Miracle-dz/UniFAR-FTUs huggingface dataset:
The nature of protein folding pathways

How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the “new view” model for protein folding. Emergent macroscopic foldon–foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the “how” and the “why” questions. The protein folding pathway depends on the same foldon units and foldon–foldon interactions that construct the native structure.
Intradecidual sign: is it effective in diagnosis of an early intrauterine pregnancy?

PURPOSE To determine if the intradecidual sign at sonography is effective in the diagnosis of early intrauterine pregnancy. MATERIALS AND METHODS In 102 pregnant patients, transvaginal sonography revealed an intrauterine fluid collection without a yolk sac or embryo. Four observers (experienced sonologist, body imaging fellow, 1st-year radiology resident, and premedical student) determined independently whether the intradecidual sign was absent, present, or indeterminate. Interpretations were limited to visualization of only the uterus. RESULTS Follow-up revealed intrauterine pregnancy in 91 patients (outcome normal in 48 and abnormal in 43) and ectopic pregnancy in 11 patients. Among the four reviewers, sensitivity for diagnosis of an intrauterine pregnancy was 34%-66%, specificity was 55%-73%, accuracy was 38%-65%, positive predictive value was 91%-93%, and negative predictive value was 12%-16%. Three to five ectopic pregnancies were categorized incorrectly as demonstrating the intradecidual sign, depending on the reviewer. CONCLUSION The intradecidual sign does not appear to be sensitive or specific in diagnosis of an early intrauterine pregnancy. When an intrauterine fluid collection is present without an embryo or yolk sac (with positive pregnancy test results), a follow-up sonogram should be obtained unless contraindicated clinically.
Study of a Business Model Related to Cultural Franchises andthe Educational Industry in Taiwan- A Case Study of CreatingMental Arithmetic - CMA

The cultural and educational industry has been quite prosperous in Taiwan’s recent past. These cultural and educational institutions now encompass large-scale facilities and include some use self-use residency with small capital. Because of rapid changes in society and the trend toward having fewer children, the numbers of student enrollment has decreased markedly. However, in order to increase relative market share, large-scale cultural and educational institutions aimed at children make use of their advantages to recruit franchisees and establish branch schools. The current study is based on the related literature of culture and education industries in Taiwan useful to investigate the Creating Mental Arithmetic Creating Great Minds (CMA) business franchaise model. It would also expand oversea markets and increase management performance for franchises involved in such enterprise.
Logistics Coordination in Dyads: Some Theoretical Foundations for EDI-Induced Redesign

Organizations are redesigning business processes in order to cope with changing organizational environments. Some of these redesigns are enabled by improved information technology. In this article, the redesign of logistics processes in dyadical partnerships is central. By focusing on the operational coordination between partners in the dyad, elements of a theory of logistics coordination are presented. A definition of coordination is given, the cause of coordination is assessed, and the factors that influence coordination are given. Uncertainty is identified as the core concept that causes and is simultaneously affected by coordination. Two process characteristics, "Degree of Freedom" and "Action Variety," are introduced to examine the potential of electronic data interchange (EDI) to redesign logistics coordination. EDI is perceived as a means that supports and intensifies coordination.
Structured Treatment Interruptions in Primary HIV-1 Infection: The ANRS 100 PRIMSTOP Trial

Background:Whether structured treatment interruptions (STIs) can induce anti-HIV immune response and control HIV replication following discontinuation of highly active antiretroviral therapy (HAART) in patients with primary HIV infection is controversial. Methods:In this multicenter, prospective trial, patients with early symptomatic primary HIV infection were given HAART continuously for 34 weeks. Afterward, patients with plasma viral load (PVL) <50 copies/mL entered the STI phase, which consisted of 3 consecutive periods of 2, 4, and 8 weeks off HAART, each separated by 12 weeks on HAART. HAART was permanently stopped at week 84 and patients were followed up for 24 weeks. The primary endpoint for definition of virologic success was a PVL <50 copies/mL during the 6 months following HAART discontinuation. Results:Of the 29 patients enrolled, 26 completed the trial. Six months after HAART discontinuation, only 1 patient (3.8%, 95% CI: 0.1% to 19.6%) had PVL <50 copies/mL, whereas 6 of 26 (23.1%, 95% CI: 9.0% to 43.7%) had PVL <1000 copies/mL. Female gender was the only parameter significantly associated with a PVL <1000 copies/mL. No other parameter, either at baseline or before HAART discontinuation, predicted virologic success at week 108. A major protease inhibitor resistance mutation (L90M) developed in 3 patients. Conclusions:This trial failed to confirm that a significant proportion of patients with primary HIV infection can maintain suppression of viremia after a sequence of HAART/STIs followed by HAART discontinuation.
Corporate governance, legal systems and value relevance of fair value estimates. Empirical evidence from the EU banking sector

ABSTRACT Scholars agree that the role played by corporate governance mechanisms is likely to be affected by the quality of the legal systems in which firms operate. This paper investigates whether the quality of firm-level corporate governance is more valuable in countries with a high- or low-quality legal system. To do so, the paper focuses on the value relevance of fair value hierarchy disclosed by the European financial entities listed in 14 stock markets over the period 2011–2015. Findings show that differences in the quality of legal systems positively affect the value relevance of fair value estimates and provide evidence that the effect of firm-level corporate governance on the value relevance of fair value assets and liabilities is stronger in countries with high-quality legal systems. Our study contributes to the literature to the extent to which it shows that the ability of corporate governance to improve the value relevance of fair value measurements depends on the quality of the legal system under which firms operate. For this reason, our results complement findings reported by prior studies that have separately investigated the effect of the quality of corporate governance and of investor protection on the value relevance of fair value measurement.
Additive models with predictors subject to measurement error

We develop a likelihood based method for fitting additive models in the presence of measurement error. We formulate the additive model using the linear mixed model representation of penalized splines. In the presence of a structural measurement error model, the resulting likelihood involves intractable integrals, and a Monte Carlo Expectation Maximization strategy is developed for obtaining estimates. The method’s performance is illustrated with a simulation study.
Trends in opioid prescribing by race/ethnicity for patients seeking care in US emergency departments.

CONTEXT National quality improvement initiatives implemented in the late 1990s were followed by substantial increases in opioid prescribing in the United States, but it is unknown whether opioid prescribing for treatment of pain in the emergency department has increased and whether differences in opioid prescribing by race/ethnicity have decreased. OBJECTIVES To determine whether opioid prescribing in emergency departments has increased, whether non-Hispanic white patients are more likely to receive an opioid than other racial/ethnic groups, and whether differential prescribing by race/ethnicity has diminished since 2000. DESIGN AND SETTING Pain-related visits to US emergency departments were identified using reason-for-visit and physician diagnosis codes from 13 years (1993-2005) of the National Hospital Ambulatory Medical Care Survey. MAIN OUTCOME MEASURE Prescription of an opioid analgesic. RESULTS Pain-related visits accounted for 156 729 of 374 891 (42%) emergency department visits. Opioid prescribing for pain-related visits increased from 23% (95% confidence interval [CI], 21%-24%) in 1993 to 37% (95% CI, 34%-39%) in 2005 (P < .001 for trend), and this trend was more pronounced in 2001-2005 (P = .02). Over all years, white patients with pain were more likely to receive an opioid (31%) than black (23%), Hispanic (24%), or Asian/other patients (28%) (P < .001 for trend), and differences did not diminish over time (P = .44), with opioid prescribing rates of 40% for white patients and 32% for all other patients in 2005. Differential prescribing by race/ethnicity was evident for all types of pain visits, was more pronounced with increasing pain severity, and was detectable for long-bone fracture and nephrolithiasis as well as among children. Statistical adjustment for pain severity and other factors did not substantially attenuate these differences, with white patients remaining significantly more likely to receive an opioid prescription than black patients (adjusted odds ratio, 0.66; 95% CI, 0.62-0.70), Hispanic patients (0.67; 95% CI, 0.63-0.72), and Asian/other patients (0.79; 95% CI, 0.67-0.93). CONCLUSION Opioid prescribing for patients making a pain-related visit to the emergency department increased after national quality improvement initiatives in the late 1990s, but differences in opioid prescribing by race/ethnicity have not diminished.
MalPEG-hemoglobin (MP4) improves hemodynamics, acid-base status, and survival after uncontrolled hemorrhage in anesthetized swine

Objectives:MalPEG-hemoglobin, 4 g/dL (MP4), is a hemoglobin-based oxygen carrier with a low hemoglobin concentration, low P50 (oxygen half-saturation pressure of hemoglobin), high colloid osmotic pressure, and high viscosity. This study evaluated resuscitation with MP4 in anesthetized swine hemorrhaged 250 mL by controlled withdrawal, followed by a 5-mm tear in the abdominal aorta. Design:Randomized, unblinded. Setting:Academic animal laboratory. Subjects:Anesthetized male and female Swedish Landrace pigs. Interventions:Four groups of pigs (n = 7 each) were randomized after hemorrhage by aortic tear to receive 250 mL of MP4, Ringer’s acetate, 10% pentastarch, or 4 g/dL of stroma-free hemoglobin, followed by aortic repair and transfusion of 250 mL of autologous blood. End points were 20-hr survival, hemodynamic variables, and acid-base status. Measurements and Main Results:Measurements included continuous aortic, pulmonary arterial, and central venous pressures, cardiac output by thermodilution, arterial and venous blood gases; electrolytes; lactate; base excess; oxygen delivery, consumption, and extraction ratio; hematocrit; hemoglobin; and urine output. Body weight (24–27 kg) and hemorrhage volume (26–33 mL/kg) were similar in the four groups. The nadir of mean arterial pressure (22–28 mm Hg) and the increase in lactic acid (5–8 mEq/L) after hemorrhage were similar in all groups, indicating equivalent shock in the four groups. Survival was greatest in the MP4-treated animals (six of seven) compared with Ringer’s acetate (two of seven), 10% pentastarch (one of seven), and stroma-free hemoglobin (two of seven) and was accompanied by an improved recovery of arterial pressure, cardiac output, and lactate. Total hemoglobin concentration was equivalent in all groups. Arterial pressure did not increase above baseline values, and systemic vascular resistance was unchanged following administration of MP4, indicating the lack of peripheral vasoconstriction. Mortality in Ringer’s acetate, stroma-free hemoglobin, and 10% pentastarch treated animals was associated with deteriorating acid-base status, low urine output, and hyperkalemia. Conclusion:These data demonstrate that restoration of oxygen delivery with a small volume of MP4 yields significant recovery from hemorrhage without systemic vasoconstriction.
Identifying hypothalamic pathways controlling food intake, body weight, and glucose homeostasis

The past decade has greatly increased our understanding and appreciation of the ability of the central nervous system (CNS) to regulate food intake and body weight. This was spearheaded by the discovery of key molecules regulating body weight homeostasis. It is now also apparent that the CNS, especially the hypothalamus, plays a primary role in directly regulating glucose homeostasis, independently of effects on body weight. These discoveries are important given the increasing incidences of obesity and type II diabetes in Western societies. In this article, we will highlight recent data from genetically modified mice. These data and other models have helped to dissect the CNS pathways regulating body weight and glucose homeostasis. Finally, although these studies have been illustrative, they also underscore our relative lack of knowledge and highlight the need for more definitive approaches to unravel the functional significance of these pathways. J. Comp. Neurol. 493:63–71, 2005. © 2005 Wiley‐Liss, Inc.
FACT, réparation par excision de bases et fixation du facteur de transcription NF-kB sur la chromatine

FACT est une proteine cle, qui joue de multiples roles, y compris dans la transcription et la reparation de l'ADN endommage. Neanmoins, comment FACT participe a la reparation et a la transcription de la chromatine n'est pas elucide. Dans ce travail nous avons tout d'abord etudie le role de FACT dans le processus de reparation par excision de base (BER). Nous avons utilise des nucleosomes reconstitues avec de l'ADN a uracile incorpore au hasard. Nous avons trouve que l'enzyme UDG est capable d'enlever les uraciles localises du cote de la solution et pas les uraciles se trouvant en face de l'octamere d'histone. La presence simultanee de FACT et de RSC (facteur de remodelage de la chromatine, implique dans la reparation) permet un enlevement efficace des uraciles localises du cote de l'octamere d'histone par l'UDG. De plus, l'action concertee de FACT et RSC contribue a l'enlevement de la lesion oxidative 8-oxoG, autrement inaccessible, de la matrice nucleosomale par l'enzyme OGG1. Ce resultat est obtenu grâce a une activite « co-remodelatrice » de la proteine FACT. Dans ce travail nous decrivons pour la premiere fois cette nouvelle propriete de FACT et nous montrons par une serie d'experiences biochimiques que FACT est capable de stimuler l'activite de remodelage du RSC. Nos experiences montrent que la presence de FACT augmente l'efficacite de RSC a transformer l'energie liberee par l'hydrolyse de l'ATP en travail « mecanique ». Les donnees obtenues suggerent une nature stochastique du BER in vivo, FACT etant un facteur cle dans le processus de reparation. Nous avons egalement investigue l'implication de l'activite co-remodelatrice de FACT dans la fixation de NF-kB aux matrices nucleosomales. La production de nucleosomes remodeles, mais non - mobilises (remosomes) n'est pas suffisante pour promouvoir la fixation de NF-kB. Pourtant, la mobilisation des nucleosomes par l'intermediaire de RSC permet une interaction efficace entre NF-kB et l'ADN nucleosomal. Toutes ces donnees sont essentielles pour le decryptage du mecanisme moleculaire par lequel FACT agit dans le BER et dans la transcription mediee par NF-kB.
Biological and genetic characterization of TnphoA mutants of Salmonella typhimurium TML in the context of gastroenteritis

TnphoA transposon insertion mutants of phoN-negative derivatives of Salmonella typhimurium TML (of human gastroenteritic origin) were selected by growing mutagenized recipient bacteria under a variety of growth conditions. Ninety-seven individual mutants, which expressed alkaline phosphatase, were collected and tested for their ability to invade HEp-2 cells. Seven smooth mutants had a reduced ability to invade HEp-2 cells, and three smooth mutants were consistently more invasive than their corresponding parental strains. One rough mutant was of similar invasiveness and two were of reduced invasiveness when compared with that of parental strains. The seven smooth hypoinvasive mutants, the three smooth hyperinvasive mutants, and the three rough mutant strains were tested for their abilities to invade ileal enterocytes by the rabbit ileal invasion assay described previously (3). All smooth mutants exhibited parental levels of invasiveness. The rough mutants were hypoinvasive in the rabbit ileal invasion assay. The HEp-2 system is therefore not a good predictor of behavior in gut tissue in this model. DNA sequences flanking the transposon were determined for five mutants which were hypoinvasive in the HEp-2 cell assay. The mutations were found to be insertions in two previously identified invasion genes, invG and invH, and in a gene not normally associated with invasion, pagC. These observations lead one to be cautious in the interpretation of the biological significance of data obtained from invasion of tissue culture monolayers when extrapolated to gut tissue.
An Energy-Efficient and Fault-Tolerant Convergecast Protocol in Wireless Sensor Networks

The simple graph theory is commonly employed in wireless sensor networks topology control. An inherent problem of small-granularity algorithms is the high computing complexity and large solution space when managing large-scale WSNs. Computed transmission paths are of low fault tolerance because of unattended sensor nodes and frail wireless transmitting channels. This paper uses hyper-graph theory to solve these practical problems and proposes a spanning hyper-tree algorithm (SHTa) to compute the minimum transmitting power delivery paths set for WSNs convergecast. There are three main contributions of this paper: (1) we present a novel hyper-graph model to abstract large-scale and high connectivity WSNs into a robust hyper-tree infrastructure; (2) we present a precise mathematical derivation that solves the “hyper-tree existence” problem; (3) SHTa is proposed to compute the delivery paths set, which is the minimum power transmitting convergecast hyper-tree. Variable scale hyper-edges represented as computing units limit solution space and reduce computing complexity. Mutual backup delivery paths in one hyper-edge improve the capability of fault tolerance. With experiment results, SHTa computes short latency paths with low energy consumption, compared with previous algorithms. Furthermore, in dynamic experiments scenes, SHTa retains its robust transmitting quality and presents high fault tolerance.
Study of load frequency control for a microgrid

This paper describes a method to enhance the load frequency control in a power system with distributed generations (DG). In this paper, a power storage system is used with solar photovoltaic generations and wind power generations. The microgrid system at Aichi Institute Technology in Japan is used as a simulation model. For each simulation, which was carried out by using a power transmission simulator, the model of the microgrid included one DG and a storage system. The effectiveness of load frequency control using the storage system was examined. It was confirmed that the electric power quality improves when load frequency control is carried out with the storage system.
Privacy and medical record information.

I first want to commend ACMI for planning this debate and for stimulating discussion of this important question. I do not believe that Americans should be prepared to accept a loss of privacy in order to achieve a cost-effective, widely accessible, high-quality health care system in the United States, for a number of reasons. In the first place, it is unclear whether a cost-effective, widely accessible, highquality health care system necessitates a medical record that would not be private in the relevant sense; nonetheless, it is reasonable to assume that some changes in the way medical information is recorded, stored, and used under health care reform will occur and that these changes will carry with them potential threats to privacy. The question is how to address the concerns for privacy. Privacy is a basic right of individuals that is anchored in the fundamental principle of autonomy or selfdetermination. I can only assert this point rather than argue it. On its basis, however, privacy should not be treated as an element to be traded off for efficiency in running some future health care system; rather, it is not only a value that needs protection, but also a complex issue that needs rigorously critical analysis and discussion. I want to sound a cautionary note that unless issues of privacy are addressed early and in a thoughtful way, they are likely to come back to stymie development and implementation of what many of you have devoted your professional lives to achieving.