Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology

Fluorescent-dye-conjugated oligonucleotides were used to classify 14 Fibrobacter strains by fluorescence microscopy. On the basis of partial 16S rRNA sequences of six Fibrobacter strains, four hybridization probes were designed to discriminate between the species Fibrobacter succinogenes and Fibrobacter intestinalis and to identify F. succinogenes subsp. succinogenes. After in situ hybridization to whole cells of the six sequenced strains, epifluorescence microscopy confirmed probe specificity. The four probes were then used to make presumptive species and subspecies assignments of eight additional Fibrobacter strains not previously characterized by comparative sequencing. These assignments were confirmed by comparative sequencing of the 16S rRNA target regions from the additional organisms. Single-mismatch discrimination between certain probe and nontarget sequences was demonstrated, and fluorescent intensity was shown to be enhanced by hybridization to multiple probes of the same specificity. The direct detection of F. intestinalis in mouse cecum samples demonstrated the application of this technique to the characterization of complex natural samples.
High C reactive protein associated with increased pulse wave velocity among urban men with metabolic syndrome in Malaysia.

OBJECTIVE To determine the association between carotid femoral pulse wave velocity (PWVCF); augmentation index (AI); and high-sensitivity C reactive protein (hs-CRP) with metabolic syndrome (MetS), and to determine the influence of ethnicity on PWVCF and AI, and the association between high hs-CRP and increased PWV, and AI in MetS. METHODS A cross-sectional study was conducted at Universiti Kebangsaan Malaysia Medical Center, Kuala Lumpur, Malaysia from September 2009 to September 2011. Three hundred and eighty men (Chinese and Malays) were recruited from the study. The PWVCF and AI were measured by Vicorder (SMT Medical, Wuerzburg, Germany). The hs-CRP level was also determined. We defined MetS using the International Diabetes Federation (IDF) and harmonized criteria. RESULTS Malays had higher AI compared to the Malaysian Chinese. Patients with MetS had higher PWVCF (IDF criteria: 8.5 [8.3-8.7] versus 8.2 [8.0-8.4] m/s, p=0.03; harmonized criteria: 8.5 [8.4-8.7] versus 8.2 [8.0-8.4] m/s, p=0.007) and hs-CRP (IDF criteria: 0.9+/-2.0 versus 0.4+/-1.1 mg/L, p=0.0007; harmonized criteria: 0.8+/-1.9 versus 0.4+/-1.1 mg/L, p=0.002) compared to non-MetS. In subjects with MetS, those with high hs-CRP (>3 mg/L) had higher PWVCF. CONCLUSION Augmentation index values were significantly higher in Malays compared with Malaysian Chinese. Metabolic syndrome was associated with increased PWVCF and hs-CRP. Patients with MetS and high hs-CRP were associated with higher PWVCF. The measurement of hs-CRP reflects the degree of subclinical vascular damage in MetS.
Systematic Correlation of Transcranial Magnetic Stimulation and Magnetic Resonance Imaging in Cervical Spondylotic Myelopathy

Study Design. A prospective study over a 3.5-year period involving transcranial magnetic stimulation and magnetic resonance imaging. Objectives. To assess the correlation of transcranial magnetic stimulation and magnetic resonance imaging in cervical spondylotic myelopathy qualitatively and statistically. Summary of Background Data. Cervical spondylotic myelopathy presents with different degrees of cord compression, which can be assessed by magnetic resonance imaging. There are no large studies correlating transcranial magnetic stimulation and magnetic resonance imaging findings in this condition. Methods. A total of 141 patients with a clinical diagnosis of cervical spondylotic myelopathy were prospectively studied over a 3.5-year period. They were classified into Groups 1 to 4 based on severity of cervical cord changes on magnetic resonance imaging. All had transcranial magnetic stimulation and central motor conduction time measurements within 2 months of the magnetic resonance imaging study. Results. Twenty-eight, 49, 28, and 36 patients were classified into Groups 1 to 4, respectively. Mean upper limb and lower limb central motor conduction times correlated with the severity of magnetic resonance cord compression. The absence of central motor conduction time abnormalities correlated reliably with the absence of cervical cord impingement as in Group 1. Statistically significant right left difference in central motor conduction time in the lower limbs was seen between Groups 1 (no cord changes) and Group 2 (mild cord impingement). Eight other patients with diagnoses other than cervical spondylotic myelopathy all showed central motor conduction time abnormalities. The sensitivity and specificity for transcranial magnetic stimulation for differentiating the presence from absence of magnetic resonance imaging cord abnormality were 100% and 84.8%, respectively. Conclusions. Transcranial magnetic stimulation showed excellent correlation with magnetic resonance imaging findings and can be considered as an effective technique for screening patients for cervical cord abnormalities before magnetic resonance imaging in the clinical setting. The findings in this study have relevant implications in the pathophysiology, management, and health costs of cervical spondylotic myelopathy.
Computational Lower Bounds for Community Detection on Random Graphs

This paper studies the problem of detecting the presence of a small dense community planted in a large Erd\H{o}s-R\'enyi random graph $\mathcal{G}(N,q)$, where the edge probability within the community exceeds $q$ by a constant factor. Assuming the hardness of the planted clique detection problem, we show that the computational complexity of detecting the community exhibits the following phase transition phenomenon: As the graph size $N$ grows and the graph becomes sparser according to $q=N^{-\alpha}$, there exists a critical value of $\alpha = \frac{2}{3}$, below which there exists a computationally intensive procedure that can detect far smaller communities than any computationally efficient procedure, and above which a linear-time procedure is statistically optimal. The results also lead to the average-case hardness results for recovering the dense community and approximating the densest $K$-subgraph.
Effect of Food Residues on Norovirus Survival on Stainless Steel Surfaces

Background In households and food processing plants, minute food residues left behind from improper cleaning may influence the survivability of human norovirus on surfaces. In this study, the survivability of norovirus on desiccated food residue-attached stainless steel coupons was investigated. Methodology/Principal Findings Using murine norovirus-1 (MNV-1) as a surrogate of human norovirus, the survivability of norovirus was investigated on lettuce, cabbage, or ground pork-attached stainless steel coupons. A 6.2 log MPN/ml of MNV-1 infectivity was completely lost at day 30 in residue-free coupons, whereas only a 1.4 log MPN/ml reduction was observed in coupons with residues. Moreover, the disinfective effect of sodium hypochlorite was reduced when residues were present on the coupons. Conclusions/Significance This study revealed that the food residues increased the survivability and the resistance to chemicals of norovirus, indicating the need of thorough cleaning in food processing plants and household settings.
Elucidating the burden of recurrent and chronic digital ulcers in systemic sclerosis: long-term results from the DUO Registry

Objectives Digital ulcers (DUs) occur in up to half of patients with systemic sclerosis (SSc) and may lead to infection, gangrene and amputation with functional disability and reduced quality of life. This study has elucidated the burden of SSc-associated DUs through identification of four patient categories based on the pattern of DU recurrence over a 2-year observation period. Methods Patients with SSc-associated DUs enrolled in the Digital Ulcers Outcome Registry between 1 April 2008 and 19 November 2013, and with ≥2 years of observation and ≥3 follow-up visits during the observation period were analysed. Incident DU-associated complications were recorded during follow-up. Work and daily activity impairment were measured using a functional assessment questionnaire completed by patients after the observation period. Potential factors that could predict incident complications were identified in patients with chronic DUs. Results From 1459 patients, four DU occurrence categories were identified: 33.2% no-DU; 9.4% episodic; 46.2% recurrent; 11.2% chronic. During the observation period, patients from the chronic category had the highest rate of incident complications, highest work impairment and greatest need for help compared with the other categories. Independent factors associated with incident complications included gastrointestinal manifestations (OR 3.73, p=0.03) and previous soft tissue infection (OR 5.86, p=0.01). Conclusions This proposed novel categorisation of patients with SSc-associated DUs based on the occurrence of DUs over time may help to identify patients in the clinic with a heavier DU burden who could benefit from more complex management to improve their functioning and quality of life.
Implementing brief Dynamic Interpersonal Therapy (DIT) in a VA Medical Center

Abstract Background: Given increasing mental health needs in the VA, identifying strategies to deliver new services is critical. Aims: This paper describes the process of navigating provider, patient and systems barriers of an initiative to increase choice, access and quality of psychotherapy at the VA by incorporating an evidence-based short-term, psychodynamic psychotherapy. Methods: Brief Dynamic Interpersonal Therapy (DIT) was selected as a viable model for implementation. Data were gathered on the process of implementation, barriers, Veterans seen, and access to psychodynamic psychotherapy. Results: Nine psychologists and 22 masters level pre-doctoral psychology externs have delivered DIT to 73 Veterans. Veterans referred for psychodynamic psychotherapy annually increased 360%. Furthermore, DIT has become the dominant form of psychodynamic psychotherapy requested of the psychology service representing 70.1% of psychodynamic psychotherapy referrals. Strategies are presented for addressing: (1) provider ability, flexibility and motivation, (2) Veteran perception of relevance, distinctiveness and adaptability to complex presenting issues and (3) administrative support. Conclusions: Implementing an evidence-based short-term psychodynamic treatment option in the VA is feasible. VA mental health providers can be trained in brief psychodynamic psychotherapy and can successfully implement those approaches in VA settings. Finally, psychodynamic treatment approaches may serve as a promising alternative to currently available treatments.
Why Do Some Firms Give Stock Options to All Employees?: An Empirical Examination of Alternative Theories

Many firms issue stock options to all employees. We consider three potential economic justifications for this practice: providing incentives to employees, inducing employees to sort, and helping firms retain employees. We gather data on firms' stock option grants to middle managers from three distinct sources, and use two methods to assess which theories appear to explain observed granting behavior. First, we directly calibrate models of incentives, sorting and retention, and ask whether observed magnitudes of option grants are consistent with each potential explanation. Second, we conduct a cross-sectional regression analysis of firms' option-granting choices. We reject an incentives-based explanation for broad-based stock option plans, and conclude that sorting and retention explanations appear consistent with the data.
Attachment of Mouse Hepatitis Virus to O-Acetylated Sialic Acid Is Mediated by Hemagglutinin-Esterase and Not by the Spike Protein

ABSTRACT The members of Betacoronavirus phylocluster A possess two types of surface projections, one comprised of the spike protein (S) and the other of hemagglutinin-esterase (HE). Purportedly, these viruses bind to O-acetylated sialic acids (O-Ac-Sias) primarily through S, with HE serving merely as receptor-destroying enzyme. Here, we show that, in apparent contrast to human and ungulate host range variants of Betacoronavirus-1, murine coronaviruses actually bind to O-Ac-Sias via HE exclusively. Apparently, expansion of group A betacoronaviruses into new hosts and niches was accompanied by changes in HE ligand and substrate preference and in the roles of HE and S in Sia receptor usage.
Benefit of exercise conditioning for patients with peripheral arterial disease.

Patients with atherosclerotic peripheral arterial disease (PAD) of the lower extremities have impaired walking ability due to exercise-induced muscle ischemia and the resultant pain of intermittent claudication. To evaluate the benefit of exercise training as a treatment for patients with PAD, as well as possible mechanisms associated with improvement, we randomly assigned 19 men with disabling claudication to treated and control groups. Treatment consisted of supervised treadmill walking (1 hr/day, 3 days/wk, for 12 weeks) with progressive increases in speed and grade as tolerated. Graded treadmill testing was performed to maximal toleration of claudication pain on entry and after 12 weeks of training to define changes in peak exercise performance. After 12 weeks, treated subjects had increased their peak walking time 123%, peak oxygen consumption 30%, and pain-free walking time 165% (all p less than 0.05). Control subjects had no change in peak oxygen consumption, but after 12 weeks, peak walking time increased 20% (p less than 0.05). In treated subjects, maximal calf blood flow (measured by a plethysmograph) increased 38 +/- 45% (p less than 0.05), but the change in flow was not correlated to the increase in peak walking time. Elevated plasma concentrations of acylcarnitines have been associated with the functional impairment of PAD and may reflect the metabolic state of ischemic skeletal muscle. In treated subjects, a 26% decrease in resting plasma short-chain acylcarnitine concentration was correlated with improvement in peak walking time (r = -0.78, p less than 0.05). (ABSTRACT TRUNCATED AT 250 WORDS)
Twenty-five year mortality of a community cohort with schizophrenia

Background People with schizophrenia have significantly raised mortality but we do not know how these mortality patterns in the UK have changed since the 1990s. Aims To measure the 25-year mortality of people with schizophrenia with particular focus on changes over time. Method Prospective record linkage study of the mortality of a community cohort of 370 people with schizophrenia. Results The cohort had an all-cause standardised mortality ratio of 289 (95% CI 247–337). Most deaths were from the common causes seen in the general population. Unnatural deaths were concentrated in the first 5 years of follow-up. There was an indication that cardiovascular mortality may have increased relative to the general population (P = 0.053) over the course of the study. Conclusions People with schizophrenia have a mortality risk that is two to three times that of the general population. Most of the extra deaths are from natural causes. The apparent increase in cardiovascular mortality relative to the general population should be of concern to anyone with an interest in mental health.
Thickness vibrations of a piezoelectric plate with dissipation

The three-dimensional (3-D) equations of linear piezoelectricity with quasi-electrostatic approximation are extended to include losses attributed to the acoustic viscosity and electrical conductivity. These equations are used to investigate effects of dissipation on the propagation of plane waves in an infinite solid and forced thickness vibrations in an infinite piezoelectric plate with general symmetry. For a harmonic plane wave propagating in an arbitrary direction in an unbounded solid, the complex eigenvalue problem is solved from which the effective elastic stiffness, viscosity, and conductivity are computed. For the forced thickness vibrations of an infinite plate, the complex coupling factor K*, input admittance Y are derived and an explicit, approximate expression for K* is obtained in terms of material properties. Effects of the viscosity and conductivity on the resonance frequency, modes, admittance, attenuation coefficient, dynamic time constant, coupling factor, and quality factor are calculated and examined for quartz and ceramic barium titanate plates.
Regulation of Wheat Seed Dormancy by After-Ripening Is Mediated by Specific Transcriptional Switches That Induce Changes in Seed Hormone Metabolism and Signaling

Treatments that promote dormancy release are often correlated with changes in seed hormone content and/or sensitivity. To understand the molecular mechanisms underlying the role of after-ripening (seed dry storage) in triggering hormone related changes and dormancy decay in wheat (Triticum aestivum), temporal expression patterns of genes related to abscisic acid (ABA), gibberellin (GA), jasmonate and indole acetic acid (IAA) metabolism and signaling, and levels of the respective hormones were examined in dormant and after-ripened seeds in both dry and imbibed states. After-ripening mediated developmental switch from dormancy to germination appears to be associated with declines in seed sensitivity to ABA and IAA, which are mediated by transcriptional repressions of PROTEIN PHOSPHATASE 2C, SNF1-RELATED PROTEIN KINASE2, ABA INSENSITIVE5 and LIPID PHOSPHATE PHOSPHTASE2, and AUXIN RESPONSE FACTOR and RELATED TO UBIQUITIN1 genes. Transcriptomic analysis of wheat seed responsiveness to ABA suggests that ABA inhibits the germination of wheat seeds partly by repressing the transcription of genes related to chromatin assembly and cell wall modification, and activating that of GA catabolic genes. After-ripening induced seed dormancy decay in wheat is also associated with the modulation of seed IAA and jasmonate contents. Transcriptional control of members of the ALLENE OXIDE SYNTHASE, 3-KETOACYL COENZYME A THIOLASE, LIPOXYGENASE and 12-OXOPHYTODIENOATE REDUCTASE gene families appears to regulate seed jasmonate levels. Changes in the expression of GA biosynthesis genes, GA 20-OXIDASE and GA 3-OXIDASE, in response to after-ripening implicate this hormone in enhancing dormancy release and germination. These findings have important implications in the dissection of molecular mechanisms underlying regulation of seed dormancy in cereals.
Concurrent Titration and Determination of Antibiotic Resistance in Ureaplasma Species with Identification of Novel Point Mutations in Genes Associated with Resistance

ABSTRACT Antibiotic resistance determination of Ureaplasma spp. (Ureaplasma parvum and Ureaplasma urealyticum) usually requires predetermination of bacterial titer, followed by antibiotic interrogation using a set bacterial input. This 96-well method allows simultaneous quantification of bacteria in the presence and absence of antibiotics. A method for determining precise MICs and a method for screening against multiple antibiotics using breakpoint thresholds are detailed. Of the 61 Ureaplasma-positive clinical isolates screened, one (1.6%) was resistant to erythromycin (MIC, >64 mg/liter) and clarithromycin (MIC, 4 mg/liter), one to ciprofloxacin (1.6%), and one to tetracycline/doxycycline (1.6%). Five isolates were also consistently found to have an elevated MIC of 8 mg/liter for erythromycin, but this may not represent true antibiotic resistance, as no mutations were found in the 23S rRNA operons or ribosome-associated L4 and L22 proteins for these strains. However, two amino acids (R66Q67) were deleted from the L4 protein of the erythromycin-/clarithromycin-resistant strain. The tetM genetic element was detected in the tetracycline-resistant clinical isolate as well as in the positive control Vancouver strain serotype 9. The tetM gene was also found in a fully tetracycline-susceptible Ureaplasma clinical isolate, and no mutations were found in the coding region that would explain its failure to mediate tetracycline resistance. An amino acid substitution (D82N) was found in the ParC subunit of the ciprofloxacin-resistant isolate, adjacent to the S83L mutation reported by other investigators in many ciprofloxacin-resistant Ureaplasma isolates. It is now possible to detect antibiotic resistance in Ureaplasma within 48 h of positive culture without prior knowledge of bacterial load, identifying them for further molecular analysis.
Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms

We have studied the metabolic gene–function network in yeast and digital organisms evolved in the artificial life platform Avida. The gene–function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene–function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with Avida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.
Implementing a user-driven online quality improvement toolkit for cancer care.

PURPOSE Peer-to-peer collaboration within integrated health systems requires a mechanism for sharing quality improvement lessons. The Veterans Health Administration (VA) developed online compendia of tools linked to specific cancer quality indicators. We evaluated awareness and use of the toolkits, variation across facilities, impact of social marketing, and factors influencing toolkit use. METHODS A diffusion of innovations conceptual framework guided the collection of user activity data from the Toolkit Series SharePoint site and an online survey of potential Lung Cancer Care Toolkit users. RESULTS The VA Toolkit Series site had 5,088 unique visitors in its first 22 months; 5% of users accounted for 40% of page views. Social marketing communications were correlated with site usage. Of survey respondents (n = 355), 54% had visited the site, of whom 24% downloaded at least one tool. Respondents' awareness of the lung cancer quality performance of their facility, and facility participation in quality improvement collaboratives, were positively associated with Toolkit Series site use. Facility-level lung cancer tool implementation varied widely across tool types. CONCLUSION The VA Toolkit Series achieved widespread use and a high degree of user engagement, although use varied widely across facilities. The most active users were aware of and active in cancer care quality improvement. Toolkit use seemed to be reinforced by other quality improvement activities. A combination of user-driven tool creation and centralized toolkit development seemed to be effective for leveraging health information technology to spread disease-specific quality improvement tools within an integrated health care system.