Miracle-dz/UniFAR-FTUs huggingface dataset:
Circadian clock in cell culture: II. In vitro photic entrainment of melatonin oscillation from dissociated chick pineal cells

The avian pineal gland contains circadian oscillators that regulate the rhythmic synthesis of melatonin. We have developed a flow-through cell culture system in order to begin to study the cellular and molecular basis of this vertebrate circadian oscillator. Pineal cell cultures express a circadian oscillation of melatonin release for at least 5 cycles in constant darkness with a period close to 24 hr. In all circadian systems, light regulates the rhythm by the process of entrainment that involves control of the phase and period of the circadian oscillator. In chick pineal cell cultures we have investigated the entraining effects of light in 2 ways: by shifting the light-dark cycle in vitro and by measuring the phase-shifting effects of single light pulses. A 6 hr advance or delay of a LD 12:12 light- dark cycle produced a corresponding shift in the melatonin rhythm. The phase shifts of the rhythms persisted after transfer to constant darkness, showing that the underlying circadian oscillator was entrained. Photic entrainment of the oscillator was further characterized by measuring the phase-shifting effects of single 6 hr light pulses. Single pulses of light shifted the phase of the circadian oscillator in a phase-dependent manner. Light pulses beginning early in the subjective night delayed the phase of the oscillation 8 hr relative to dark controls. Conversely, light pulses beginning late in the subjective night advanced the phase of the oscillation nearly 8 hr. Thus, photoreceptors within the cell cultures can mediate entrainment of the pineal oscillators.
Supply Chain as a Service: A Cloud Perspective on Supply Chain Systems

Supply chains are characterized by multiple firms providing their resources and processes to meeting customer demand in an efficient manner. There exists a great variety of approaches for solving the inherent coordination problem. It has been acknowledged that the autonomy of supply chain participants - and their business objectives - as well as the contractual relations between participants have to be maintained when designing a coordination mechanism. Often, new mechanisms are triggered by innovation in the software industry. This paper adopts the basic idea of Cloud Computing and takes a Cloud perspective on supply chain systems: It proposes to represent supply chains as a set of service offerings and customer demand as service requests; coordination is then a problem of determining optimal service compositions. We evaluate our proposal in a case study of airport service supply chains.
Mining communities in networks: a solution for consistency and its evaluation

Online social networks pose significant challenges to computer scientists, physicists, and sociologists alike, for their massive size, fast evolution, and uncharted potential for social computing. One particular problem that has interested us is community identification. Many algorithms based on various metrics have been proposed for communities in networks [18, 24], but a few algorithms scale to very large networks. Three recent community identification algorithms, namely CNM [16], Wakita [59], and Louvain [10], stand out for their scalability to a few millions of nodes. All of them use modularity as the metric of optimization. However, all three algorithms produce inconsistent communities every time the ordering of nodes to the algorithms changes. We propose two quantitative metrics to represent the level of consistency across multiple runs of an algorithm: pairwise membership probability and consistency. Based on these two metrics, we propose a solution that improves the consistency without compromising the modularity. We demonstrate that our solution to use pairwise membership probabilities as link weights generates consistent communities within six or fewer cycles for most networks. However, our iterative, pairwise membership reinforcing approach does not deliver convergence for Flickr, Orkut, and Cyworld networks as well for the rest of the networks. Our approach is empirically driven and is yet to be shown to produce consistent output analytically. We leave further investigation into the topological structure and its impact on the consistency as future work. In order to evaluate the quality of clustering, we have looked at 3 of the 48 communities identified in the AS graph. Surprisingly, all have either hierarchical, geographical, or topological interpretations to their groupings. Our preliminary evaluation of the quality of communities is promising. We plan to conduct more thorough evaluation of the communities and study network structures and their evolutions using our approach.
Learning to Identify the Best Contexts for Knowledge-based WSD

We outline a learning framework that aims at identifying useful contextual cues for knowledge-based word sense disambiguation. The usefulness of individual context words is evaluated based on diverse lexico-statistical and syntactic information, as well as simple word distance. Experiments using two different knowledge-based methods and benchmark datasets show significant improvements due to context modeling, beating the conventional window-based approach.
Obesogenic environments: exploring the built and food environments

Obesity is a significant health and social problem which has reached pandemic levels. The obesogenicity of an environment has been defined as ‘the sum of influences that the surroundings, opportunities, or conditions of life have on promoting obesity in individuals or populations’. 1 Prevention and treatment of obesity has focused on pharmacological, educational and behavioural interventions, with limited overall success. A novel and a longer-term approach would be to investigate the environments that promote high energy intake and sedentary behaviour; this has not yet been fully understood. The obesity epidemic has attracted attention at all levels, from general media interest to policy and practice from health and other professions including urban designers and planners. Shaping the environment to better support healthful decisions has the potential to be a key aspect of a successful obesity prevention intervention. Thus in order to develop effective environmental interventions, in relation to obesity, we need to understand how individuals, and different groups of individuals, interact with their environments in terms of physical activity and food intake.
DNA vaccines targeting human papillomavirus-associated diseases: progresses in animal and clinical studies

Human papillomavirus (HPV) infection is a major cause of cervical cancer and its precancerous diseases. Cervical cancer is the second deadliest cancer killer among women worldwide. Moreover, HPV is also known to be a causative agent of oral, pharyngeal, anal and genital cancer. Recent application of HPV structural protein (L1)-targeted prophylactic vaccines (Gardasil® and Cervarix®) is expected to reduce the incidence of HPV infection and cervical cancer, and possibly other HPV-associated cancers. However, the benefit of the prophylactic vaccines for treating HPV-infected patients is unlikely, underscoring the importance of developing therapeutic vaccines against HPV infection. In this regard, numerous types of therapeutic vaccine approaches targeting the HPV regulatory proteins, E6 and E7, have been tested for their efficacy in animals and clinically. In this communication, we review HPV vaccine types, in particular DNA vaccines, their designs and delivery by electroporation and their immunologic and antitumor efficacy in animals and humans, along with the basics of HPV and its pathogenesis.
Do Bullied Children Become Anxious and Depressed Adults?: A Cross-Sectional Investigation of the Correlates of Bullying and Anxious Depression

There is little empirical research examining the historical and clinical correlates of exposure to childhood bullying in adult clinical subjects. Using structured clinical assessments, the authors studied a group of adult males and females presenting to an outpatient depression clinic, to examine the childhood risk factors and the distinguishing comorbid features associated with those reporting exposure to bullying. Just over a quarter of both men and women reported having experienced bullying that was severe and traumatic. More of these subjects also reported several other well studied childhood risk factors. Childhood correlates that were particularly relevant for exposure to bullying were parental overcontrol, illness or disability, and the tendency to have an inhibited temperament early in life. The experience of childhood bullying was strongly related to high levels of comorbid anxiety, both in terms of greater levels of state anxiety and a higher prevalence of both social phobia and agoraphobia. Independent of other childhood risk factors, exposure to bullying was especially predictive of subjects’ higher levels of general state anxiety and the tendency to express anxious arousal externally when under stress. These results are compatible with both cross-sectional and prospective studies of child and adolescent samples, and highlight the potential etiological significance of early peer victimization experiences for a percentage of adults suffering from depression with comorbid anxiety.
Computers and Mathematics with Applications Bankruptcy Prediction in Firms with Statistical and Intelligent Techniques and a Comparison of Evolutionary Computation Approaches

In this paper, we compare some traditional statistical methods for predicting financial distress to some more ''unconventional'' methods, such as decision tree classification, neural networks, and evolutionary computation techniques, using data collected from 200 Taiwan Stock Exchange Corporation (TSEC) listed companies. Empirical experiments were conducted using a total of 42 ratios including 33 financial, 8 non-financial and 1 combined macroeconomic index, using principle component analysis (PCA) to extract suitable variables. This paper makes four critical contributions: (1) with nearly 80% fewer financial ratios by the PCA method, the prediction performance is still able to provide highly-accurate forecasts of financial bankruptcy; (2) we show that traditional statistical methods are better able to handle large datasets without sacrificing prediction performance, while intelligent techniques achieve better performance with smaller datasets and would be adversely affected by huge datasets; (3) empirical results show that C5.0 and CART provide the best prediction performance for imminent bankruptcies; and (4) Support Vector Machines (SVMs) with evolutionary computation provide a good balance of high-accuracy short-and long-term performance predictions for healthy and distressed firms. Therefore, the experimental results show that the Particle Swarm Optimization (PSO) integrated with SVM (PSO–SVM) approach could be considered for predicting potential financial distress.
Regulation of Hsp90 ATPase activity by tetratricopeptide repeat (TPR)‐domain co‐chaperones

The in vivo function of the heat shock protein 90 (Hsp90) molecular chaperone is dependent on the binding and hydrolysis of ATP, and on interactions with a variety of co‐chaperones containing tetratricopeptide repeat (TPR) domains. We have now analysed the interaction of the yeast TPR‐domain co‐chaperones Sti1 and Cpr6 with yeast Hsp90 by isothermal titration calorimetry, circular dichroism spectroscopy and analytical ultracentrifugation, and determined the effect of their binding on the inherent ATPase activity of Hsp90. Sti1 and Cpr6 both bind with sub‐micromolar affinity, with Sti1 binding accompanied by a large conformational change. Two co‐chaperone molecules bind per Hsp90 dimer, and Sti1 itself is found to be a dimer in free solution. The inherent ATPase activity of Hsp90 is completely inhibited by binding of Sti1, but is not affected by Cpr6, although Cpr6 can reactivate the ATPase activity by displacing Sti1 from Hsp90. Bound Sti1 makes direct contact with, and blocks access to the ATP‐binding site in the N‐terminal domain of Hsp90. These results reveal an important role for TPR‐domain co‐chaperones as regulators of the ATPase activity of Hsp90, showing that the ATP‐dependent step in Hsp90‐mediated protein folding occurs after the binding of the folding client protein, and suggesting that ATP hydrolysis triggers client‐protein release.
Induction of Chimerism Permits Low-Dose Islet Grafts in the Liver or Pancreas to Reverse Refractory Autoimmune Diabetes

OBJECTIVE To test whether induction of chimerism lowers the amount of donor islets required for reversal of diabetes and renders the pancreas a suitable site for islet grafts in autoimmune diabetic mice. RESEARCH DESIGN AND METHODS The required donor islet dose for reversal of diabetes in late-stage diabetic NOD mice after transplantation into the liver or pancreas was compared under immunosuppression or after induction of chimerism. Recipient mice were monitored for blood glucose levels and measured for insulin-secretion capacity. Islet grafts were evaluated for β-cell proliferation, β-cell functional gene expression, and revascularization. RESULTS With immunosuppression, transplantation of 1,000, but not 600, donor islets was able to reverse diabetes when transplanted into the liver, but transplantation of 1,000 islets was not able to reverse diabetes when transplanted into the pancreas. In contrast, after induction of chimerism, transplantation of as few as 100 donor islets was able to reverse diabetes when transplanted into either the liver or pancreas. Interestingly, when lower doses (50 or 25) of islets were transplanted, donor islets in the pancreas were much more effective in reversal of diabetes than in the liver, which was associated with higher β-cell replication rate, better β-cell functional gene expression, and higher vascular density of graft islets in the pancreas. CONCLUSIONS Induction of chimerism not only provides immune tolerance to donor islets, but also markedly reduces the required amount of donor islets for reversal of diabetes. In addition, this process renders the pancreas a more superior site than the liver for donor islets in autoimmune mice.
Comparative Performance and Complementarity of Four Sampling Methods and Arthropod Preference Tests from Human and Porcine Remains at the Forensic Anthropology Center in Knoxville, Tennessee

Abstract Comparative performance and complementarity tests of four arthropod sampling methods (aerial netting, hand collection, pitfall traps, and sticky traps), used by forensic entomologists in death investigations, training workshops, and research trials, were conducted from simultaneously placed human and porcine subjects inside the Forensic Anthropology Center at the University of Tennessee, Knoxville, TN. A secondary aim investigated the widely held claim that pig carcasses are reliable surrogates for human corpses. Over a 35-d period in summer 1989, >72,000 invertebrates from three subjects (one human, two pigs) were sampled of which 93% were members of the forensically important (FI) fauna. Performance tests revealed that hand collections, when performed by an experienced forensic entomologist, consistently yielded the largest fraction of FI arthropods from the total invertebrate catch, followed by aerial netting, sticky traps, and pitfall traps, regardless of subject. Pitfall traps and hand collections were broadly effective at sampling both fly and beetle populations, whereas aerial netting and sticky traps mostly targeted flies. The best two-method combination, based on the highest combined catches of FI taxa, were hand collections and pitfall traps, regardless of subject. Between-subject comparisons revealed negligible preference by FI arthropods for human over pig remains. Insofar as our limited comparisons allow with only three study subjects, these results validated the concept of transferability of “best practices” from one subject to another and confirmed the claim that pig carcasses (of 23–27-kg starting mass) can substitute for human corpses in research and training programs, at least for summer-exposed and unconcealed remains in the first 5 wk postmortem.
Toll-Like Receptor 1 Polymorphisms and Associated Outcomes in Sepsis After Traumatic Injury: A Candidate Gene Association Study

Objective:To determine whether single nucleotide polymorphisms (SNPs) in TLR1 are associated with mortality, specifically sepsis-associated mortality, in a traumatically injured population. Background:Innate immune responses mediated by toll-like receptors (TLRs) induce early inflammatory responses to pathogen and damage-associated molecular patterns. Genetic variation in TLRs has been associated with susceptibility and outcomes in a number of infectious and noninfectious disease states. Methods:Patients admitted to the trauma intensive care unit at a level 1 trauma center serving 4 states were enrolled and followed for development of infection, sepsis, and death. Genomic DNA was genotyped and logistic regression analysis was performed to determine associations between TLR1 SNPs and mortality. We further examined for associations between TLR1 SNPs and mortality in subgroups on the basis of the presence of sepsis and the type of sepsis-associated organism. Results:We enrolled 1961 patients. TLR1−7202G (rs5743551) was associated with increased mortality after traumatic injury and this association was primarily observed in the subset of patients who developed sepsis [adjusted odds ratio (OR): 3.16; 95% confidence interval (CI): 1.43–6.97, P = 0.004]. This association persisted after further restriction to gram-positive sepsis. TLR1742A/G(Asn248Ser) (rs4833095), a coding SNP in LD with TLR1−7202G, was also associated with mortality in gram-positive sepsis (adjusted OR: 4.16; 95% CI: 1.22–14.19, P = 0.023). Conclusions:Genetic variation in TLR1 is associated with increased mortality in patients with sepsis after traumatic injury and may represent a novel marker of risk for death in critically injured patients.
Nitric Oxide Protects against Infection-Induced Neuroinflammation by Preserving the Stability of the Blood-Brain Barrier

Nitric oxide (NO) generated by inducible NO synthase (iNOS) is critical for defense against intracellular pathogens but may mediate inflammatory tissue damage. To elucidate the role of iNOS in neuroinflammation, infections with encephalitogenic Trypanosoma brucei parasites were compared in inos -/- and wild-type mice. Inos -/- mice showed enhanced brain invasion by parasites and T cells, and elevated protein permeability of cerebral vessels, but similar parasitemia levels. Trypanosome infection stimulated T cell- and TNF-mediated iNOS expression in perivascular macrophages. NO nitrosylated and inactivated pro-inflammatory molecules such as NF-κΒp65, and reduced TNF expression and signalling. iNOS-derived NO hampered both TNF- and T cell-mediated parasite brain invasion. In inos -/- mice, TNF stimulated MMP, including MMP9 activity that increased cerebral vessel permeability. Thus, iNOS-generated NO by perivascular macrophages, strategically located at sites of leukocyte brain penetration, can serve as a negative feed-back regulator that prevents unlimited influx of inflammatory cells by restoring the integrity of the blood-brain barrier.
Oscillatory behavior of two nonlinear microbial models of soil carbon decomposition

A number of nonlinear models have recently been proposed for simulating soil carbon decomposition. Their predictions of soil carbon responses to fresh litter input and warming differ significantly from conventional linear mod- els. Using both stability analysis and numerical simulations, we showed that two of those nonlinear models (a two-pool model and a three-pool model) exhibit damped oscillatory re- sponses to small perturbations. Stability analysis showed the
A prospective study on buprenorphine use during pregnancy: effects on maternal and neonatal outcome

Background. Exposure to illicit drugs in utero is associated with low birth weight and premature birth. Therefore, maintenance therapy for opioid dependence during pregnancy has been recommended to help withdrawal from street drugs, in order to improve maternal health and decrease risks to the fetus. Methods. In 2002–2005, 67 pregnancies of 66 buprenorphine users were followed prospectively in an outpatient multidisciplinary antenatal setting by an obstetrician, a midwife, a psychiatric nurse and a social worker. Decreasing doses or even abstinence from buprenorphine was encouraged. Outcome measures were daily buprenorphine dose, fetal growth, gestational age at birth, mode of delivery, birth weight, Apgar scores, umbilical pH values, and occurrence of neonatal abstinence syndrome [NAS]. National statistics were used as reference values. Results. The daily dose of buprenorphine decreased by 2.3 mg (median, range increase of 8 mg to decrease of 24 mg). There were no more incidences of premature birth, cesarean section, low Apgar scores (≤6) or umbilical artery pH <7.05 at birth than in the national register, despite the lower birth weight. A total of 91% of the infants needed treatment in a neonatal care unit, 76% had NAS, and 57% needed morphine replacement therapy. Seven infants were taken into care directly from the maternity hospital. Two sudden infant deaths occurred later. Conclusions. The pregnancies and deliveries of buprenorphine‐using women were uneventful, but severe NAS and need for morphine replacement therapy was seen in 57% of the buprenorphine‐exposed newborns. A high number of sudden infant deaths occurred.
A Wearable EEG-HEG-HRV Multimodal System With Simultaneous Monitoring of tES for Mental Health Management

A multimodal mental management system in the shape of the wearable headband and earplugs is proposed to monitor electroencephalography (EEG), hemoencephalography (HEG) and heart rate variability (HRV) for accurate mental health monitoring. It enables simultaneous transcranial electrical stimulation (tES) together with real-time monitoring. The total weight of the proposed system is less than 200 g. The multi-loop low-noise amplifier (MLLNA) achieves over 130 dB CMRR for EEG sensing and the capacitive correlated-double sampling transimpedance amplifier (CCTIA) has low-noise characteristics for HEG and HRV sensing. Measured three-physiology domains such as neural, vascular and autonomic domain signals are combined with canonical correlation analysis (CCA) and temporal kernel canonical correlation analysis (tkCCA) algorithm to find the neural-vascular-autonomic coupling. It supports highly accurate classification with the 19% maximum improvement with multimodal monitoring. For the multi-channel stimulation functionality, after-effects maximization monitoring and sympathetic nerve disorder monitoring, the stimulator is designed as reconfigurable. The 3.37 × 2.25 mm 2 chip has 2-channel EEG sensor front-end, 2-channel NIRS sensor front-end, NIRS current driver to drive dual-wavelength VCSEL and 6-b DAC current source for tES mode. It dissipates 24 mW with 2 mA stimulation current and 5 mA NIRS driver current.
Linking Uncertainty in Physicians’ Narratives to Diagnostic Correctness

In the medical domain, misdiagnoses and diagnostic uncertainty put lives at risk and incur substantial financial costs. Clearly, medical reasoning and decision-making need to be better understood. We explore a possible link between linguistic expression and diagnostic correctness. We report on an unusual data set of spoken diagnostic narratives used to computationally model and predict diagnostic correctness based on automatically extracted and linguistically motivated features that capture physicians' uncertainty. A multimodal data set was collected as dermatologists viewed images of skin conditions and explained their diagnostic process and observations aloud. We discuss experimentation and analysis in initial and secondary pilot studies. In both cases, we experimented with computational modeling using features from the acoustic-prosodic and lexical-structural linguistic modalities.