated with mutant TDP-43.
Blood First Assay Screening Trial (BFAST) in Treatment-Naive Advanced or Metastatic NSCLC: Initial Results of the Phase 2 ALK-Positive Cohort (2021)

These results reveal the clinical application of blood-based NGS as a method to inform clinical decision-making in ALK-positive NSCLC.
Effectiveness and Safety of Therapeutic Vaccines for Precancerous Cervical Lesions: A Systematic Review and Meta-Analysis (2022)

PROSPERO https://www.crd.york.ac.uk/PROSPERO/, CRD42021275452.
Impact of Proportional Valves' Differences to Ensure Uniform Motion of Hydraulic Motors (2021)

Ensuring uniform motion of hydraulic actuators is one of the most demanding tasks in the field of Hydraulic Drive Technology. Various, more or less demanding and precise, mechanical-hydraulic or electro-hydraulic solutions are used depending on the accuracy requirements of uniform motion. In addition to more precise uniform motion, the electro-hydraulic solutions also enable compensation and elimination of many inequalities.
Association study of the NF1 gene and autistic disorder (1999)

Neurofibromatosis type 1 (NF1) is increased about 150-fold in autistic patients. The aim of this study was to test for an association between the NF1 locus and autistic disorder. The allele distributions of three markers of the NF1 gene were studied in 85 autistic patients and 90 controls. No differences in allele distributions were observed. However, we found a new allele (allele 5) of the GXAlu marker in four autistic patients. Allele 5 was absent in a larger control population (213 individuals). The patients with allele 5 had a more severe clinical picture, mainly in the fields of motility and tonus. Our preliminary results suggest that the NF1 region is not a major susceptibility locus for autism. However, the GXAlu marker of the NF1 gene appears as a possible candidate for a susceptibility locus in a small subgroup of severely affected autistic patients. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 88:729-732, 1999.
A Química Medicinal e o Paradigma do Composto-Protótipo (2009)

Este manuscrito descreve brevemente a aplicacao da estrategia da abordagem fisiologica para a invencao de novos compostos-prototipo, candidatos a farmacos de distintas classes terapeuticas, exemplificando com a descoberta de alguns prototipos no Laboratorio de Avaliacao e Sintese de Substâncias Bioativas (LASSBio®) da Universidade Federal do Rio de Janeiro. DOI: 10.5935/1984-6835.20090005
An alternative interpretation of the HETCOR NMR spectra of poly(lactide) (1998)

An alternative to the assignments proposed recently by Chisholm et al. for the 1H and 13C NMR resonances of poly(lactide) based on their HETCOR spectra is presented; we find that the HETCOR spectra are consistent with older assignments of the tetrad and hexad stereosequence resonances in the 1H and 13C NMR spectra and we believe that the influence of adjacent chiral units on the NMR chemical shift extends asymmetrically and is opposite in the case of 1H and 13C nuclei; this is in contrast to the assumption that the observed chiral repeat unit for any particular stereosequence resonance is the same for 1H and 13C NMR spectra as used by Chisholm et al. in their analysis.
Human salivary α‐amylase Trp58 situated at subsite −2 is critical for enzyme activity (2004)

The nonreducing end of the substrate-binding site of human salivary alpha-amylase contains two residues Trp58 and Trp59, which belong to beta2-alpha2 loop of the catalytic (beta/alpha)(8) barrel. While Trp59 stacks onto the substrate, the exact role of Trp58 is unknown. To investigate its role in enzyme activity the residue Trp58 was mutated to Ala, Leu or Tyr. Kinetic analysis of the wild-type and mutant enzymes was carried out with starch and oligosaccharides as substrates. All three mutants exhibited a reduction in specific activity (150-180-fold lower than the wild type) with starch as substrate. With oligosaccharides as substrates, a reduction in k(cat), an increase in K(m) and distinct differences in the cleavage pattern were observed for the mutants W58A and W58L compared with the wild type. Glucose was the smallest product generated by these two mutants in the hydrolysis oligosaccharides; in contrast, wild-type enzyme generated maltose as the smallest product. The production of glucose by W58L was confirmed from both reducing and nonreducing ends of CNP-labeled oligosaccharide substrates. The mutant W58L exhibited lower binding affinity at subsites -2, -3 and +2 and showed an increase in transglycosylation activity compared with the wild type. The lowered affinity at subsites -2 and -3 due to the mutation was also inferred from the electron density at these subsites in the structure of W58A in complex with acarbose-derived pseudooligosaccharide. Collectively, these results suggest that the residue Trp58 plays a critical role in substrate binding and hydrolytic activity of human salivary alpha-amylase.
Vaginal Microflora Associated With Bacterial Vaginosis inNonpregnant Women: Reliability of Sialidase Detection (2000)

Our data demonstrate a strong association between G. vaginalis, M. hominis, and P. bivia and BV. Sialidase activity and Gram stain of vaginal fluid represent accurate methods for diagnosing BV.
Fin pitch effect on the frosting cycle in a fin-and-tube heat exchanger operating at low temperatures (2017)

International audience
Linear Simulation of Spaced Microphone Arrays Using B-Format Recordings (2010)

A novel approach for linear post-processing of B-Format recordings is presented. The goal is to simulate spaced microphone arrays by approximating and virtually recording the sound field at the position of each single microphone. The delays occurring in non-coincident recordings are simulated by translating an ap- proximative plane wave representation of the sound field to the positions of the microphones. The directional responses of the spaced microphones are approximated by linear combination of the corresponding translated B-format channels.
A comparison of auction and flat pricing for differentiated service networks (2004)

In a network with quality of service (QoS) support, pricing is an effective means of dealing with congestion control and revenue generation. In the Internet, the needs of the customers and their applications are constantly evolving. An auction based algorithm is the best choice for this environment because it needs minimal a priori information. In this paper, we propose an auction based pricing algorithm which lets customers choose the price as well as the services required, and in which the service provider decides on the admission price threshold and the service level of the differentiated service provided. We then investigate the system's adaptive behavior by simulating it in various environments and situations.
Nutzung von Datenbankdiensten in Data-Warehouse-Anwendungen (Connecting Data Warehouse Applications with Database Services) (2003)

Zusammenfassung Zentral für eine effiziente Analyse der in Data-Warehouse-Systemen gespeicherten Daten ist das Zusammenspiel zwischen Anwendung und Datenbanksystem. Der vorliegende Artikel klassifiziert und diskutiert unterschiedliche Wege, Data-Warehouse-Anwendungen mit dem Datenbanksystem zu koppeln, um komplexe OLAP-Szenarien zur Berechnung dem Datenbankdienst zu überlassen. Dabei werden vier unterschiedliche Kategorien, die Spracherweiterung (SQL), die anwendungsspezifische Sprachneuentwicklung (MDX), die Nutzung spezifischer Objektmodelle (JOLAP) und schließlich der Rückgriff auf XML-basierte WebServices (XCube) im einzelnen diskutiert und vergleichend gegenübergestellt.
Periosteal autograft for articular cartilage defects in dogs: MR imaging and ultrasonography of the repair process (2011)

MR imaging is capable of depicting the repair characteristics following periosteal grafting for articular cartilage defects. MR imaging may provide useful information in the assessment of the graft appearance with definite implications regarding the degree and success of incorporation.
Multiscale detection of curvilinear structures in 2-D and 3-D image data (2002)

Presents a novel, parameter-free technique for the segmentation and local description of line structures on multiple scales, both in 2D and in 3D. The algorithm is based on a nonlinear combination of linear filters and searches for elongated, symmetric line structures, while suppressing the response to edges. The filtering process creates one sharp maximum across the line-feature profile and across the scale-space. The multi-scale response reflects local contrast and is independent of the local width. The filter is steerable in both the orientation and scale domains, leading to an efficient, parameter-free implementation. A local description is obtained that describes the contrast, the position of the center-line, the width, the polarity, and the orientation of the line. Examples of images from different application domains demonstrate the generic nature of the line segmentation scheme. The 3D filtering is applied to magnetic resonance volume data in order to segment cerebral blood vessels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Influence of land use on stream ecosystem function in a Mediterranean catchment (2008)

Summary 1. Due to the hierarchical organization of stream networks, land use changes occurring at larger spatial scales (i.e. the catchment) can affect physical, chemical and biological characteristics at lower spatial scales, ultimately altering stream structure and function. Anthropogenic effects on streams have primarily been documented using structural metrics such as water chemistry, channel alteration and algal biomass. Functional parameters, including metrics of nutrient retention and metabolism, are now being widely used as indicators of stream condition. 2. Within this hierarchical context, we used a multivariate approach to examine how structural and functional (i.e. nutrient retention and metabolism) attributes of streams are related to catchment variables, including land use. The study was done in 13 streams located within a single Mediterranean catchment, but draining sub‐catchments with contrasting land use. 3. At the catchment scale, results showed two contrasting land use gradients: (i) from forested‐ to urban‐dominated catchments and (ii) from low to moderate agricultural‐dominated catchments. Variation in structural and functional parameters was strongly related to these land use gradients. Specifically, NH 4 + demand (measured as the uptake velocity, V f ) decreased along the gradient from forested‐ to urban‐dominated catchments primarily in response to increases in stream nutrient concentrations [NH 4 + , dissolved organic nitrogen (DON) and carbon (DOC)]. Both primary production and respiration increased along the gradient of agricultural development in response to increases in algal biomass (chlorophyll a ). Soluble reactive phosphorus demand was not related to any of the land use gradients. 4. Our results illustrate the connections among factors operating at different spatial scales (i.e. from catchments to streams) and their distinct influence on stream ecosystem function. Managers should take into consideration these connections when designing stream management and restoration plans. Because ecologically successful stream management and restoration is expected to restore function as well as structure to streams, the use of appropriate measures of functional processes is required. Nutrient retention and metabolism parameters are good candidates to fill this gap.