Miracle-dz/UniFAR-FTUs huggingface dataset:
25-Dihydroxyvitamin D 3 is a negative endocrine regulator of the renin-angiotensin system

The renin-angiotensin system is a regulatory cascade that plays an essential role in the regulation of blood pressure, electrolyte, and volume homeostasis. The first and rate-limiting component of this cascade is renin, a protease synthesized and secreted predominantly by the juxtaglomerular (JG) apparatus in the nephron. Renin cleaves angiotensin I (Ang I) from liver-derived angiotensinogen, which is then converted to Ang II by the angiotensin-converting enzyme. Ang II, through binding to its receptors, exerts diverse actions that affect the electrolyte, volume, and blood pressure homeostasis (1). Inappropriate stimulation of the renin-angiotensin system has been associated with hypertension, heart attack, and stroke. The renin-producing granulated cells are mainly located in the afferent glomerular arterioles in the kidney (2). It is well established that renin secretion is regulated by renal perfusion pressure, renal sympathetic nerve activity, and tubular sodium load (1, 2). Renin secretion is stimulated by factors such as prostaglandins, NO, and adrenomedullin, and inhibited by other factors, including Ang II (feedback), endothelin, vasopressin, and adenosine (1, 2). Stimulation of renin secretion is often mediated by an increase in intracellular cAMP and is accompanied by increases in renin gene transcription (3). In the renin gene promoter, several cAMP response elements have been identified. Recently, steroid hormone receptors LXRα and RAR/RXR complex, transcriptional factors CREB/CREM and USF1/USF2, and HOX gene family members have been found to be involved in the activation of murine renin gene transcription (4–7). Vitamin D is a primary regulator of calcium homeostasis. Genetic inactivation of either the vitamin D receptor (VDR), a member of the nuclear receptor superfamily that mediates the action of 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], or 25-hydroxyvitamin D3 1α-hydroxylase, the rate-limiting enzyme for the biosynthesis of 1,25(OH)2D3, results in impaired calcium homeostasis, leading to hypocalcemia, secondary hyperparathyroidism, and rickets (8–11). However, the wide tissue distribution of VDR suggests that the vitamin D endocrine system has additional physiological functions beyond calcium homeostasis. Indeed, vitamin D and VDR have been shown to play important roles in the immune system, cardiovascular system, reproductive system, and hair growth.
Table: Object oriented editing of complex structures

This research adopts the point of view that much of software development is a process of editing complex structures, structures that represent a tightly coupled integration of textual and graphical material. In the context of text and table objects, this research explores a Smalltalk-like, object oriented architecture for editors of such complex structures. Based on this experience, we propose certain design and operation principles for such editors.
Proteomic Analysis of Matched Formalin-Fixed, Paraffin-Embedded Specimens in Patients with Advanced Serous Ovarian Carcinoma

Objective: The biology of high grade serous ovarian carcinoma (HGSOC) is poorly understood. Little has been reported on intratumoral homogeneity or heterogeneity of primary HGSOC tumors and their metastases. We evaluated the global protein expression profiles of paired primary and metastatic HGSOC from formalin-fixed, paraffin-embedded (FFPE) tissue samples. Methods: After IRB approval, six patients with advanced HGSOC were identified with tumor in both ovaries at initial surgery. Laser capture microdissection (LCM) was used to extract tumor for protein digestion. Peptides were extracted and analyzed by reversed-phase liquid chromatography coupled to a linear ion trap mass spectrometer. Tandem mass spectra were searched against the UniProt human protein database. Differences in protein abundance between samples were assessed and analyzed by Ingenuity Pathway Analysis software. Immunohistochemistry (IHC) for select proteins from the original and an additional validation set of five patients was performed. Results: Unsupervised clustering of the abundance profiles placed the paired specimens adjacent to each other. IHC H-score analysis of the validation set revealed a strong correlation between paired samples for all proteins. For the similarly expressed proteins, the estimated correlation coefficients in two of three experimental samples and all validation samples were statistically significant (p < 0.05). The estimated correlation coefficients in the experimental sample proteins classified as differentially expressed were not statistically significant. Conclusion: A global proteomic screen of primary HGSOC tumors and their metastatic lesions identifies tumoral homogeneity and heterogeneity and provides preliminary insight into these protein profiles and the cellular pathways they constitute.
A Transformation Framework for Optimizing Task-Parallel Programs

Task parallelism has increasingly become a trend with programming models such as OpenMP 3.0, Cilk, Java Concurrency, X10, Chapel and Habanero-Java (HJ) to address the requirements of multicore programmers. While task parallelism increases productivity by allowing the programmer to express multiple levels of parallelism, it can also lead to performance degradation due to increased overheads. In this article, we introduce a transformation framework for optimizing task-parallel programs with a focus on task creation and task termination operations. These operations can appear explicitly in constructs such as async, finish in X10 and HJ, task, taskwait in OpenMP 3.0, and spawn, sync in Cilk, or implicitly in composite code statements such as foreach and ateach loops in X10, forall and foreach loops in HJ, and parallel loop in OpenMP. Our framework includes a definition of data dependence in task-parallel programs, a happens-before analysis algorithm, and a range of program transformations for optimizing task parallelism. Broadly, our transformations cover three different but interrelated optimizations: (1) finish-elimination, (2) forall-coarsening, and (3) loop-chunking. Finish-elimination removes redundant task termination operations, forall-coarsening replaces expensive task creation and termination operations with more efficient synchronization operations, and loop-chunking extracts useful parallelism from ideal parallelism. All three optimizations are specified in an iterative transformation framework that applies a sequence of relevant transformations until a fixed point is reached. Further, we discuss the impact of exception semantics on the specified transformations, and extend them to handle task-parallel programs with precise exception semantics. Experimental results were obtained for a collection of task-parallel benchmarks on three multicore platforms: a dual-socket 128-thread (16-core) Niagara T2 system, a quad-socket 16-core Intel Xeon SMP, and a quad-socket 32-core Power7 SMP. We have observed that the proposed optimizations interact with each other in a synergistic way, and result in an overall geometric average performance improvement between 6.28× and 10.30×, measured across all three platforms for the benchmarks studied.
Water Absorption and Modification of Kenaf and Flax Fibres

The experimental work for this project involved several strands; to study the water absorption characteristic of kenaf and flax in composites, to investigate the influence of fibre types on water absorption, and finally to investigate the influence of chemical treatment on water absorption. Hydrophilic character of natural fibres is responsible for the water absorption in the composites. Water absorption of kenaf and flax reinforced polyester composites was occurred via fibres lumen. Mechanical properties are affected by water absorption. After water absorption test, the specimens present poor mechanical properties such as lower value of flexural strength and flexural modulus. The matrix structure was also affected by water absorption by processes such as chain orientation and shrinkage. It was found that the different fibre types had influenced the different percentage of water absorption in composite. It seems that the compatibilization between fibres and matrix has influenced the water absorption of fibres. Acetylation of kenaf and flax fibres has reduced the hygroscopic nature of natural fibres and increased the dimensional stability of composites. The flexural strength properties of acetylated fibres were higher than untreated fibres composites.
Robust Navigation Execution by Planning in Belief Space

We consider robot navigation in environments given a known static map, but where dynamic obstacles of varying and unknown lifespans appear and disappear over time. We describe a roadmap-based formulation of the problem that takes the sensing and transition uncertainty into account, and an efficient online planner for this problem. The planner displays behaviors such as persistence and obstacle timeouts that would normally be hardcoded into an executive. It is also able to make inferences about obstacle types even with impoverished sensors. We present empirical results on simulated domains and on a PR2 robot.
Pilot Study with Adriamycin and Ifosfamide in Small Cell Lung Cancer

Twenty-one patients with limited (12 cases) or extensive (9 cases) small cell lung cancer entered a pilot study with adriamycin (ADM) plus ifosfamide (IFX) as first line treatment for six planned cycles. ADM was administered at the dose of 60 mg/m2 iv push on day 1 and IFX at 3 g/m2/iv in 1-hour infusion on days 1 and 2. To prevent IFX-induced hemorrhagic cystitis, mercaptoethane sulfonate sodium (Mesna) was given after the admnistration of IFX at the dose of 500 mg/m2 by iv push four times (hour 0, 4, 8, 12) on days 1 and 2. In the absence of disease progression, chemotherapy was repeated every 3 weeks for 6 cycles. All patients were evaluable for analysis of response, toxicity and survival. The overall response rate clinically and radiologically assessed after four treatment cycles was 95.3% (CR 28.6%, PR 66.7%). However, by continuing the same drug treatment up to the sixth cycle, 7 of 14 partial responders showed tumor progression within the intrathoracic region. Therefore, at the end of the planned chemotherapy program the partial remission rate fell to 33.3%, for a total remission rate of 61.9% and a median total survival of 9 months (range 5 to 36+). The regimen was well tolerated with only one case presenting hemorrhagic cystitis. The results achieved with this drug combination appear comparable to those obtained with other conventional regimens. However, the high response rate achieved after four cycles and the low incidence of marrow toxicity suggest the use of this regimen for a short period with increased dose levels.
Time course of nicotinamide adenine dinucleotide diaphorase staining after renal radiofrequency ablation influences viability assessment.

BACKGROUND AND PURPOSE Nicotinamide adenine dinucleotide (NADH) diaphorase staining has been used to confirm cell viability or death after radiofrequency ablation (RFA) of renal tissue. The time course over which NADH staining status converts from viable to non-viable after a lethal insult has not been defined for renal RFA, but the change may not be immediate. Our objective was to assess porcine renal tissue for viability using NADH diaphorase staining at various times after RFA. MATERIALS AND METHODS Seven pigs underwent monopolar RFA of both kidneys followed by needle biopsy of the ablation zone before and immediately after ablation and at 15-minute intervals thereafter. Initially, a single kidney was treated, and the contralateral kidney was treated 2 weeks later. Biopsies were taken from untreated renal parenchyma in a similar time course after nephrectomy to examine the effect of ischemia. All biopsy specimens, as well as representative sections of the ablation zone, were subjected to NADH staining and reviewed by a pathologist who was blinded to the tissue treatment. RESULTS Most of the post-RFA biopsy specimens (86%) showed non-viable tissue. However, 14% of the specimens revealed viable tissue as late as 150 minutes after RFA. Therefore, none were positive. In the nephrectomy parenchyma, 92% of the biopsy specimens showed viable tissue as late as 4 hours after the onset of ischemia. CONCLUSION Staining for NADH can establish tissue non-viability after RFA, but the timing of staining after treatment must be considered when interpreting results to avoid false positive tests. Tissue that is apparently viable by NADH staining within 2.5 hours of RFA may in fact have been ablated.
Measurement of the Σπ photoproduction line shapes near the Λ(1405)

The reaction {gamma} + p -> K{sup +} + {Sigma} + {p}i was used to determine the invariant mass distributions or "line shapes" of the {Sigma}{sup +} {pi}{sup -}, {Sigma}{sup -} {pi}{sup +} and {Sigma}{sup 0} {pi}{sup 0} final states, from threshold at 1328 MeV/c^2 through the mass range of the {Lambda}(1405) and the {Lambda}(1520). The measurements were made with the CLAS system at Jefferson Lab using tagged real photons, for center-of-mass energies 1.95 < W < 2.85 GeV. The three mass distributions differ strongly in the vicinity of the I=0 {Lambda}(1405), indicating the presence of substantial I=1 strength in the reaction. Background contributions to the data from the {Sigma}{sup 0}(1385) and from K* {Sigma} production were studied and shown to have negligible influence. To separate the isospin amplitudes, Breit-Wigner model fits were made that included channel-coupling distortions due to the Nkbar threshold. A best fit to all the data was obtained after including a phenomenological I=1, J{sup P} = 1/2{sup -} amplitude with a centroid at 1394\pm20 MeV/c^2 and a second I=1 amplitude at 1413\pm10 MeV/c^2. The centroid of the I=0 {Lambda}(1405) strength was found at the {Sigma} {pi} threshold, with the observed shape determined largely by channel-coupling, leadingmore » to an apparent overall peak near 1405 MeV/c^2. « less
Plasma kallikrein-kinin system and diabetic retinopathy

Abstract Diabetic retinopathy (DR) occurs, to some extent, in most people with at least 20 years’ duration of diabetes mellitus. The progression of DR to its sight-threatening stages is usually associated with the worsening of underlying retinal vascular dysfunction and disease. The plasma kallikrein-kinin system (KKS) is activated during vascular injury, where it mediates important functions in innate inflammation, blood flow, and coagulation. Recent findings from human vitreous proteomics and experimental studies on diabetic animal models have implicated the KKS in contributing to DR. Vitreous fluid from people with advanced stages of DR contains increased levels of plasma KKS components, including plasma kallikrein (PK), coagulation factor XII, and high-molecular-weight kininogen. Both bradykinin B1 and B2 receptor isoforms (B1R and B2R, respectively) are expressed in human retina, and retinal B1R levels are increased in diabetic rodents. The activation of the intraocular KKS induces retinal vascular permeability, vasodilation, and retinal thickening, and these responses are exacerbated in diabetic rats. Preclinical studies have shown that the administration of PK inhibitors and B1R antagonists to diabetic rats ameliorates retinal vascular hyperpermeability and inflammation. These findings suggest that components of plasma KKS are potential therapeutic targets for diabetic macular edema.
Differential Roles of NMDA Receptor Subtypes in Ischemic Neuronal Cell Death and Ischemic Tolerance

Background and Purpose— Activation of NMDA subtypes of glutamate receptors is implicated in cell damage induced by ischemia as well as for the establishment of ischemic tolerance after ischemic preconditioning in animal models. We investigated the contributions of NR2A- and NR2B-containing NMDA receptors to ischemic cell death and ischemic tolerance in a rat model of transient global ischemia. Methods— Transient global ischemia was produced in rats by 4-vessel occlusion. Neuronal injury was analyzed by Fluoro-Jade B and Nissl staining. Phosphorylation of CREB was detected by Western blotting and immunohistochemistry. In situ hybridization and reverse transcriptase–polymerase chain reaction were used to evaluate the mRNA level of cpg15 and bdnf. Results— NR2A subtype-specific antagonist NVP-AAM077 enhanced neuronal death after transient global ischemia and abolished the induction of ischemic tolerance. In contrast, NR2B subtype-specific antagonist ifenprodil attenuated ischemic cell death and enhanced preconditioning-induced neuroprotection. Furthermore, selectively blocking NR2A-, but not NR2B-, containing NMDA receptors inhibited ischemia-induced phosphorylation of CREB and the subsequent upregulation of CREB target genes such as cpg15 and bdnf. Conclusions— We found that NR2A- and NR2B-containing NMDA receptor subtypes play differential roles in ischemic neuronal death and ischemic tolerance, suggesting attractive new strategies for the development of drugs for patients with stroke.
Molecular Identification of a Malaria Merozoite Surface Sheddase

Proteolytic shedding of surface proteins during invasion by apicomplexan parasites is a widespread phenomenon, thought to represent a mechanism by which the parasites disengage adhesin-receptor complexes in order to gain entry into their host cell. Erythrocyte invasion by merozoites of the malaria parasite Plasmodium falciparum requires the shedding of ectodomain components of two essential surface proteins, called MSP1 and AMA1. Both are released by the same merozoite surface “sheddase,” but the molecular identity and mode of action of this protease is unknown. Here we identify it as PfSUB2, an integral membrane subtilisin-like protease (subtilase). We show that PfSUB2 is stored in apical secretory organelles called micronemes. Upon merozoite release it is secreted onto the parasite surface and translocates to its posterior pole in an actin-dependent manner, a trafficking pattern predicted of the sheddase. Subtilase propeptides are usually selective inhibitors of their cognate protease, and the PfSUB2 propeptide is no exception; we show that recombinant PfSUB2 propeptide binds specifically to mature parasite-derived PfSUB2 and is a potent, selective inhibitor of MSP1 and AMA1 shedding, directly establishing PfSUB2 as the sheddase. PfSUB2 is a new potential target for drugs designed to prevent erythrocyte invasion by the malaria parasite.
Self-Taught Active Learning from Crowds

The emergence of social tagging and crowdsourcing systems provides a unique platform where multiple weak labelers can form a crowd to fulfill a labeling task. Yet crowd labelers are often noisy, inaccurate, and have limited labeling knowledge, and worst of all, they act independently without seeking complementary knowledge from each other to improve labeling performance. In this paper, we propose a Self-Taught Active Learning (STAL) paradigm, where imperfect labelers are able to learn complementary knowledge from one another to expand their knowledge sets and benefit the underlying active learner. We employ a probabilistic model to characterize the knowledge of each labeler through which a weak labeler can learn complementary knowledge from a stronger peer. As a result, the self-taught active learning process eventually helps achieve high classification accuracy with minimized labeling costs and labeling errors.
The WalkTrainer—A New Generation of Walking Reeducation Device Combining Orthoses and Muscle Stimulation

This paper presents a novel reeducation device for paraplegics that combines hybrid orthoses and closed-loop electrical muscle stimulation. Based on the so called cyberthosis concept, the WalkTrainer enables an active muscular participation of the subject in the walking reeducation process by the mean of closed-loop muscle stimulation. The WalkTrainer is also equipped with a leg and pelvic orthosis, an active bodyweight support, and motorized wheels to allow true over ground deambulation. This paper will focus on the development of the WalkTrainer, the presentation of the control strategies, and also give some preliminary results of the first clinical trials.
Nucleosynthesis in Type II Supernovae and the Abundances in Metal-poor Stars

We explore the effects on nucleosynthesis in Type II supernovae of various parameters (mass cut, neutron excess, explosion energy, progenitor mass) in order to explain the observed trends of the iron-peak element abundance ratios ([Cr/Fe], [Mn/Fe], [Co/Fe], and [Ni/Fe]) in halo stars as a function of metallicity for the range -4≤[Fe/H]≤-2.5. [Cr/Fe] and [Mn/Fe] decrease with decreasing [Fe/H], whereas [Co/Fe] increases. We show that such behavior can be explained by a variation of mass cuts in Type II supernovae as a function of progenitor mass, which provides a changing mix of nucleosynthesis from an alpha-rich freeze-out of Si burning and incomplete Si burning. This explanation is consistent with the amount of ejected 56Ni determined from modeling the early light curves of individual supernovae. We also suggest that the ratio [H/Fe] of halo stars is mainly determined by the mass of interstellar hydrogen mixed with the ejecta of a single supernova, which is larger for larger explosion energy and the larger Strömgren radius of the progenitor.
Dynamics of Aggregation and Emergence of Cooperation

Aggregation is one of the most basic social phenomena, and many activities of social insects are linked to it. For instance, the selection of a valuable site and the spatial organization of the population are very often by-products of amplifications based on the local density of nestmates. The patterns of aggregation are very diverse, ranging from the gathering of all animals in a unique site to their splitting between several ones. One might question how these multiple patterns emerge. Do ants actively initiate the formation of such patterns by modulating the emission of an attracting signal such as the trail pheromone? Alternatively, do patterns result from quantitative changes in the duration of interaction between animals once they have reached the gathering site, without any active modulation of the communications? To discuss these questions, we present two empirical studies: the gregarious behavior of cockroaches (Blatella) and self-assembly in the weaver ant (Oecophylla). Through experimental and theoretical studies, we show how a single behavior—the resting time—leads to a collective choice in both species. This behavior is a response to the density of conspecifics and can also be modulated by heterogeneities in the environment. In weaver ants, it allows the colony to focus the formation of chains in a given area among several potential sites. In cockroaches, it allows the gathering of individuals in particular shelters, depending on the proximity between strains. These results are discussed with emphasis on the role of aggregation processes in the emergence of cooperativity and task allocation.
Uncertainty Reduction as a Measure of Cognitive Processing Effort

The amount of cognitive effort required to process a word has been argued to depend on the word's effect on the uncertainty about the incoming sentence, as quantified by the entropy over sentence probabilities. The current paper tests this hypothesis more thoroughly than has been done before by using recurrent neural networks for entropy-reduction estimation. A comparison between these estimates and word-reading times shows that entropy reduction is positively related to processing effort, confirming the entropy-reduction hypothesis. This effect is independent from the effect of surprisal.