Miracle-dz/UniFAR-FTUs huggingface dataset:
Replication-directed sister chromosome alignment in Escherichia coli

Non‐replicating Escherichia coli chromosomes are organized as sausage‐shaped structures with the left (L) and the right (R) chromosome arms (replichores) on opposite cell halves and the replication origin (oriC) close to midcell. The replication termination region (ter) therefore passes between the two outer edges of the nucleoid. Four alignment patterns of the two sister chromosomes within a cell have been detected in an asynchronous population, with the pattern predominating. We test the hypothesis that the minority and patterns arise because of pausing of DNA replication on the right and left replichores respectively. The data resulting from transient pausing or longer‐term site‐specific blocking of replication show that paused/blocked loci remain close to midcell and the normally replicated‐segregated loci locate to the outer regions of the nucleoid, therefore providing experimental support for a direct mechanistic link between DNA replication and chromosome organization.
Recombination in animal mitochondrial DNA: evidence from published sequences.

The question of whether animal mitochondrial DNA (mtDNA) undergoes recombination has recently been the subject of intense debate. In a recent paper (Ladoukakis and Zouros 2001), we presented evidence for mtDNA recombination from direct recovery of recombinant molecules in the gonads of several males of the mussel Mytilus galloprovincialis. Because in this species there exist two lineages of mitochondrial genomes, each with a different mode of transmission (a phenomenon known as doubly uniparental inheritance [DUI] of mtDNA; Zouros et al. 1994), the possibility existed that mtDNA recombination was a peculiarity of DUI. Here, we present evidence for recombination in three different species with standard maternal mtDNA inheritance: a crustacean, an amphibian, and a mammal. Our initial objective was to apply the method of Awadalla, Eyre-Walker, and Maynard Smith (1999) to cases drawn from the literature. We used the study by Meyran, Gielly, and Taberlet (1998) of a segment of cytochrome oxidase I in Gammarus fossarum as one such case. In the process of analyzing these data, we realized that the signature of recombination was clearly preserved in the amino acid sequences. As a result, we turned our search to studies that reported coding mtDNA sequences with substantial differences at the amino acid level, even if the sequences were drawn from different species of a genus. We confined the search to within volume 16 (year 2000) of Molecular Phylogenetics and Evolution, from which we selected the study by Martin et al. (2000) on rodents of the genus Apodemus and the study by Sumida, Ogata, and Nishioka (2000) on frogs of the genus Rana. These two studies report only parts of the known sequences of the cytochrome b gene, but our analysis was based on the full DNA sequences, which we retrieved from GenBank (accession numbers and references in fig. 1). The protocol of the analysis was as follows:
Reliability in assigning ICF codes to children with special health care needs using a developmentally structured interview

Purpose. The purpose of this study was to determine if two teams of raters could reliably assign codes and performance qualifiers from the Activities and Participation component of the International Classification of Functioning, Disability, and Health (ICF) to children with special health care needs based on the results of a developmentally structured interview. Method. Children (N = 40), ages 11 months to 12 years 10 months, with a range of health conditions, were evaluated using a structured interview consisting of open-ended questions and scored using developmental guidelines. For each child, two raters made a binary decision indicating whether codes represented an area of need or no need for that child. Raters assigned a performance qualifier, based on the ICF guidelines, to each code designated as an area of need. Cohen's κ statistic was used as the measure of inter-rater reliability. Results. Team I reached good to excellent agreement on 39/39 codes and Team II on 38/39 codes. Team I reached good to excellent agreement on 5/5 qualifiers and Team II on 10/14 qualifiers. Conclusions. A developmentally structured interview was an effective clinical tool for assigning ICF codes to children with special health care needs. The interview resulted in higher rates of agreement than did results from standardized functional assessments. Guidelines for assigning performance qualifiers must be modified for use with children.
Spotsize contraction in standard single-mode fibers by use of a GI-fiber tip with a high focusing parameter

A spotsize reducer for single-mode fibers (SMFs) was fabricated by use of the quarter-pitch length of a parabolic-index fiber tip having a high focusing parameter. The modal-field diameter of a standard SMF at a wavelength of 1.55 /spl mu/m has been reduced from 10.4 to 5.8 /spl mu/m, with the use of the tip. The reducer appears promising for low-loss coupling between standard SMFs and various waveguides, such as dispersion compensated fibers, erbium-doped fibers, and planar waveguides.
A User-Oriented Webpage Ranking Algorithm Based on User Attention Time

We propose a new webpage ranking algorithm which is personalized. Our idea is to rely on the attention time spent on a document by the user as the essential clue for producing the user-oriented webpage ranking. The prediction of the attention time of a new webpage is based on the attention time of other previously browsed pages by this user. To acquire the attention time of the latter webpages, we developed a browser plugin which is able to record the time a user spends reading a certain webpage and then automatically send that data to a server. Once the user attention time is acquired, we calibrate it to account for potential repetitive occurrences of the webpage before using it in the prediction process. After the user's attention times of a collection of documents are known, our algorithm can predict the user's attention time of a new document through document content similarity analysis, which is applied to both texts and images. We evaluate the webpage ranking results from our algorithm by comparing them with the ones produced by Google's Pagerank algorithm.
Sibling Support During Post-Divorce Adjustment: An Idiographic Analysis of Support Forms, Functions, and Relationship Types

This research examines social support from siblings following parental divorce, based on retrospective interviews and ratings obtained from adult children of divorced parents. Sibling relationships were diverse in the extent, form, and direction of support, as reflected in seven types of sibling support relationships (separates, pals, allies, opponents, parent, protector, encourager). Availability/companionship with siblings predicted improved adjustment to divorce, whereas multiple dimensions of maternal support predicted adjustment. Qualitative analyses suggested that the company of a sibling provided reassurance and promoted resilience, even in the absence of explicit support messages or tangible assistance. Supportive siblings appeared to buffer children by providing a sense of continuity and shared experience during family reorganization. Sibling support typically served a complementary role to parental support. However, siblings sometimes provided more extensive and direct compensatory support in situations where competent parental support was unavailable. Such assistance helped children to weather especially stressful family breakups but did not mitigate bad feelings about the divorce. The results illustrate the situational and relational nature of effective social support in families.
When Does Gender Trump Money? Bargaining and Time in Household Work1

Using data from Australia and the United States, the authors explore the effect of spouses’ contribution to family income on how housework is divided. Consistent with exchange‐bargaining theory, women decrease their housework as their earnings increase, up to the point where both spouses contribute equally to income. In other respects, gender trumps money. The base level of housework for women is much higher. Among the small percentage of couples who are in the range where women provide 51%–100% of household income, the change in housework is opposite what exchange theory predicts: couples that deviate from the normative income standard (men make more money than women) seem to compensate with a more traditional division of household work.
Perspectives of Child Therapists as Revealed Through Therapist Drawings

Abstract This report describes a qualitative study of the perceptions of child mental health practitioners about their own profession, as revealed through their drawings (N = 66). Thirty-three therapists participated in a developmental play therapy training workshop and drew “a picture of a child therapist” pre- and post-training. A content analysis generated 6 categories that were used to rate the drawings: the perceived age of the therapist figure, its body posture, the position of the figure to the ground line, its attentiveness toward the child figure, its differentiation from the child figure, and the placement of play and art materials depicted in the picture. Post-training drawings suggested that participant perceptions had changed. Although the figures representing therapists did not appear as adults in most of the drawings, there were a greater number of child images pictured with the therapist in the post-training drawings, and play and art materials were placed more peripherally. Overall findings provided insight into participants’ perspectives about the essential characteristics of therapists who work with children.
Low prevalence of Connexin 26 (GJB2) variants in Pakistani families with autosomal recessive non‐syndromic hearing impairment

The Pakistani population has become an important resource for research on autosomal recessive non‐syndromic hearing impairment (ARNSHI) due to the availability of large extended and highly consanguineous pedigrees. Here is presented the first report on the prevalence of gap junction beta‐2 (GJB2) variants in Pakistan. One hundred and ninety‐six unrelated Pakistani families with ARNSHI were recruited for a study on the genetics of NSHI. DNA sequencing of the GJB2 coding region was done on two affected individuals per family. Evolutionary conservation and predicted effect on the protein product were studied in order to hypothesize whether or not a variant was potentially deleterious. Homozygous putatively functional GJB2 variants were identified in 6.1% of families. None of the putatively functional GJB2 variants were observed in the compound heterozygous state. The six putatively causative variants noted were 231G > A(W77X), 71G > A(W24X), 167delT, 95G > A(R32H), 358–360delGAG(delE120), and 269T > C(L90P), with 231G > A(W77X) and 71G > A(W24X) being the most common. In addition, five benign polymorphisms, 380G > A(R127H), 457G > A(V153I), 493C > T(R165W), 79G > A(V27I), and 341 A > G(E114G), were identified within this population. In a few individuals, benign polymorphisms were observed to occur on the same haplotype, namely [457G > A(V153I); 493C > T(R165W)] and [79G > A(V27I); 341 A > G(E114G)]. The spectrum of GJB2 sequence variants in Pakistan may reflect shared origins of hearing impairment alleles within the Indian subcontinent. The high degree of consanguinity within Pakistan may have maintained the GJB2 prevalence at a much lower rate than within India and other populations.
WISER: Cooperative Sensing Using Mobile Robots

This paper presents an overview of WISER which is a communication architecture for multiple mobile robots with short-range wireless links aiming at cooperative sensing. WISER deals with several features which were not observed in conventional wireless ad hoc networks: intentional mobility and allowance for disconnection. In this paper we describe the design and the prototype implementation of WISER
Joint interference suppression and power allocation techniques for multiuser multiantenna relay broadcast systems

In this work, we study the downlink of multiuser multiantenna systems which employ one multiple-input multiple-output (MIMO) relay and the amplify-and-forward (AF) relay strategy. We propose joint constrained optimization frameworks that consider the allocation of power levels between the base station (BS) and the relay station (RS) subject to a total power constraint and the joint design of BS precoders, relay beamformers and mobile station (MS) receivers. In terms of the perfect channel state information (CSI), we derive constrained minimum mean square error (MMSE) expressions for the BS precoding and RS beamforming matrices that determine the optimal power levels across the BS and the RS, and the MS receiver matrices. Simulation results show that the performance of the proposed techniques is significantly better than prior art in terms of perfect CSI.
An Angel on the Wind: How Heroic Policy Narratives Shape Policy Realities

Narrative Policy Framework (NPF) is a new and maturing theory of the policy process that takes a systematic, scientific approach to understanding the social construction of policy realities. As such, NPF serves as a bridge between postpositivists, who assert that public policymaking is contextualized through narratives and social construction, and positivists, who contend that legitimacy is grounded in falsifiable claims. The central questions of NPF are: What is the empirical role of policy narratives in the policy process and do policy narratives influence policy outcomes? First, the contributions of NPF scholarship at three levels of analysis—micro, meso, and macro—are examined. Next, necessary conditions of a policy narrative are specified, accompanied by detailed discussion of the narrative components: narrative elements, narrative strategies, and policy beliefs. Finally, an empirical illustration of NPF—a case study of Cape Wind's proposal to install wind turbines off Nantucket—is presented. Although intercoalitional differences have long been studied in the NPF scholarship, this is the first study to examine intracoalitional cohesion or the extent to which a coalition tells the same story across narrative elements, narrative strategies, and policy beliefs. NPF is a new approach to the study of the policy process that offers empirical pathways to better speculating the role of narrative in the policy process.
Trochanteric Fractures

Four hundred and thirty trochanteric fractures operated upon with McLaughlin, Ender or Richard's osteosynthesis were divided into 6 different types based on their radiographic appearance before and immediately after reposition with special reference to the medial cortical support. A significant correlation was found between the fracture type and subseq
Exploring Residents' Perceptions of Expertise and Expert Development

Background Given the expectation that trainees develop into adaptive experts, able to effectively solve both routine and nonroutine problems of practice, and that they do so by actively guiding and shaping their own learning, the purpose of this study was to explore how residents at the postgraduate level of training conceptualize expertise, expert development, and their own learning in the developing expert trajectory. Method This research was a grounded theory study conducted during an 11-month period at a large, urban, Canadian university. Results Three major themes were identified from the data analysis: (1) the dominance of routinization as the pathway to expert practice, (2) a sophisticated conceptualization of the role and complexity of routine practice, and (3) a recognition that nonroutine problems are an important part of physician practice. Conclusions The results highlight our participants' emerging understanding of the complementary nature of routine and nonroutine problem solving by demonstrating their engagement in a process of progressive problem solving, as well as their inclusion of nonroutine problem solving as a crucial part of expert practice.
Multiple modality biomarker prediction of cognitive impairment in prospectively followed de novo Parkinson disease

Objectives To assess the neurobiological substrate of initial cognitive decline in Parkinson’s disease (PD) to inform patient management, clinical trial design, and development of treatments. Methods We longitudinally assessed, up to 3 years, 423 newly diagnosed patients with idiopathic PD, untreated at baseline, from 33 international movement disorder centers. Study outcomes were four determinations of cognitive impairment or decline, and biomarker predictors were baseline dopamine transporter (DAT) single photon emission computed tomography (SPECT) scan, structural magnetic resonance imaging (MRI; volume and thickness), diffusion tensor imaging (mean diffusivity and fractional anisotropy), cerebrospinal fluid (CSF; amyloid beta [Aβ], tau and alpha synuclein), and 11 single nucleotide polymorphisms (SNPs) previously associated with PD cognition. Additionally, longitudinal structural MRI and DAT scan data were included. Univariate analyses were run initially, with false discovery rate = 0.2, to select biomarker variables for inclusion in multivariable longitudinal mixed-effect models. Results By year 3, cognitive impairment was diagnosed in 15–38% participants depending on the criteria applied. Biomarkers, some longitudinal, predicting cognitive impairment in multivariable models were: (1) dopamine deficiency (decreased caudate and putamen DAT availability); (2) diffuse, cortical decreased brain volume or thickness (frontal, temporal, parietal, and occipital lobe regions); (3) co-morbid Alzheimer’s disease Aβ amyloid pathology (lower CSF Aβ 1–42); and (4) genes (COMT val/val and BDNF val/val genotypes). Conclusions Cognitive impairment in PD increases in frequency 50–200% in the first several years of disease, and is independently predicted by biomarker changes related to nigrostriatal or cortical dopaminergic deficits, global atrophy due to possible widespread effects of neurodegenerative disease, co-morbid Alzheimer’s disease plaque pathology, and genetic factors.
Whole-Body Proteolysis Rate Is Elevated in HIV-Associated Insulin Resistance

Type 2 diabetes is characterized by impaired glucose tolerance (IGT) and insulin resistance with respect to glucose metabolism but not amino acid metabolism. We examined whether whole-body leucine and protein metabolism are dysregulated in HIV-infected individuals with IGT. Glucose and leucine kinetics were measured under fasting insulin conditions and during euglycemic hyperinsulinemia using primed-constant infusions of 2H2-glucose and 13C-leucine in 10 HIV-seronegative control subjects, 16 HIV+ subjects with normal glucose tolerance, and 21 HIV+IGT subjects. Glucose disposal rate during hyperinsulinemia was lower in HIV+IGT than the other two groups. Absolute plasma leucine levels and rate of appearance (whole-body proteolysis) were higher in HIV+IGT at all insulin levels but declined in response to hyperinsulinemia in parallel to those in the other two groups. HIV+IGT had greater visceral adiposity, fasting serum interleukin (IL)-8 and free fatty acid levels, and higher lipid oxidation rates during the clamp than the other two groups. These findings implicate several factors in the insulin signaling pathway, which may be further dysregulated in HIV+IGT, and support the notion that insulin signaling pathways for glucose and leucine metabolism may be disrupted by increased proinflammatory adipocytokines (IL-8) and increased lipid oxidation. Increased proteolysis may provide amino acids for gluconeogenesis, exacerbating hyperglycemia in HIV.
Improved method for testing susceptibility of Mycobacterium tuberculosis to pyrazinamide

The acid medium required to test susceptibility of Mycobacterium tuberculosis to pyrazinamide (PZA) is a major problem in obtaining reliable test results. Satisfactory growth is usually obtained on Middlebrook and Cohn 7H10 medium at pH 5.5 if albumin-dextrose-catalase (ADC) supplement rather than oleic acid-albumin-dextrose-catalase is used; however, some lots of ADC supplement still fail to support growth at this low pH. A rapid turbidimetric test was developed to determine the growth-supporting potential of ADC enrichment for M. tuberculosis at pH 5.5. An atmosphere supplemented with 5 to 10% carbon dioxide, used to stimulate growth of tubercle bacilli on 7H10 medium, counteracted the growth-inhibiting effects of PZA. By using optimum conditions of medium and pH, the susceptibility of 90% of M. tuberculosis strains to PZA was determined.
Entropy-Compressed Indexes for Multidimensional Pattern Matching

In this talk, we will discuss the challenges involved in developing a multidimensional generalizations of compressed text indexing structures. These structures depend on some notion of Burrows-Wheeler transform (BWT) for multiple dimensions, though naive generalizations do not enable multidimensional pattern matching. We study the 2D case to possibly highlight combinatorial properties that do not emerge in the 1D case. We also present related work in 2D pattern matching and indexing. Introduction Suffix arrays and suffix trees are ubiquitous data structures at the heart of several text and string algorithms. They are used in a wide variety of applications, including pattern matching, text and information retrieval, Web searching, and sequence analysis in computational biology [14]. Compressed suffix arrays [13, 18, 19] and opportunistic FM-indexes [7, 8] represent new trends in the design of advanced indexes for full-text searching of documents, in that they support the functionalities of suffix arrays and suffix trees, which are more powerful than classical inverted files, yet they also overcome the aforementioned space limitations by exploiting, in a novel way, the notion of text compressibility and the techniques developed for succinct data structures and bounded-universe dictionaries. Grossi and Vitter [13] developed the compressed suffix array using 2n log |Σ| bits in the worst case with o(m) searching time. Sadakane [18, 19] related the space bound to the order-0 empirical entropy H0. Ferragina and Manzini devised the FM-index [7, 8], which is based on the Burrows-Wheeler transform (BWT) and is the first to encode the index size with respect to the hth-order empirical entropy Hh of the text. Navarro [17] recently developed an index requiring 4nHh + o(n) bits, and boasts fast search. Grossi, Gupta, and Vitter [11] exploited the higher-order entropy Hh of the text to represent a compressed suffix array in just nHh + O(n log log n/ log|Σ| n) bits. The index is optimal in space, apart from lower-order terms, achieving asymptotically the empirical entropy of the text (with a multiplicative constant 1). These data structures also have practical significance, as detailed in [12].