Miracle-dz/UniFAR-FTUs huggingface dataset:
The Tools to Understand

SUMMARY A collaborative research process engaging Alaska Native communities in the study of protective factors in Alaska Native sobriety and the design of a preventative intervention using its findings is described. Study 1 was discovery oriented qualitative research whose objectives were identification of protective factors and development of a heuristic model. Study 2 involved quantitative survey methods to develop and test a measure of protective factors identified by the qualitative study. Empirical data from these studies is presented, and the role of Alaska Native co-researchers who did not possess specialist research training is described in the design and implementation of the study, interpretation of findings, and design of the intervention model and tools. Benefits that emerged from co-researcher involvement in this process, to the community and to the co-researchers themselves, are described.
Kinesin's step dissected with single-motor FRET

The motor protein Kinesin-1 drives intracellular transport along microtubules, with each of its two motor domains taking 16-nm steps in a hand-over-hand fashion. The way in which a single-motor domain moves during a step is unknown. Here, we use Förster resonance energy transfer (FRET) between fluorescent labels on both motor domains of a single kinesin. This approach allows us to resolve the relative distance between the motor domains and their relative orientation, on the submillisecond timescale, during processive stepping. We observe transitions between high and low FRET values for certain kinesin constructs, depending on the location of the labels. These results reveal that, during a step, a kinesin motor domain dwells in a well-defined intermediate position for ≈3 ms.
The Marine Indo-West Pacific Break: Contrasting the Resolving Power of Mitochondrial and Nuclear Genes1

Abstract Simultaneous studies of both nuclear and mitochondrial markers were undertaken in two widespread Indo-West Pacific (IWP) marine invertebrates to compare and contrast the ability of these markers to resolve genetic structure. In particular, we were interested in the resolution of a genetic break between the Indian and Pacific Oceans due to historical isolation. Sequence variation from the nuclear gene encoding myosin heavy chain (MyHC) and the mitochondrial gene cytochrome oxidase I (COI) were examined for the snapping shrimp Alpheus lottini from wide-ranging populations throughout the Indian and Pacific Oceans. A previously identified genetic break between oceans based on COI sequences appears to have been an artifact caused by the inadvertent inclusion of pseudogene sequences; our new COI data provide evidence only of a break between IWP and East Pacific populations. Distribution of a single nucleotide polymorphism in MyHC, on the other hand, shows evidence of a cline between Indian and Pacific Oceans. New allozyme and mtDNA sequence data were also obtained for the starfish Linckia laevigata. Allozyme data show a clear genetic break between Indian Ocean populations and Pacific (including western Australian) populations, whereas the distribution of mtDNA haplotypes shows a region of overlap in the central IWP. Comparisons of our data for both Alpheus and Linckia with data from other population genetic studies in the IWP suggest that nuclear markers (allozymes, sequence data and morphological characters) may in some instances reveal historical patterns of genetic population structure whereas mtDNA variation better reflects present day patterns of gene flow.
A Collaborative Approach for Monitoring Nodes Behavior during Spectrum Sensing to Mitigate Multiple Attacks in Cognitive Radio Networks

Spectrum sensing is the first step to overcome the spectrum scarcity problem in Cognitive Radio Networks (CRNs) wherein all unutilized subbands in the radio environment are explored for better spectrum utilization. Adversary nodes can threaten these spectrum sensing results by launching passive and active attacks that prevent legitimate nodes from using the spectrum efficiently. Securing the spectrum sensing process has become an important issue in CRNs in order to ensure reliable and secure spectrum sensing and fair management of resources. In this paper, a novel collaborative approach during spectrum sensing process is proposed. It monitors the behavior of sensing nodes and identifies the malicious and misbehaving sensing nodes. The proposed approach measures the node’s sensing reliability using a value called belief level. All the sensing nodes are grouped into a specific number of clusters. In each cluster, a sensing node is selected as a cluster head that is responsible for collecting sensing-reputation reports from different cognitive nodes about each node in the same cluster. The cluster head analyzes information to monitor and judge the nodes’ behavior. By simulating the proposed approach, we showed its importance and its efficiency for achieving better spectrum security by mitigating multiple passive and active attacks.
Insurance Crisis or Liability Crisis? Medical Malpractice Claiming in Illinois, 1980–2010

Since 1980, Illinois has experienced three med mal insurance crises – in the mid-1980s, mid-1990s, and early-2000s. Each time, Illinois responded by enacting tort reform. Using a previously unavailable database of closed medical malpractice (“med mal”) claims, maintained by the Illinois Department of Insurance, we analyze statewide trends in med mal claiming from 1980-2010, covering all three crises. Paid claim rates rose sharply from 1980-1985, roughly leveled off from 1986-1993, and then began a sustained decline. By 2010, paid claims rates were 75% lower than in the peak year (1991). Payout per claim has steadily increased since 1980, but these increases can be entirely explained by the virtual disappearance of smaller paid claims and claims involving less severe injuries. The total direct cost of med mal litigation (payouts and defense costs) rose sharply from 1980-1992, with a jump in 1991 and then declined steadily, with a more modest jump during 2000-2002, which persists through 2006. Thus, of the three Illinois insurance crises, only the first coincided in time with a major change in claiming. Rather than becoming more generous over time, Illinois’ med mal system has squeezed out claimants with less severe injuries and smaller claims.
Learning to Aggregate: An Automated Aggregation Method for Software Quality Model

Quality models are regarded as a well-acceptedapproach for assessing high-level abstract quality characteristics(e.g., maintainability) by aggregation from low-level metrics. However, most of the existing quality models adopt the weightedlinear aggregation method which suffers from a lack of consensusin how to decide the correct weights. To address this issue, wepresent an automated aggregation method which adopts a kind ofprobabilistic weight instead of the subjective weight in previousaggregation methods. In particular, we utilize a topic modelingtechnique to estimate the probabilistic weight by learning froma software benchmark. In this manner, our approach can enableautomated quality assessment by using the learned knowledgewithout manual effort. In addition, we conduct an application onthe maintainability assessment of the systems in our benchmark. The result shows that our approach can reveal the maintainabilitywell through a correlation analysis with the changed lines of code.
Prospectively assessed incidence, severity, and determinants of respiratory symptoms in the first year of life

Respiratory symptoms are common in infancy. Nevertheless, few prospective birth cohort studies have studied the epidemiology of respiratory symptoms in normal infants. The aim of this study was to prospectively obtain reliable data on incidence, severity, and determinants of common respiratory symptoms (including cough and wheeze) in normal infants and to determine factors associated with these symptoms. In a prospective population‐based birth cohort, we assessed respiratory symptoms during the first year of life by weekly phone calls to the mothers. Poisson regression was used to examine the association between symptoms and various risk factors. In the first year of life, respiratory symptoms occurred in 181/195 infants (93%), more severe symptoms in 89 (46%). The average infant had respiratory symptoms for 4 weeks and 90% had symptoms for less than 12 weeks (range 0 to 23). Male sex, higher birth weight, maternal asthma, having older siblings and nursery care were associated with more, maternal hay fever with fewer respiratory symptoms. The association with prenatal maternal smoking decreased with time since birth. This study provides reliable data on the frequency of cough and wheeze during the first year of life in healthy infants; this may help in the interpretation of published hospital and community‐based studies. The apparently reduced risk in children of mothers with hayfever but no asthma, and the decreasing effect of prenatal smoke exposure over time illustrate the complexity of respiratory pathology in the first year of life. Pediatr Pulmonol. 2007; 42:41–50. © 2006 Wiley‐Liss, Inc.
A hybrid heuristic algorithm based on Mean-Field Theory with a Simple Local Search for the Quadratic Knapsack Problem

In statistical physics, Mean-Field Theory is a probabilistic model which has three different approaches, one of them is Mean-Field variational that replaces a difficult distribution by an easier one. An optimization problem can be associated with a probability distribution that involves the structure of the problem, and is generally difficult to treat. This paper presents a novel method based on the Mean-Field Theory and a Local Search procedure to build good feasible solutions for the Quadratic Knapsack Problem. Basically, Mean-Field is used as a constructive heuristic that offers initial solutions and the quality of the solution is improved by a Local Search. To compare the performance of the proposed algorithm a Greedy constructive heuristic is implemented, and the same Local Search procedure was used. In order to test the efficiency of both algorithms, computational experiments were done on a set of benchmark instances in literature and another set is created. The experimental results show that Mean-Field like a constructive method provides similar solutions as Greedy in less time. And, incorporate them in a Local Search the response time for Mean-FIeld is less than Greedy but the quality of solutions is slightly smaller than Greedy.
Dual Role of the β2-Adrenergic Receptor C Terminus for the Binding of β-Arrestin and Receptor Internalization*

Homologous desensitization of β2-adrenergic and other G-protein-coupled receptors is a two-step process. After phosphorylation of agonist-occupied receptors by G-protein-coupled receptor kinases, they bind β-arrestins, which triggers desensitization and internalization of the receptors. Because it is not known which regions of the receptor are recognized by β-arrestins, we have investigated β-arrestin interaction and internalization of a set of mutants of the human β2-adrenergic receptor. Mutation of the four serine/threonine residues between residues 355 and 364 led to the loss of agonist-induced receptor-β-arrestin2 interaction as revealed by fluorescence resonance energy transfer (FRET), translocation of β-arrestin2 to the plasma membrane, and receptor internalization. Mutation of all seven serine/threonine residues distal to residue 381 did not affect agonist-induced receptor internalization and β-arrestin2 translocation. A β2-adrenergic receptor truncated distal to residue 381 interacted normally with β-arrestin2, whereas its ability to internalize in an agonist-dependent manner was compromised. A similar impairment of internalization was observed when only the last eight residues of the C terminus were deleted. Our experiments show that the C terminus distal to residue 381 does not affect the initial interaction between receptor and β-arrestin, but its last eight amino acids facilitate receptor internalization in concert with β-arrestin2.
Catabolite repression of α amylase gene expression in Bacillus subtilis involves a trans‐acting gene product homologous to the Escherichia coli lacl and galR repressors

Expression of the α‐amylase gene of Bacillus subtilis is controlled at the transcriptional level, and responds to the growth state of the cell as well as the availability of rapidly metabolizable carbon sources. Glucose‐mediated repression has previously been shown to involve a site near the transcriptional start‐point of the amyE gene. In this study, a transposon insertion mutation was characterized which resulted in loss of glucose repression of amyE gene expression. The gene affected by this mutation, which was localized near 263° on the B. subtilis chromosomal map, was isolated and its DNA sequence was determined. This gene, designated ccpA, exhibited striking homology to repressor genes of the lac and gal repressor family. The ccpA gene was found to be allelic to alsA, previously identified as a regulator of acetoin biosynthesis, and may be involved in catabolite regulation of other systems as well.
Effects of high CO2 level during early incubation and late incubation in ovo dexamethasone injection on perinatal embryonic parameters and post-hatch growth of broilers

1. A total of 1200 Cobb broiler breeder eggs were incubated under either standard conditions (C group) or high CO2 levels (CO2 group) during the first 10 d of incubation. The CO2 level of the CO2 incubator was attained gradually by a natural build-up of CO2 due to air-tight closure of the incubator. From d 10 of incubation onwards, all eggs were incubated under standard incubation conditions. At d 18 of incubation, the eggs of both incubation groups (CO2 and C group) were either injected with water-soluble dexamethasone (DEXA group) or with saline (0·9% NaCl; saline group) or were not injected (control). 2. Body weights, plasma hormonal concentrations (T3, T4 and corticosteroid) and glucose concentrations were measured regularly during the perinatal (at IP, internal pipping) and post-hatch period (at 1, 2, 4 and 6 weeks post-hatch). Additionally, hatchability and pattern of embryonic mortality were determined after hatch. 3. The results showed that high CO2 levels during the first 10 d of incubation or dexamethasone injection at d 18 of incubation decreased embryo mortality, mainly because of a reduction in embryo malpositioning. However, a combination of a CO2 incubation and a dexamethasone injection led to an increase in embryo mortality and therefore a decrease in hatchability. 4. Although dexamethasone injection at embryonic d 18 decreased body weight in the second week of the rearing period and CO2 incubation increased body weight during the first 2 weeks of the rearing period, no consistent effect of both the incubation and injection treatments on body weight at slaughter age was observed.
In situ behavior of human Langerhans cells in skin organ culture.

BACKGROUND Epidermal Langerhans cells (ELC) play a critical role in the initiation of cutaneous immune responses. ELC are characterized by the expression of major histocompatibility complex (MHC) class II Ag and a number of adhesion/costimulatory molecules. Evidence suggests that cytokines induced within the epidermis regulate the functions of ELC, including their phenotypic expression. In the human system, no information is available regarding the behavior of the ELC in situ: their changes in morphology, expression of functional molecules or migration within the microenvironment. In the present study, using an ex vivo human skin organ culture model, we addressed the above questions and also examined the phenotypic modulation of ELC in situ by cytokines. EXPERIMENTAL DESIGN Skin explants were cultured either in a Trowell-type method or free in the medium. Skin explants were cultured with and without cytokines and were processed for light and electron microscopy and for immunohistochemical definition of ELC phenotypes. RESULTS In the Trowell-type skin organ culture, morphologic integrity of ELC, CD1a molecule, and Birbeck granules could be preserved intact up to 3 to 4 days in culture. During the first 3 days of culture, the intensity of MHC-II (HLA-DR, DP, and DQ) and CD1a expression on ELC increased sharply, and the dendritic appearance of ELC became more prominent at Day 3. Adhesion molecules, ICAM-1, LFA-3, HECA-452, sLx, and B7/BB1 were also spontaneously acquired in varying amounts by CD1a+ ELC after 3 days in culture. Significant increase of CD1a and ICAM-1 expression on ELC was observed within 12 hours, when skin explants were cultured free in the medium with GM-CSF and TNF-alpha, respectively. Further, we demonstrated spontaneous migration of ELC within the epidermis and then to the dermis during the Trowell-type skin culture. We also showed the migration of ELC out of the human skin when skin explants were cultured directly in the medium. CONCLUSIONS Human ELC showed significant phenotypic changes within the epidermis and acquired migratory capacity during the skin organ culture. ELC in skin organ culture appear to undergo a phenotypic maturation within the epidermis. ELC in situ rapidly respond to GM-CSF and TNF-alpha by increasing the expression of CD1a and ICAM-1 molecules, respectively. These results suggest the modulation of phenotypic characteristics of ELC and their migration in response to the changes of epidermal microenvironment and cytokines and implicate the potential use of skin organ culture model to elucidate the role of human ELC in the immunopathology of skin diseases.
Multipoint Linkage Analysis

Multipoint linkage analysis is commonly used to evaluate linkage of a disease to multiple markers in a small region. Multipoint analysis is particularly powerful when the IBD relations of family members at the trait locus are ambiguous. The increased power arises because, unlike single-marker analyses, multipoint analysis uses haplotype information from several markers to infer the IBD relations. We wish to temper this advantage with a cautionary note: multipoint analysis is sensitive to power loss due to misspecification of intermarker distances. Such misspecification is especially problematic when dealing with closely spaced markers. We present computer simulations comparing the power of single-point and multipoint analyses, both when IBD relations are ambiguous, and when the intermarker distances are misspecified. We conclude that when evaluating markers in a small region to confirm or refute previous findings, a situation in which p values of modest statistical significance are important, single marker analyses may provide more reliable measures of the strength of support for linkage than multipoint statistics.
Pain, Sedation, and Delirium Management in the Neurocritically Ill: Lessons Learned from Recent Research

Abstract Critically ill patients with a primary neurological injury or illness pose unique challenges for pain, agitation, and delirium management in intensive care units (ICUs). Detection and monitoring can be limited by contextual level of consciousness (LOC) alterations, cognition, expression, or language deficits. Recent data suggest that existing pain assessment tools may not be applicable to all neurocritically ill patients, especially in those with LOC alterations and atypical pain-associated behaviors. Targeted sedation goals may be neurologically disease specific; for instance, intracranial pressure (ICP) targets will supersede sedation titration by other criteria. Technology such as bispectral index (BIS) may be beneficial in avoiding excessive medication administration in deeply sedated neurologically injured ICU patients. Given the wide variety of pathology in the neurocritically ill patients, it is unclear if delirium can be diagnosed and unequivocally differentiated from symptoms of the underlying neurological pathology. However, delirium symptoms may herald life-threatening primary insult progression or result from a new secondary neurological injury and should be monitored. Patients with neurological injury or illness are often excluded from ICU studies addressing pain, sedation, and delirium, but this need not be the case. We review what is understood in this area based on current evidence.
Capsular serotype-specific attack rates and duration of carriage of Streptococcus pneumoniae in a population of children.

BACKGROUND The relative invasiveness rates (attack rates) of Streptococcus pneumoniae of different capsular serotypes in children are not known. Estimates of capsular serotype invasiveness (designated "invasive odds ratios") that are based on cross-sectional prevalence carriage data have been published, but these estimates could be biased by variation in the duration of carriage. METHODS The relative attack rates of invasive pneumococci were measured using national UK surveillance data on invasive pneumococcal disease (IPD) incidence and data on incidence of pneumococcal acquisition from longitudinal studies of nasopharyngeal pneumococcal carriage. RESULTS We found significant differences in capsular serotype-specific attack rates. For example, capsular serotypes 4, 14, 7F, 9V, and 18C were associated with rates of >20 IPD cases/100,000 acquisitions, whereas capsular serotypes 23F, 6A, 19F, 16F, 6B, and 15B/C were associated with <10 IPD cases/100,000 acquisitions. There was an inverse relationship between duration of carriage and attack rate by capsular serotype (P<.0001). Attack rates were significantly correlated with invasive odds ratios (P<.0001). CONCLUSIONS The capsular serotype is a major determinant of both pneumococcal duration of carriage and attack rate. Published invasive odds ratios are a reliable and practical method of determining capsular serotype invasiveness and will be valuable for investigating and characterizing emerging capsular serotypes in the context of conjugate vaccination.
Alzheimer's disease and Parkinson's disease

Speech and language alterations were assessed in 51 patients with Parkinson's disease (PD) and 10 patients with dementia of the Alzheimer type (DAT). Thirty-five of the PD patients had no evidence of intellectual impairment on a conventional mental status questionnaire and 16 of the PD patients had dementia syndromes of comparable severity to the DAT patients. DAT produced significantly greater language disturbances, including anomia, decreased information content of spontaneous speech, and diminished word list generation. PD patients had significantly decreased phrase length, impaired speech melody, dysarthria, and agraphia. The results suggest that the dementia of PD is distinguishable from that of DAT: PD patients have prominent motor speech abnormalities, whereas DAT patients exhibit more profound language alterations.
β-Thalassemia Mutations Found During 1 Year of Prenatal Diagnoses in Fars Province, Iran

We report the spectrum of β-thalassemia (β-thal) mutations observed in a cohort of at-risk couples, who presented for prenatal diagnosis at the Thalassemia, Hemophilia and Prenatal Diagnosis Genetic Research Center, Shiraz Medical University, Fars, Iran, from March 2001 to April 2002. Using polymerase chain reaction-amplification refractory mutation system (PCR-ARMS), restriction fragment length polymorphism (RFLP) and direct sequencing technologies, in different combinations, we were able to provide preventive medical abortions to 55 couples at-risk of having an affected fetus. Fetal samples of chorionic villus (63.6%) or amniocentesis (37.6%) were collected according to the gestational age. The average presentation age was 11.6 ± 2.6 weeks. The expected prevalent mutations were IVS-II-1 (G>A, 23.6%) and IVS-I-110 (G>A, 10.0%) followed by IVS-I-5 (G>C, 6.4%) and IVS-I, 25 bp deletion (8.2%).