gebhart/patrepeval huggingface dataset:
Devitalized Stem Cell Microsheets for Sustainable Release of Osteogenic and Vasculogenic Growth Factors and Regulation of Anti‐Inflammatory Immune Response (2017)

The objective of this work was to investigate the effect of devitalized human mesenchymal stem cells (hMSCs) and endothelial colony-forming cells (ECFCs) seeded on mineralized nanofiber microsheets on protein release, osteogenesis, vasculogenesis, and macrophage polarization. Calcium phosphate nanocrystals were grown on the surface of aligned, functionalized nanofiber microsheets. The microsheets were seeded with hMSCs, ECFCs, or a mixture of hMSCs+ECFCs, cultured for cell attachment, differentiated to the osteogenic or vasculogenic lineage, and devitalized by lyophilization. The release kinetic of total protein, bone morphogenetic protein-2 (BMP2), and vascular endothelial growth factor (VEGF) from the devitalized microsheets was measured. Next, hMSCs and/or ECFCs were seeded on the devitalized cell microsheets and cultured in the absence of osteo-/vasculo-inductive factors to determine the effect of devitalized cell microsheets on hMSC/ECFC differentiation. Human macrophages were seeded on the microsheets to determine the effect of devitalized cells on macrophage polarization. Based on the results, devitalized undifferentiated hMSC and vasculogenic-differentiated ECFC microsheets had highest sustained release of BMP2 and VEGF, respectively. The devitalized hMSC microsheets did not affect M2 macrophage polarization while vascular-differentiated, devitalized ECFC microsheets did not affect M1 polarization. Both groups stimulated higher M2 macrophage polarization compared to M1.
Time-dependent inhibition of Bacillus stearothermophilus alanine racemase by (1-aminoethyl)phosphonate isomers by isomerization to noncovalent slowly dissociating enzyme-(1-aminoethyl)phosphonate complexes (1986)

An alanine racemase encoded by a gene from the thermophilic Gram-positive bacterium Bacillus stearothermophilus is overproduced to 0.3% of the soluble protein when carried on plasmid pICR4 in Escherichia coli [Inagaki, K., Tanizawa, K., Badet, B., Walsh, C. T., Tanaka, H., & Soda, K. (1986) Biochemistry (third paper of four in this issue)]. Purification of large quantities (50 mg) of racemase permits study of time-dependent inactivation by D and L isomers of the antibacterial (1-aminoethyl)phosphonate (Ala-P), the phosphonate analogue of alanine. The time-dependent activity loss by this compound now appears general to Gram-positive but not to Gram-negative racemases [Badet, B., & Walsh, C. (1985) Biochemistry 24, 1333] and is shown to occur by extremely slow dissociation of a noncovalent E X Ala-P complex. Ala-P binds initially in a weak, reversible (KI = 1 mM) competitive manner but is slowly isomerized (kinact = 6-9 min-1) to a stoichiometric enzyme complex, which in turn dissociates extremely slowly, with a half-time about 25 days. Thus, Ala-P is a slow but not a tight-binding inhibitor. The E X Ala-P complex is not reducible by borohydride but does perturb the fluorescence of bound pyridoxal 5'-phosphate coenzyme. Determination of the sequence of an active site octapeptide of the B. stearothermophilus alanine racemase shows homology with the sequence of a Gram-negative Salmonella typhimurium alanine racemase that is not susceptible to time-dependent inhibition by Ala-P. Studies with Ala-P analogues suggest the phosphonate dianion is crucial for stable formation of an isomerized long-lived E X Ala-P-inhibited complex.
Design fragments (2007)

Frameworks are a valuable way to share designs and implementations on a large scale. Client programmers, however, find it difficult to: understand non-local client-framework interactions, design solutions when they do not own the architectural skeleton, gain confidence that they have engaged with the framework correctly, represent their successful engagement with the framework in a way that can be shared with others, ensure their design intent is expressed in their source code, and connect with external files. 
A design fragment is a specification of how a client program can use framework resources to accomplish a goal. From the framework, it identifies the minimal set of classes, interfaces, and methods that should be employed. For the client program, it specifies the client-framework interactions that must be implemented. Annotations express design intent; specifically, that it is the intention of the client programs to interact with the framework as specified by the design fragment. 
The thesis of this dissertation is: We can provide pragmatic help for programmers to use frameworks by providing a form of specification, called a design fragment, to describe how a client program can correctly employ a framework and by providing tools to assure conformance between the client program and the design fragments. 
We built tools into an IDE to demonstrate how design fragments could alleviate the difficulties experienced by client programmers. We performed two case studies on commercial Java frameworks, using demo client programs from the framework authors, and client programs we found on the internet. 
This work provides three primary contributions to software engineering. First, it provides a new technique to help programmers use frameworks. Second, it provides a systematic way to increase code quality. Design fragments provide a means to communicate known-good designs to programmers. Third, it provides an empirically-based understanding of how clients use frameworks, which aids researchers in choosing research directions and aids framework authors in delivery of new frameworks.
Resource allocation and budgetary mechanisms for decentralized health systems: experiences from Balochistan, Pakistan. (2000)

This paper identifies key political and technical issues involved in the development of an appropriate resource allocation and budgetary system for the public health sector, using experience gained in the Province of Balochistan, Pakistan. The resource allocation and budgetary system is a critical, yet often neglected, component of any decentralization policy. Current systems are often based on historical incrementalism that is neither efficient nor equitable. This article describes technical work carried out in Balochistan to develop a system of resource allocation and budgeting that is needs-based, in line with policies of decentralization, and implementable within existing technical constraints. However, the development of technical systems, while necessary, is not a sufficient condition for the implementation of a resource allocation and decentralized budgeting system. This is illustrated by analysing the constraints that have been encountered in the development of such a system in Balochistan.
Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death (2023)

Pregnancy loss and perinatal death are devastating events for families. We assessed 'genomic autopsy' as an adjunct to standard autopsy for 200 families who had experienced fetal or newborn death, providing a definitive or candidate genetic diagnosis in 105 families. Our cohort provides evidence of severe atypical in utero presentations of known genetic disorders and identifies novel phenotypes and disease genes. Inheritance of 42% of definitive diagnoses were either autosomal recessive (30.8%), X-linked recessive (3.8%) or autosomal dominant (excluding de novos, 7.7%), with risk of recurrence in future pregnancies. We report that at least ten families (5%) used their diagnosis for preimplantation (5) or prenatal diagnosis (5) of 12 pregnancies. We emphasize the clinical importance of genomic investigations of pregnancy loss and perinatal death, with short turnaround times for diagnostic reporting and followed by systematic research follow-up investigations. This approach has the potential to enable accurate counseling for future pregnancies.
A Survey-Based Empirical Evaluation of Bad Smells in LabVIEW Systems Models (2021)

Bad smells are indications of poor designs that decrease the quality and maintainability of software. Compared with extensive research on bad smells in the context of Object-Oriented Programming (code smells), bad smells in systems models (model smells) need much more investigation. Although some works have proposed several model smells in a few modeling domains, the understanding and perception of different types of model smells may vary due to depth of knowledge and area of expertise. To fill this gap, we conducted an empirical study to evaluate the model smells summarized in the existing literature within the context of LabVIEW systems models through an anonymous online survey. Based on the 45 complete responses received from a diverse group of systems modelers, we observed that there exist differences regarding the perception of various model smells. Furthermore, depth of knowledge (experienced and inexperienced users) was observed as a factor that affects a user's understanding of different model smells. However, area of expertise (academia/industry, as well as domain of focus) did not show significant difference in model smells perception. Moreover, we identified additional model smells from this empirical study. In this paper, we provide several recommendations to avoid common model smells and we summarize the lessons learned from this investigation. Our exploratory research provides empirical evidence that drives deeper insights into model smells and lays out recommendations to practitioners on how to avoid some of the prominent smells, thus improving the quality of software artifacts in systems models.
Orientation dependence of piezoelectric properties and mechanical quality factors of 0.27Pb(In1/2Nb1/2)O3-0.46Pb(Mg1/3Nb2/3)O3-0.27PbTiO3:Mn single crystals (2013)

The complete set of material constants of single domain rhombohedral phase 0.27Pb(In1/2Nb1/2)O3-0.46Pb(Mg1/3Nb2/3)O3-0.27PbTiO3:Mn single crystal has been determined. The orientation dependence of piezoelectric, dielectric, and electromechanical properties was calculated based on these single domain data. The maximum piezoelectric and electromechanical properties were found to exist near the [001]C pseudo-cubic direction. In addition, the piezoelectric properties of [001]C poled crystals with “4R” multi-domain configuration were experimentally measured and compared with the calculated values. Only a small difference (3%) was found between experimental and theoretical values, indicating the high piezoelectric properties in the “4R” state are mainly from intrinsic contributions. The mechanical quality factors Q33 are significantly improved by the Mn-doping for the “4R” domain engineered crystals but almost no change for the single domain “1R” state. On the other hand, Q15 of both single domain and multidomain crystals were found to increase with Mn-doping, due to the internal bias induced by acceptor dopants, which clamps the domain wall motions and restricts polarization rotation.
P3814A novel risk stratification scheme for long QT syndrome based on genetic substrate and QTc duration (2018)

People's Republic of Doxorubicin (DOX) is a highly effective antineoplastic anthracycline drug; however, the adverse effect of the cardiotoxicity has limited its widespread application. Melatonin, a highly conserved molecule that is mainly produced by the pineal gland, is well known for its free radical scavenging and anti-oxidative roles. The aim of this study was to investigate the possible protective effects of melatonin against DOX-induced cardiomyopathy. We preliminarily established DOX-induced cardiotoxicity models in H9c2 cells, and C57 mice, which clearly showed cardiac dysfunction and injury, oxidative stress, and apoptotic damage. Treatment with melatonin obviously attenuated the DOX-induced cardiac dysfunction and pathological changes. The anti-oxidative stress activity of melatonin was achieved via reduced generation of reactive oxygen species through regulation of AMPK and PGC1 signaling. Its anti-apoptotic activity was shown by reductions in the number of TUNEL-positive cells and DNA fragments along with a decreased ratio of Bax/Bcl-2 expression. In a further mechanistic study, melatonin exerted improvement on the cardiac function, oxidative stress, and apoptosis were inhibited by Compound C treatment or AMPK/PGC1 siRNA.
CD103+ tumor-infiltrating lymphocytes are tumor-reactive intraepithelial CD8+ T cells associated with prognostic benefit and therapy response in cervical cancer (2017)

Human papilloma virus (HPV)-induced cervical cancer constitutively expresses viral E6/E7 oncoproteins and is an excellent target for T cell-based immunotherapy. However, not all tumor-infiltrating T cells confer equal benefit to patients, with epithelial T cells being superior to stromal T cells. To assess whether the epithelial T cell biomarker CD103 could specifically discriminate the beneficial antitumor T cells, association of CD103 with clinicopathological variables and outcome was analyzed in the TCGA cervical cancer data set (n = 304) and by immunohistochemistry (IHC) in an independent cohort (n = 460). Localization of CD103+ cells in the tumor was assessed by immunofluorescence. Furthermore, use of CD103 as a response biomarker was assessed in an <i>in vivo</i> E6/E7+ tumor model. Our results show that CD103 gene expression was strongly correlated with cytotoxic T cell markers (e.g. CD8/GZMB/PD1) in the TCGA series. In line with this, CD103+ cells in the IHC series co-expressed CD8 and were preferentially located in cervical tumor epithelium. High CD103+ cell infiltration was strongly associated with an improved prognosis in both series, and appeared to be a better predictor of outcome than CD8. Interestingly, the prognostic benefit of CD103 in both series seemed limited to patients receiving radiotherapy. In a preclinical mouse model, HPV E6/E7-targeted therapeutic vaccination in combination with radiotherapy increased the intratumoral number of CD103+ CD8+ T cells, providing a potential mechanistic basis for our results. In conclusion, CD103 is a promising marker for rapid assessment of tumor-reactive T cell infiltration of cervical cancers and a promising response biomarker for E6/E7-targeted immunotherapy.
Molecular Cloning and Expression of a Functional Snake Venom Serine Proteinase, with Platelet Aggregating Activity, from the <i>Cerastes cerastes</i> Viper<sup>,</sup> (2003)

The venoms of Viperidae snakes contain numerous serine proteinases that have been recognized to possess one or more of the essential activities of thrombin on fibrinogen and platelets. Among them, a platelet proaggregant protein, cerastocytin, has been isolated from the venom of the Tunisian viper Cerastes cerastes. Using the RACE-PCR technique, we isolated and identified the complete nucleotide sequence of a cDNA serine proteinase precursor. The recombinant protein was designated rCC-PPP (for C. cerastes platelet proaggregant protein), since its deduced amino acid sequence is more than 96% identical to the partial polypeptide sequences that have been determined for natural cerastocytin. The structure of the rCC-PPP cDNA is similar to that of snake venom serine proteinases. The expression of rCC-PPP in Escherichia coli system allowed, for the first time, the preparation and purification of an active protein from snake venom with platelet proaggregant and fibrinogenolytic activities. Purified rCC-PPP efficiently activates blood platelets at nanomolar (8 nM) concentrations, as do natural cerastocytin (5 nM) and thrombin (1 nM). It is able to clot purified fibrinogen and to hydrolyze α-chains. Thus, rCC-PPP could be therefore considered a cerastocytin isoform. By comparison with other snake venom serine proteinases, a Gly replaces the conserved Cys42. This implies that rCC-PPP lacks the conserved Cys42−Cys58 disulfide bridge. A structural analysis performed by molecular modeling indicated that the segment of residues Tyr67−Arg80 of rCC-PPP corresponds to anion-binding exosite 1 of thrombin that is involved in its capacity to induce platelet aggregation. Furthermore, the surface of the rCC-PPP molecule is characterized by a hydrophobic pocket, comprising the 90 loop (Phe90−Val99), Tyr172, and Trp215 residues, which might be involved in the fibrinogen clotting activity of rCC-PPP.
Cardiac 123I-MIBG scintigraphy in patients with drug induced parkinsonism (2005)

Cardiac sympathetic dysfunction was investigated using 123I-metaiodobenzylguanidine (MIBG) myocardial scintigraphy in 20 patients with drug induced parkinsonism (DIP). The mean heart to mediastinum ratio was significantly greater in patients with DIP than in those with Parkinson's disease (mean (SD): 2.07 (0.39) v 1.28 (0.15), p<0.001). MIBG uptake was not different between the DIP patients and controls. Two DIP patients whose MIBG uptake was significantly reduced showed persistent parkinsonism and responded dramatically to levodopa.
Functional anatomy of distant-acting mammalian enhancers (2013)

Transcriptional enhancers are a major class of functional element embedded in the vast non-coding portion of the human genome. Acting over large genomic distances, enhancers play critical roles in the tissue and cell type-specific regulation of genes, and there is mounting evidence that they contribute to the aetiology of many human diseases. Methods for genome-wide mapping of enhancer regions are now available, but the functional architecture contained within human enhancer elements remains unclear. Here, we review recent approaches aimed at understanding the functional anatomy of individual enhancer elements, using systematic qualitative and quantitative assessments of mammalian enhancer variants in cultured cells and in vivo. These studies provide direct insight into common architectural characteristics of enhancers including the presence of multiple transcription factor-binding sites and the mixture of both transcriptionally activating and repressing domains within the same enhancer. Despite such progress in understanding the functional composition of enhancers, the inherent complexities of enhancer anatomy continue to limit our ability to predict the impact of sequence changes on in vivo enhancer function. While providing an initial glimpse into the mutability of mammalian enhancers, these observations highlight the continued need for experimental enhancer assessment as genome sequencing becomes routine in the clinic.
Prevalence of comorbid conditions among adult patients diagnosed with phenylketonuria (2018)

The prevalence of selected comorbidities across several organ systems is significantly higher among PKU patients than for general population controls. Regular screening for common co-morbidities may be warranted as part of PKU management.
Improvement of Coherency of the Panel Level Package by Integrated Dry Process (2016)

Abstract Lately, Semi Additive process has been considered to dry processing for the downsizing of the emiconductor packages. WET process is a process depending on the chemical reaction of the chemical solution. There are many problems with the formation of the minute redistribution layer. We repeated the study of the Photodesmear technology as a new technology of the dry process, reported result in IMAPS in 2013 and 2015. We completed a panel level experiment tool equipped with a high power irradiation light source. We reported findings of the coherency improvement by integrated dry process which fused in a Photodesmear technology and a dry seed technology. We confirmed the following effects in integrated dry process. Desmear of micro via was difficult at a panel level. We were able to keep flatness characteristics of the resin before the plating low. We were able to confirm strong coherence of the via filled plating. VUV light irradiation is effective for the residue that is left when removing the protective film before the pre-dry seed layer process. Integrated dry process is a key technology to establish the next generation semi additive process.
Plasminogen Activation in Cheese Milk: Influence on Swiss Cheese Ripening (1997)

Our objective was to increase plasmin activity, proteolysis, and flavor development of Swiss cheese. Swiss cheese was manufactured from milk containing no added urokinase (control), low concentrations of urokinase (0.05 U/L), or high concentrations of urokinase (0.5 U/L). Composition of cheese, plasmin activity, and urea-PAGE of cheese proteins were analyzed after 6, 12, and 24 wk of ripening. Sensory evaluation and HPLC analysis were done after 12 and 24 wk. Plasmin activity increased in Swiss cheese made from milk that contained high concentrations of urokinase. Urea-PAGE showed that higher plasmin activity resulted in more rapid hydrolysis of b-casein during 12 wk of ripening. After 24 wk, there were no differences in b-casein contents among the cheeses. Sensory evaluation showed that propionic acid, nutty flavor, and overall flavor intensity were higher for cheese ripened for 12 wk and made from milk that contained urokinase. After 24 wk, there were no sensory differences among cheeses.
Effect of Low-temperature Plasma Pre-treatment on the Chemical Silver-plated Polyester Fabrics (2006)

Low-temperature plasma (LTP) has been increasingly employed for polymer surface modifications. In this paper, plasma gases of oxygen and argon were used for pre-treating polyester fabrics before conducting chemical silver plating, aiming to increase the amount of metal content and improve the performance of the polyester fabrics. After LTP pre-treatment, there was a thin plasma layer generation on the fabric surface which was in good contact with the fibre. Based on the observation of micro-structure using scanning electron microscopy (SEM), it was found that there was an increase in the amount of silver particles deposited on the fibre surface after the LTP pre-treatment. The surface observation implies that the LTP pre-treatment could enhance the hydrophilicity of fibre surface and help facilitate the absorption of silver particle layer to reach the necessary level of uniformity and adhesive strength.
Extragradient method in optimization: convergence and complexity (2018)

We consider the extragradient method to minimize the sum of two functions, the first one being smooth and the second being convex. Under the Kurdyka-Aojasiewicz assumption, we prove that the sequence produced by the extragradient method converges to a cri
CFA-aware features for steganalysis of color images (2015)

Color interpolation is a form of upsampling, which introduces constraints on the relationship between neighboring pixels in a color image. These constraints can be utilized to substantially boost the accuracy of steganography detectors. In this paper, we introduce a rich model formed by 3D co-occurrences of color noise residuals split according to the structure of the Bayer color filter array to further improve detection. Some color interpolation algorithms, AHD and PPG, impose pixel constraints so tight that extremely accurate detection becomes possible with merely eight features eliminating the need for model richification. We carry out experiments on non-adaptive LSB matching and the content-adaptive algorithm WOW on five different color interpolation algorithms. In contrast to grayscale images, in color images that exhibit traces of color interpolation the security of WOW is significantly lower and, depending on the interpolation algorithm, may even be lower than non-adaptive LSB matching.