gebhart/patrepeval huggingface dataset:
Idiopatinės skoliozės gydymo programos parinkimas. Sisteminė analizė (2013)

Kiekvienoje pasaulio šalyje vaikų, turinčių laikysenos sutrikimų daugėja. Idiopatinė skoliozė yra diagnozuojama 2-3 proc. augančio amžiaus vaikų. Kalbant apie skoliozę yra labai svarbu parinkti tinkamą diagnozavimo metodiką, tinkamą gydymą. Daugelis autorių teigia, kad yra reikalingas konservatyvus gydymas, ne operacinis. Tikslas. Atlikti įvairiose duomenų bazėse rastų straipsnių sisteminę analizę, publikuotų 2006-2010 metais apie atliktus tyrimus vaikams, turintiems idiopatinę skoliozę. Uždaviniai. 1. Sukurti sisteminei apžvalgai atrankos kriterijus. 2. Pagal suskurtus atrankos kriterijus atlikti paiešką duomenų bazėse. 3. Atrinkti mokslines publikacijas, susijusias su vaikų idiopatine skolioze. 4. Atlikti rastų mokslinių publikacijų analizę. Metodika. Mokslinių straipsnių atranka buvo vykdoma pagal iš anksto numatytus kriterijus. Atrinktuose strapsniuose nagrinėjamos problemos, susijusios su laikysennos sutrikimu – skolioze. Sukūrus paieškos strategiją PubMed duomenų bazei, ji buvo naudojama ir kitose Lietuvos sveikatos mokslų universiteto prenumeruojamose duomenų bazėse – Cochrane Library, Lippicott Williams & Wilkins, taip pat buvo naudojama EBSCO HOST duomenų bazė. Vykdyta 2006-2012 metais publikuotų mokslinių straipsnių paieška. Pasirinkti raktiniai žodžiai: (angl.) children, asymmetric posture, exercise. Straipsniai ieškoti pilnu tekstu, anglų kalba, straipsniai ne senesni kaip 5 metų, tačiau dėl mažo kiekio straispnių pasirinkti ir du 2006 metų straipsniai. Mokslinių publikacijų atranka atlikta atmetant straipsnius, nesusijusius su skolioze. Rezultatai. Atlikus paiešką, rasta 63 mokslinės publikacijos. Iš šių publikacijų atrinkta 11 straipsnių aiateminei analizei. Kiti 52 atmesti, nes neatitiko atrankos kriterijų – straipsniai nebuvo susiję su vaikų skoliozine laikysena. [...].
Nodal marginal zone lymphoma: gene expression and miRNA profiling identify diagnostic markers and potential therapeutic targets (2011)

Nodal marginal zone lymphoma (NMZL) is a small B-cell neoplasm whose molecular pathogenesis is still essentially unknown and whose differentiation from other small B-cell lymphomas is hampered by the lack of specific markers. We have analyzed gene expression, miRNA profile, and copy number data from 15 NMZL cases. For comparison, 16 follicular lymphomas (FLs), 9 extranodal marginal zone lymphomas, and 8 reactive lymph nodes and B-cell subtypes were included. The results were validated by quantitative RT-PCR in an independent series, including 61 paraffin-embedded NMZLs. NMZL signature showed an enriched expression of gene sets identifying interleukins, integrins, CD40, PI3K, NF-κB, and TGF-β, and included genes expressed by normal marginal zone cells and memory B cells. The most highly overexpressed genes were SYK, TACI, CD74, CD82, and CDC42EP5. Genes linked to G(2)/M and germinal center were down-regulated. Comparison of the gene expression profiles of NMZL and FL showed enriched expression of CHIT1, TGFB1, and TACI in NMZL, and BCL6, LMO2, and CD10 in FL. NMZL displayed increased expression of miR-221, miR-223, and let-7f, whereas FL strongly expressed miR-494. Our study identifies new candidate diagnostic molecules for NMZL and reveals survival pathways activated in NMZL.
Correction: HIV-Infected Men Who Have Sex with Men Who Identify Themselves as Belonging to Subcultures Are at Increased Risk for Hepatitis C Infection (2013)

Background: Hepatitis C virus (HCV) emerged as sexually transmitted infection among HIV-infected men who have sex with men (MSM). We studied whether HCV circulated in identifiable high-risk MSM subcultures and performed phylogenetic analysis.
Non-stop monitoring and debugging on shared-memory multiprocessors (2002)

Monitoring and debugging parallel programs is a difficult activity. There are many situations where the traditional "stop the world, I want to get off" approach to debugging is simply unsuitable. Frequently, nonintrusive monitoring of the program execution is more productive in locating sources of error and also in monitoring "correct" programs for such purposes as performance measurement and tuning. This paper presents a number of space- and time-efficient tools and techniques to support nonintrusive, non-stop monitoring and debugging of parallel programs running on a shared-memory multiprocessor. The techniques include the use of spy tasks, circular history buffers, vectors of use bits, and data structure audits. Particular emphasis is placed on issues that pertain to parallel computing, such as dealing with concurrent execution, shared memory and data caches.
Quantifying the Hydrophobic Effect. 2. A Computer Simulation−Molecular-Thermodynamic Model for the Micellization of Nonionic Surfactants in Aqueous Solution (2007)

In this article, the validity and accuracy of the CS-MT model introduced in article 1 for oil aggregates and in article 2 for nonionic surfactants is further evaluated by using it to model the micellization behavior of ionic and zwitterionic surfactants in aqueous solution. In the CS-MT model, two separate free-energy contributions to the hydrophobic driving force for micelle formation are computed using hydration data obtained from computer simulation: gdehydr, the free-energy change associated with dehydration, and ghydr, the change in the hydration free energy. To enable straightforward estimation of gdehydr and ghydr for ionic and zwitterionic surfactants, a number of simplifying approximations were made. Reasonable agreement between the CMCs predicted using the CS-MT model and the experimental CMCs was obtained for sodium dodecyl sulfate (SDS), dodecylphophocholine (DPC), cetyltrimethylammonium bromide (CTAB), two 3-hydroxy sulfonate surfactants (AOS-12 and AOS-16), and a homologous series of four DCNA bromide surfactants with a dimethylammonium head attached to a dodecyl alkyl tail and to an alkyl side chain of length CN, having the chemical formula C12H25CNH2N+1N(CH3)2Br, with N = 1 (DC1AB), 2 (DC2AB), 4 (DC4AB), and 6 (DC6AB). For six of these nine surfactants, the CMCs predicted using the CS-MT model are closer to the experimental CMCs than the CMCs predicted using the traditional molecular-thermodynamic (MT) model. For DC2AB, DC4AB, and DC6AB, which are the most structurally complex of the ionic surfactants modeled, the CMCs predicted using the CS-MT model are in remarkably good agreement with the experimental CMCs, and the CMCs predicted using the traditional MT model are quite inaccurate. Our results suggest that the CS-MT model accurately quantifies the hydrophobic driving force for micelle formation for ionic and zwitterionic surfactants in aqueous solution. For complex ionic and zwitterionic surfactants where it is difficult to accurately quantify the hydrophobic driving force for micelle formation using the traditional MT modeling approach, the CS-MT model represents a very promising alternative.
Decarbonization Reactions between Sodium Metaborate and Sodium Carbonate (2004)

Autocausticizing, used for the recovery of kraft pulping chemicals, is nearing commercialization. This technology produces sodium hydroxide directly on dissolving the molten salts produced in the kraft recovery furnace in water. Thus, the dependence on the lime cycle for sodium hydroxide is reduced. Ongoing trials in several kraft mills are in progress to implement this technology. In this study, the reactions between sodium metaborate (NaBO2) and sodium carbonate (Na2CO3)the anticipated reactantswere studied in a tubular reactor heated in an electric furnace. It was found that the reaction begins in the solid phase, followed by a liquid phase reaction. The reaction rate is extremely rapid once the system melts. It was proposed that these reactions could proceed through the intermediate formation of sodium diborate (Na4B2O5).
Strategies and Limitations in Dendrimeric Immunogen Synthesis. The Influenza Virus M2e Epitope as a Case Study (2009)

Dendrimeric platforms such as multiple antigen peptides (MAPs) are regarded as one of the most efficacious approaches for antigenic presentation. Originally described as available by stepwise solid-phase peptide synthesis (SPPS), MAPs have also been prepared by chemical (thioether, oxime, hydrazone) ligation of appropriately functionalized tetra- or octavalent polylysine scaffolds with the peptide antigen to be multiply displayed. In this work, the advantages and limitations of two of the most frequent methods of MAP preparation, namely, chemoselective thioether ligation in solution, and all-solid-phase synthesis, have been tested in the case of a particularly troublesome epitope model, the ectodomain of protein M2 from influenza virus (M2e). The strong tendency of M2e to self-associate is a serious inconvenient for conjugation in solution, which as a result fails to produce the target MAPs with the specified number of M2e copies. In contrast, the fully stepwise SPPS approach is shown to be quite practical, especially when 6-aminohexanoic acid spacer units providing increased internal flexibility are inserted at each branching point.
SULFATION PATHWAYS: Alternate steroid sulfation pathways targeted by LC–MS/MS analysis of disulfates: application to prenatal diagnosis of steroid synthesis disorders (2018)

The steroid disulfates (<i>aka</i> bis-sulfates) are a significant but minor fraction of the urinary steroid metabolome that have not been widely studied because major components are not hydrolyzed by the commercial sulfatases commonly used in steroid metabolomics. In early studies, conjugate fractionation followed by hydrolysis using acidified solvent (solvolysis) was used for the indirect detection of this fraction by GC-MS. This paper describes the application of a specific LC-MS/MS method for the direct identification of disulfates in urine, and their use as markers for the prenatal diagnosis of disorders causing reduced estriol production: STSD (steroid sulfatase deficiency), SLOS (Smith-Lemli-Opitz syndrome) and PORD (P450 oxidoreductase deficiency). Disulfates were detected by monitoring a constant ion loss (CIL) from the molecular di-anion. While focused on disulfates, our methodology included an analysis of intact steroid glucuronides and monosulfates because steroidogenic disorder diagnosis usually requires an examination of the complete steroid profile. In the disorders studied, a few individual steroids (as disulfates) were found particularly informative: pregn-5-ene-3β,20<i>S</i>-diol, pregn-5-ene-3β,21-diol (STSD, neonatal PORD) and 5α-pregnane-3β,20<i>S</i>-diol (pregnancy PORD). Authentic steroid disulfates were synthesized for use in this study as aid to characterization. Tentative identification of 5ξ-pregn-7-ene-3ξ,20<i>S</i>-diol and 5ξ-pregn-7-ene-3ξ,17,20<i>S</i>-triol disulfates was also obtained in samples from SLOS affected pregnancies. Seven ratios between the detected metabolites were applied to distinguish the three selected disorders from control samples. Our results show the potential of the direct detection of steroid conjugates in the diagnosis of pathologies related with steroid biosynthesis.
Association between emergency department pediatric readiness and transfer of noninjured children in small rural hospitals (2021)

Abstract Purpose Pediatric readiness scores may be a useful measure of a hospital's preparedness to care for children. However, there is limited evidence linking these scores with patient outcomes or other metrics, including the need for interfacility transfer. This study aims to determine the association of pediatric readiness scores with the odds of interfacility transfer among a cohort of noninjured children (&lt; 18 years old) presenting to emergency departments (EDs) in small rural hospitals in the state of California. Methods Data from the National Pediatric Readiness Project assessment were linked with the California Office of Statewide Health Planning and Development's ED and inpatient databases to conduct a cross‐sectional study of pediatric interfacility transfers. Hospitals were manually matched between these data sets. Logistic regression was performed with random intercepts for hospital and adjustment for patient‐level confounders. Findings A total of 54 hospitals and 135,388 encounters met the inclusion criteria. EDs with a high pediatric readiness score (&gt;70) had lower adjusted odds of transfer (aOR: 0.55, 95% CI: 0.33–0.93) than EDs with a low pediatric readiness score (≤ 70). The pediatric readiness section with strongest association with transfer was the “policies, procedures, and protocols” section; EDs in the highest quartile had lower odds of transfer than EDs in the lowest quartile (aOR: 0.54, 95% CI: 0.31–0.91). Conclusions Pediatric patients presenting to EDs at small rural hospitals with high pediatric readiness scores may be less likely to be transferred. Additional studies are recommended to investigate other pediatric outcomes in relation to hospital ED pediatric readiness.
miR-138–Mediated Regulation of KINDLIN-2 Expression Modulates Sensitivity to Chemotherapeutics (2015)

Targeted inhibition of Kindlin-2 in combination with chemotherapy represents an effective treatment option for mCRPC.
Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and the Ph1 locus (2018)

ABSTRACT Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologues and homoeologues at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-Seq data derived from six different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologues is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. This suggests that post-transcriptional and post-translational processes are likely to be more important. Thus, further studies will be required to reveal whether these observations are specific to wheat meiosis, and whether there are significant changes in post-transcriptional and post-translational modifications in wheat and other polyploid species associated with their polyploidisation.
Static and Rotordynamic Characteristics for a New Hole-Pattern Annular Gas Seal Design Incorporating Larger Diameter Holes (2013)

To reduce manufacturing cost and time, a new larger-diameter hole-pattern seal incorporating hole diameters of 12.27 mm, versus prior hole diameters of 3.175 mm has been proposed. The 12.27 mm hole-diameter seal had substantially better stability performance with higher effective damping and a markedly lower crossover frequency. It had negative direct stiffness coefficients at low frequency, while the 3.175 mm hole-diameter seal did not. Predictions for the rotordynamic coefficients of this new seal were made based on a two-control-volume model developed by Kleynhans and Childs in 1997. The two control volumes consisted of a through-flow control-volume and a control-volume B that extended from the surface of the stator at the top of the holes to the bottom of holes. Predictions agreed poorly with measured results, because the model used, assumes gas flows only radially within control-volume B. With the large hole-diameters axial and circumferential flow is readily accomplished. Compared to the prior 3.175 mm hole-diameter seals, the 12.27 mm hole-diameter seal design leaked approximately 37.5% more which probably precludes its commercial application. Leakage for the seal was well predicted. Although the larger hole diameters were initially proposed to reduce costs, the fabrication was more challenging than originally thought. The larger holes could not be manufactured with a single pass. Hence, manufacturing costs and time were not reduced.
Damage-Associated Molecular Patterns in Myocardial Infarction and Heart Transplantation: The Road to Translational Success (2020)

In the setting of myocardial infarction (MI), ischemia reperfusion injury (IRI) occurs due to occlusion (ischemia) and subsequent re-establishment of blood flow (reperfusion) of a coronary artery. A similar phenomenon is observed in heart transplantation (HTx) when, after cold storage, the donor heart is connected to the recipient's circulation. Although reperfusion is essential for the survival of cardiomyocytes, it paradoxically leads to additional myocardial damage in experimental MI and HTx models. Damage (or danger)-associated molecular patterns (DAMPs) are endogenous molecules released after cellular damage or stress such as myocardial IRI. DAMPs activate pattern recognition receptors (PRRs), and set in motion a complex signaling cascade resulting in the release of cytokines and a profound inflammatory reaction. This inflammatory response is thought to function as a double-edged sword. Although it enables removal of cell debris and promotes wound healing, DAMP mediated signalling can also exacerbate the inflammatory state in a disproportional matter, thereby leading to additional tissue damage. Upon MI, this leads to expansion of the infarcted area and deterioration of cardiac function in preclinical models. Eventually this culminates in adverse myocardial remodeling; a process that leads to increased myocardial fibrosis, gradual further loss of cardiomyocytes, left ventricular dilation and heart failure. Upon HTx, DAMPs aggravate ischemic damage, which results in more pronounced reperfusion injury that impacts cardiac function and increases the occurrence of primary graft dysfunction and graft rejection via cytokine release, cardiac edema, enhanced myocardial/endothelial damage and allograft fibrosis. Therapies targeting DAMPs or PRRs have predominantly been investigated in experimental models and are potentially cardioprotective. To date, however, none of these interventions have reached the clinical arena. In this review we summarize the current evidence of involvement of DAMPs and PRRs in the inflammatory response after MI and HTx. Furthermore, we will discuss various current therapeutic approaches targeting this complex interplay and provide possible reasons why clinical translation still fails.
A form of sensorineural deafness is determined by a mitochondrial and an autosomal locus: Evidence from pedigree segregation analysis (1993)

We have previously reported a large Israeli-Arab pedigree with sensorineural deafness possibly determined simultaneously by two loci--one mitochondrial, and one autosomal recessive. This was analyzed by extending classic segregation analysis methods to the many nuclear families derived from the maternal line pedigree. Here we expand this pedigree and extend our analysis by using the regressive models for segregation analysis on the entire pedigree. The corresponding REGD computer program was utilized and the marrying-in males' and paternal line members' affection statuses were assigned as unknown to accommodate the exclusive maternal transmission pattern. For the autosomal locus, a simple autosomal recessive (q = 0.52) model with a nearly complete penetrance (0.93) was found to be the best-fitting model. Equally importantly, we were also able to use the power of the regressive models to test the hypothesis of mitochondrial heteroplasmy as an alternative for the proposed autosomal locus. We found no evidence for the heteroplasmy hypothesis as an explanation for the incomplete maternal transmission of deafness in this pedigree. Thus, even if the mitochondrial mutation occurred in a heteroplasmic distribution in the family members, this could not explain the familial aggregation in this pedigree, and an autosomal recessive locus is still required. These results provide further support for the concept that the sensorineural deafness occurring in this large Israeli-Arab pedigree results from simultaneous involvement of two genes at two different loci, one mitochondrial and likely homoplasmic, and the other autosomal and recessive.
Common Elements Regulating Gene Expression in Temperate and Lytic Bacteriophages of Lactococcus Species (1998)

ABSTRACT A phage-inducible middle promoter (P 15A10 ) from the lytic, lactococcal bacteriophage φ31, a member of the P335 species, is located in an 888-base pair fragment near the right cohesive end. Sequence analysis revealed extensive homology (&gt;95%) to the right cohesive ends of two temperate phages of the P335 species, φr1t and φLC3. Sequencing upstream and downstream of P 15A10 showed that the high degree of homology between φ31 and φr1t continued beyond the phage promoter. With the exception of one extra open reading frame in φ31, the sequences were highly homologous (95 to 98%) between nucleotides 13448 and 16320 of the published φr1t sequence. By use of a β-galactosidase (β-Gal) gene under the control of a smaller, more tightly regulated region within the P 15A10 promoter, P 566–888 , it was established that mitomycin C induction of a lactococcal strain harboring the prophage φr1t induced the P 566–888 promoter, as determined from an increase in β-Gal activity. Hybridization of nine other lactococcal strains with 32 P-labeled P 566–888 showed that the Lactococcus lactis strains C10, ML8, and NCK203 harbored sequences homologous to that of the phage-inducible promoter. Mitomycin C induced the resident prophages in all these strains and concurrently induced the P 566–888 promoter, as determined from an increase in β-Gal activity. DNA restriction analysis revealed that the prophages in C10, ML8, and NCK203 had identical restriction patterns which were different from that of φr1t. In addition, DNA sequencing showed that the promoter elements in the three phages were identical to each other and to P 566–888 from the lytic phage φ31. These results point to a conserved mechanism in the regulation of gene expression between the lytic phage φ31 and at least two temperate bacteriophages and provide further evidence for a link in the evolution of certain temperate phages and lytic phages.
Attitude control without angular velocity measurement for flexible satellites (2018)

In this paper, by using quaternion models, the problem of attitude control is investigated for a class of flexible satellites. Two control laws are presented for the considered flexible satellite models to guarantee convergence of the closed-loop systems without using angular velocity measurement. One is in the form of a partial state feedback for the case where the modal variable is available, and the other is in the form of an observer-based partial state feedback for the case where the modal variable cannot be measured. Finally, an example is employed to illustrate the effectiveness of the proposed control laws.