gebhart/patrepeval huggingface dataset:
Interplay of primary bovine lymphocytes and Mycobacterium avium subsp. paratuberculosis shows distinctly different proteome changes and immune pathways in host-pathogen interaction (2019)

Abstract Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogen causing paratuberculosis in cattle and small ruminants. During the long asymptomatic subclinical stage, high numbers of MAP are excreted and can be transmitted to food, where they survive many of the standard techniques of food decontamination. If these MAP are harmful to the consumers is currently under debate. In general, there is a lack of information regarding interaction of the hosts immune system with MAP. In this study, we tested the interaction of peripheral blood lymphocytes (PBL) from cattle with MAP in their exoproteomes/secretomes. Because in other mycobacterial infections, the immune phenotype correlates with susceptibility, we additionally tested the interaction of MAP with recently detected immune deviant cows. In PBL, different biological pathways were enhanced in response to MAP dependent on the immune phenotype of the host. PBL of control cows activated members of cell activation and chemotaxis of leukocytes pathway as well as IL-12 mediated signaling. In contrast, in ID cows CNOT1 was detected as highly abundant protein, pointing to a different immune response, which could be favorable for MAP. Additionally, MAP reacted different to the hosts. Their exoproteomes differed in either GroEL1 or DnaK abundance, depending on the interacting immune response. These findings point to an interdependent, tightly regulated response of MAP and the immune system.
Towards a Functional Performance Validation Standard for Industrial Low-Back Exoskeletons: State of the Art Review (2021)

While the research interest for exoskeletons has been rising in the last decades, missing standards for their rigorous evaluation are potentially limiting their adoption in the industrial field. In this context, exoskeletons for worker support have the aim to reduce the physical effort required by humans, with dramatic social and economic impact. Indeed, exoskeletons can reduce the occurrence and the entity of work-related musculoskeletal disorders that often cause absence from work, resulting in an eventual productivity loss. This very urgent and multifaceted issue is starting to be acknowledged by researchers. This article provides a systematic review of the state of the art for functional performance evaluation of low-back exoskeletons for industrial workers. We report the state-of-the-art evaluation criteria and metrics used for such a purpose, highlighting the lack of a standard for this practice. Very few studies carried out a rigorous evaluation of the assistance provided by the device. To address also this topic, the article ends with a proposed framework for the functional validation of low-back exoskeletons for the industry, with the aim to pave the way for the definition of rigorous industrial standards.
Radiation-Associated Lung Cancer: A Comparison of the Histology of Lung Cancers in Uranium Miners and Survivors of the Atomic Bombings of Hiroshima and Nagasaki (1993)

A binational panel of Japanese and American pulmonary pathologists reviewed tissue slides of lung cancer cases diagnosed among Japanese A-bomb survivors and American uranium miners and classified the cases according to histological subtype. Blind reviews were completed on slides from 92 uranium miners and 108 A-bomb survivors, without knowledge of population, sex, age, smoking history, or level of radiation exposure. Consensus diagnoses were obtained with respect to principal subtype, including squamous-cell cancer, small-cell cancer, adenocarcinoma, and less frequent subtypes. The results were analyzed in terms of population, radiation dose, and smoking history. As expected, the proportion of squamous-cell cancer was positively related to smoking history in both populations. The relative frequencies of small-cell cancer and adenocarcinoma were very different in the two populations, but this difference was accounted for adequately by differences in radiation dose or, more specifically, dose-based relative risk estimates based on published data. Radiation-induced cancers appeared more likely to be of the small-cell subtype, and less likely to be adenocarcinomas, in both populations. The data appeared to require no additional explanation in terms of radiation quality (alpha particles vs gamma rays), uniform or local irradiation, inhaled vs external radiation source, or other population difference.
Whole-Body Diffusion Imaging Applying Simultaneous Multi-Slice Excitation (2016)

•Whole-body diffusion-weighted imaging (WB-DWI) using simultaneous multi-slice and blipped-CAIPIRINHA reduces the measurement time strongly without having a significant impact on image quality. •The reduction in measurement time might strongly contribute to the clinical applicability of WB-DWI. •However, further refinement of the slice-accelerated EPI sequence, and the WB-DWI protocol applying this sequence type seems necessary; and the value of such WB-DWI protocols for assessment of systemic oncological diseases needs to be investigated in further clinical studies.
Simplicial sets and triangular patches (2002)

This work fits into the domain of topology-based geometric modeling. An assembling of non-overlapping patches can be interpreted as a subdivision of a geometric object into cells of different dimensions and a combinatorial structure can be associated with it. More precisely, our study deals with the manipulation of simplicial sets imbedded on triangular patches. We give the definition and properties of simplicial sets and triangular Bezier spaces and discuss the relationship between these two entities. The advantages of this approach are developed and some construction operations for the manipulation of this structure are presented.
Molecular definition of the shortest region of deletion overlap in the Langer-Giedion syndrome. (1991)

The Langer-Giedion syndrome (LGS), which is characterized by craniofacial dysmorphism and skeletal abnormalities, is caused by a genetic defect in 8q24.1. We have used 13 anonymous DNA markers from an 8q24.1-specific microdissection library, as well as c-myc and thyroglobulin gene probes, to map the deletion breakpoints in 16 patients with LGS. Twelve patients had a cytogenetically visible deletion, two patients had an apparently balanced translocation, and two patients had an apparently normal karyotype. In all cases except one translocation patient, loss of genetic material was detected. The DNA markers fall into 10 deletion intervals. Clone L48 (D8S51) defines the shortest region of deletion overlap (SRO), which is estimated to be less than 2 Mbp. Three clones--p17-2.3 EE (D8S43), L24 (D8S45), and L40 (D8S49) - which flank the SRO recognize evolutionarily conserved sequences.
Advantages and Disadvantages of Cytidine Deamination (2004)

Cytidine deamination of nucleic acids underlies diversification of Ig genes and inhibition of retroviral infection, and thus, it would appear to be vital to host defense. The host defense properties of cytidine deamination require two distinct but homologous cytidine deaminases-activation-induced cytidine deaminase and apolipoprotein B-editing cytidine deaminase, subunit 3G. Although cytidine deamination has clear benefits, it might well have biological costs. Uncontrolled cytidine deamination might generate misfolded polypeptides, dominant-negative proteins, or mutations in tumor suppressor genes, and thus contribute to tumor formation. How cytidine deaminases target a given nucleic acid substrate at specific sequences is not understood, and what protects cells from uncontrolled mutagenesis is not known. In this paper, I shall review the functions and regulation of activation-induced cytidine deaminase and apolipoprotein B-editing cytidine deaminase, subunit 3G, and speculate about the basis for site specificity vis-à-vis generalized mutagenesis.
A Global Clustering Algorithm to Identify Long Intergenic Non-Coding RNA - with Applications in Mouse Macrophages (2011)

Identification of diffuse signals from the chromatin immunoprecipitation and high-throughput massively parallel sequencing (ChIP-Seq) technology poses significant computational challenges, and there are few methods currently available. We present a novel global clustering approach to enrich diffuse CHIP-Seq signals of RNA polymerase II and histone 3 lysine 4 trimethylation (H3K4Me3) and apply it to identify putative long intergenic non-coding RNAs (lincRNAs) in macrophage cells. Our global clustering method compares favorably to the local clustering method SICER that was also designed to identify diffuse CHIP-Seq signals. The validity of the algorithm is confirmed at several levels. First, 8 out of a total of 11 selected putative lincRNA regions in primary macrophages respond to lipopolysaccharides (LPS) treatment as predicted by our computational method. Second, the genes nearest to lincRNAs are enriched with biological functions related to metabolic processes under resting conditions but with developmental and immune-related functions under LPS treatment. Third, the putative lincRNAs have conserved promoters, modestly conserved exons, and expected secondary structures by prediction. Last, they are enriched with motifs of transcription factors such as PU.1 and AP.1, previously shown to be important lineage determining factors in macrophages, and 83% of them overlap with distal enhancers markers. In summary, GCLS based on RNA polymerase II and H3K4Me3 CHIP-Seq method can effectively detect putative lincRNAs that exhibit expected characteristics, as exemplified by macrophages in the study.
Different activities of viral enhancer elements before and after stable integration of transfected DNAs. (1987)

Analysis of the RNA and DNA levels of a selectable gene linked to a murine retroviral enhancer demonstrated a correlation between RNA levels and tissue-specific enhancer activity during transient expression in T cells but not in stably transformed cell lines.
Cellular signalling pathways involved in muscle atrophy in cancer cachexia (2004)

Cancer cachexia encompases severe weight loss, characterised by the debilitating atrophy of adipose and skeletal muscle mass. Skeletal muscle proteolysis in cancer cachexia is mediated by a sulphated glycoprotein with a relative molecular mass of 24kDa, termed Proteolysis-Inducing Factor (PIF). PIF induced a significant increase in protein degradation, peaking at 4.2nM PIF (p&lt;0.001), ‘chymotrypsin-like’ activity of the proteasome (p&lt;0.001) and increased expression of components of the ATP-ubiquitin dependent proteolytic pathway. This was attenuated in vitro by pre-incubation with the PKC inhibitor calphostin C (100µM) and NF-kB the inhibitors SN50 (18µM), curcumin (50µM) and resveratrol (30µM), 2 hours prior to the addition of PIF. In vivo studies found the IKK inhibitor resveratrol (1mg/kg) to be successful in attenuating protein degradation (p&lt;0.001) and upregulation of ubiquitin-dependent proteolysis in MAC16 tumour bearing mice. C2C12 myoblasts transfected with mutant IkBα and PKCα inserts did not elicit a PIF-induced response, suggesting the importance of the transcription factor NF-kB and PKC involvement in PIF signal transduction. 15(S)-HETE acts as an intracellular mediator of PIF and exerts an effect through the activation of PKC and subsequently IKK, which phosphorylates IkBα and allows NF-kB to migrate to the nucleus. This effect was negated with the PKC inhibitor calphostin C (300nM). A commercially produced PIF receptor antibody was raised in rabbits immunised with a peptide containing the partial N-terminal sequence of the PIF receptor. The PIF receptor antibody was successful in attenuating the PIF-induced increase in skeletal muscle catabolism and protein degradation in vitro at 10µg/ml (p&lt;0.001) and 3.47mg/kg in vivo (p&lt;0.001). The data suggest great potential in the development of this antibody as a therapy against cancer cachexia.
Synthesis and Thermal Properties of Cyclotriphosphazene Containing Polyamides (1993)

Abstract A series of cyclotriphosphazene containing polyamides has been prepared by polycondensation of bis-(p-aminophenoxy) tetra (phenoxy) chlorocyclotriphosphazene and some diacid chlorides. The characterization, thermal stability and fire resistance of the synthesized polymers were studied. TGA showed that the polymers prepared were stable to above 320°C in nitrogen and exhibited high char contents at elevated temperature.
THE CONTEXT for Nursing Home Resident Care: THE ROLE OF LEADERS IN DEVELOPING STRATEGIES (2005)

Data obtained from three Midwestern nursing homes were used to identify and describe contextual factors that influenced resident care. A qualitative, emergent, case study design guided the study. In addition to 17 residents and 16 family members or friends of the respective residents, participants included 66 staff members and 9 managers involved in the planning and delivery of care to the participating residents. Data were collected via observation, semi-structured interview, and resident record audit. Contextual factors seemed to integrate or fragment care planning and delivery. Important integrators were shared values, the role of the Minimum Data Set coordinator, the role of other leaders, and family influence. Two fragmenting factors, competing demands for the staff members' time and a task orientation to care, appeared to be ubiquitous. External accountability also fragmented care to a discernible degree.
Direct Synthesis of Allyl Sulfides from Allyl Alcohols and Thiols (1993)

In the presence of boron trifluoride-diethyl ether complex, various allyl alcohols [(-)-myrtenol, geraniol, cinnamyl alcohol, linalool, 1-octen-3-ol, 2-hydroxybenzyl alcohol and bicyclic diols] were reacted with thiophenol, 1-butanethiol, trimethyl(phenylthio)silane or hexamethylsilane in dichloromethane at room temperature to give the corresponding allyl sulfides in good to excellent yields. The mild conditions for this transformation allowed chemoselectivity.
A toolbox for developing bioinformatics software (2011)

Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and have identified a set of practices for software development in an academic environment. We found them useful to plan a project, support the involvement of experts (e.g. experimentalists), and to promote higher quality and maintainability of the resulting programs. This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers.
Individual participant data meta‐analysis for external validation, recalibration, and updating of a flexible parametric prognostic model (2021)

Individual participant data (IPD) from multiple sources allows external validation of a prognostic model across multiple populations. Often this reveals poor calibration, potentially causing poor predictive performance in some populations. However, rather than discarding the model outright, it may be possible to modify the model to improve performance using recalibration techniques. We use IPD meta-analysis to identify the simplest method to achieve good model performance. We examine four options for recalibrating an existing time-to-event model across multiple populations: (i) shifting the baseline hazard by a constant, (ii) re-estimating the shape of the baseline hazard, (iii) adjusting the prognostic index as a whole, and (iv) adjusting individual predictor effects. For each strategy, IPD meta-analysis examines (heterogeneity in) model performance across populations. Additionally, the probability of achieving good performance in a new population can be calculated allowing ranking of recalibration methods. In an applied example, IPD meta-analysis reveals that the existing model had poor calibration in some populations, and large heterogeneity across populations. However, re-estimation of the intercept substantially improved the expected calibration in new populations, and reduced between-population heterogeneity. Comparing recalibration strategies showed that re-estimating both the magnitude and shape of the baseline hazard gave the highest predicted probability of good performance in a new population. In conclusion, IPD meta-analysis allows a prognostic model to be externally validated in multiple settings, and enables recalibration strategies to be compared and ranked to decide on the least aggressive recalibration strategy to achieve acceptable external model performance without discarding existing model information.
Technology Development Decision Economics for Real-Time Rolling Resistance Monitoring of Haul Roads (2007)

Proponents of advanced technologies for the delivery of constructed facilities assert that information and automation technologies can significantly reduce construction costs. However, technology transfer has been greatly limited as practitioners are reluctant to adopt new technologies for myriad reasons including concerns over expertise requirements, value versus traditional approaches, implementation practicality, and risk. All of these concerns ultimately relate to cost versus benefit. While considerable automation research has been documented, thorough economic justifications in the literature have been rare in comparison. In this paper, the writers present and illustrate a model to assess the economics of construction equipment automation using a case illustration focused on the allowable cost of sensor technologies for real-time, in-field rolling resistance monitoring. Rolling resistance is vital in determining power train requirements, fuel consumption, and travel time associated with hauling operations. The absence of a true understanding of field changes in rolling resistance may result in a lack of insight regarding the interaction of jobsite characteristics and the performance potential of hauling operations.
Pharmacokinetics and Lipid-Lowering Effect of Fluvastatin in Hypercholesterolaemic Patients on Maintenance Haemodialysis (2004)

Patients undergoing haemodialysis are predisposed to serum lipid abnormalities that can accelerate the development of atherosclerosis. Serum lipid levels must therefore be controlled over a long period. For patients with reduced renal function (including dialysis patients), special attention must be paid to hyperlipidaemia therapy, particularly drug selection. In this study, 30 mg/day fluvastatin was administered orally to five patients receiving maintenance haemodialysis. Their serum lipid levels and blood biochemistry were monitored during the 6 months of fluvastatin administration, and the pharmacokinetic parameters calculated. The therapeutic efficacy and safety of fluvastatin were demonstrated in this patient group. Furthermore, fluvastatin is not influenced by the dialysis membrane and does not accumulate in haemodialysis patients with hyperlipidaemia.
New classes of non-crystalline photonic band gap materials (2009)

The paper shows that existence of photonic bandgap (PBG) in a disordered structures called hyperuniform photonic structures . The common feature of hyperuniform photonic structures is that they are derived from hyperuniform point patterns. Hyperuniform point patterns are those whose number variance within a spherical sampling window of radius R (in d dimensions) grows more slowly than the window volume for large R. This classification includes all crystals and quasicrystals, as well as a special subset of disordered structures. Due to their compatibility with general boundary constraints, photonic band gap structures based on disordered hyperuniform patterns can provide a fexible optical insulator platform for planar optical circuits.
Hydrogen flux through the heat transfer tube wall in the steam generator of Monju (2013)

In fast breeder reactors (FBRs), hydrogen, one of the major impurities in sodium coolant, is used for water leak detection and tritium control in the interest of operating nuclear plant safety. It is essential to evaluate the hydrogen flux into the sodium coolant through the heat transfer tubes in a steam generator to understand the hydrogen behavior in an FBR plant. This study shows the time and temperature dependence of hydrogen flux using data obtained in the power rising test of the prototype FBR, Monju, and using the analysis code that can simulate the hydrogen distribution in an FBR plant. The hydrogen flux evaluated by the code gradually decreased with operating time, following the parabolic oxidation law and the Arrhenius relation over a wide range of steam temperatures. The results agreed with the hydrogen fluxes of other FBR plants evaluated in the past. It was also found that the hydrogen flux was mainly controlled by permeation through the heat transfer tubes, rather than the corrosion at the water side of the heat transfer tubes.
A multiresolution restoration method for cardiac SPECT imaging (1998)

In this study we present a multiresolution based method for restoring cardiac SPECT projections. Original projections were decomposed into a set of sub-band frequency images by using analyzing functions localized in both the space and frequency domain. This representation allows a simple denoising and restoration procedure by discarding high-frequency channels and performing inversion only in low frequencies. The method was evaluated in bull's eye reconstructions of a realistic cardiac chest phantom with a custom-made liver insert and 99mTc liver-to-heart activity ratios (LHAR) of 0:1, 1.5:1, 2.5:1, and 3.5:1. The cardiac phantom in free air was used as the reference standard. Reconstructions were performed by filtered backprojection using (1) no correction; (2) restoration without attenuation correction; (3) attenuation correction without restoration; and (4) restoration and attenuation correction. The attenuation correction was carried out with the Chang's method for one iteration. Results were compared with those obtained using an optimized prereconstruction Metz filter. Quantitative analysis was performed by calculating the normalized chi-square measure and mean +/- s.d. of bull's eye counts. In reconstructions with high liver activity (LHAR > 2), attenuation correction without restoration severely distorted the polar maps due to the spill-over of liver activity into the inferior myocardial wall. Both restoration methods when combined with an attenuation correction compensated this artifact and yielded uniform polar maps similar to that of the standard reference. There was no visual or quantitative difference between the performance of Metz filtering and multiresolution restoration. However, the main advantage of the multiresolution method is that it states a more concise and straightforward approach to the restoration problem. Multiresolution based methods does not require information about the object image or optimization processes, such as in conventional nuclear medicine restoration filters. In addition, the method is easy to implement using DFT techniques and potentially can be extended to noniterative spatially shift-invariant restorations in SPECT.