Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for PDZ domains in bacteria, yeast, and plants

Several dozen signaling proteins are now known to contain 80‐100 residue repeats, called PDZ (or DHR or GLGF) domains, several of which interact with the C‐terminal tetrapeptide motifs X‐Ser/Thr‐X‐Val‐COO− of ion channels and/or receptors. PDZ domains have previously been noted only in mammals, flies, and worms, suggesting that the primordial PDZ domain arose relatively late in eukaryotic evolution. Here, techniques of sequence analysis—including local alignment, profile, and motif database searches—indicate that PDZ domain homologues are present in yeast, plants, and bacteria. It is suggested that two PDZ domains occur in bacterial high‐temperature requirement A (htrA) and one in tail‐specific protease (tsp) homologues, and that a yeast htrA homologue contains four PDZ domains. Sequence comparisons suggest that the spread of PDZ domains in these diverse organisms may have occurred via horizontal gene transfer. The known affinity of Escherichia coli tsp for C‐terminal polypeptides is proposed to be mediated by its PDZ‐like domain, in a similar manner to the binding of C‐terminal polypeptides by animal PDZ domains.
Numerical Study of Lightly Doped Drain and Source Carbon Nanotube Field Effect Transistors

In this paper, we investigate the transport properties of carbon nanotube field-effect transistors (CNTFETs), with a nonequilibrium Green's function (NEGF) method. Tunneling leakage currents with respect to gate voltages are known effects for MOSFET-like CNTFETs (MOSCNTs). To minimize this phenomenon, we have proposed a structure with a simple modification of the MOSCNT by using lightly doped regions between the intrinsic channel and the highly doped source and drain regions, which we call the ¿lightly doped drain and source CNTFET (LDDS-CNTFET). ¿ Simulations have shown that LDDS-CNTFET characteristics are related to the lightly doped region concentration. In comparison with an MOSCNT and a linearly doped CNTFET (LD-CNTFET), an LDDS-CNTFET with appropriately doped lightly doped drain and source regions has demonstrated a larger on current (I on), a larger on -off ratio (I on/I off), a superior ambipolar characteristic, a shorter delay time, and also a smaller power-delay product. Furthermore, our results show that the channel length for an LDDS-CNTFET is shorter than that for an LD-CNTFET having the same off-state characteristics. Finally, the effect of the unavoidable Schottky barriers at the interface of the heavily doped source/drain regions and their metal electrodes has been taken into account. Simulations have demonstrated that these Schottky barriers have almost the same deteriorating effects on the characteristics for both LD-CNTFETs and LDDS-CNTFETs. Hence, all discussions regarding the superiority of the proposed structure are also valid in presence of the Schottky barriers.
Bacteriology of Moderate-to-Severe Diabetic Foot Infections and In Vitro Activity of Antimicrobial Agents

ABSTRACT As part of a United States-based multicenter clinical trial, conducted from 2001 to 2004, that compared ertapenem to piperacillin-tazobactam for the treatment of moderate-to-severe diabetic foot infections (DFIs), we obtained 454 pretreatment specimens from 433 patients. After debridement, the investigators collected wound specimens, mostly by curettage or biopsy, and sent them to the R. M. Alden Research Laboratory for aerobic and anaerobic culture. Among the 427 positive cultures, 83.8% were polymicrobial, 48% grew only aerobes, 43.7% had both aerobes and anaerobes, and 1.3% had only anaerobes. Cultures yielded a total of 1,145 aerobic strains and 462 anaerobic strains, with an average of 2.7 organisms per culture (range, 1 to 8) for aerobes and 2.3 organisms per culture (range, 1 to 9) for anaerobes. The predominant aerobic organisms were oxacillin-susceptible Staphylococcus aureus (14.3%), oxacillin-resistant Staphylococcus aureus (4.4%), coagulase-negative Staphylococcus species (15.3%), Streptococcus species (15.5%), Enterococcus species (13.5%), Corynebacterium species (10.1%), members of the family Enterobacteriaceae (12.8%), and Pseudomonas aeruginosa (3.5%). The predominant anaerobes were gram-positive cocci (45.2%), Prevotella species (13.6%), Porphyromonas species (11.3%), and the Bacteroides fragilis group (10.2%). Pure cultures were noted for 20% of oxacillin-resistant Staphylococcus aureus cultures, 9.2% of Staphylococcus epidermidis cultures, and 2.5% of P. aeruginosa cultures. Two or more species of Staphylococcus were present in 13.1% of the patients. Ertapenem and piperacillin-tazobactam were each active against >98% of the enteric gram-negative rods, methicillin-sensitive S. aureus, and anaerobes. Among the fluoroquinolones, 24% of anaerobes, especially the gram-positive cocci, were resistant to moxifloxacin; 27% of the gram-positive aerobes but only 6% of the members of the family Enterobacteriaceae were resistant to levofloxacin. Moderate-to-severe DFIs are typically polymicrobial, and almost half include anaerobes. Our antibiotic susceptibility results can help to inform therapeutic choices.
Changes in Foxp3-Positive Regulatory T Cell Number in the Intestine of Dogs With Idiopathic Inflammatory Bowel Disease and Intestinal Lymphoma

Although regulatory T cells (Tregs) play an integral role in immunologic tolerance and the maintenance of intestinal homeostasis, their involvement in canine gastrointestinal diseases, including idiopathic inflammatory bowel disease (IBD) and intestinal lymphoma, remains unclear. Here we show altered numbers of forkhead box P3 (Foxp3)–positive Tregs in the intestine of dogs with IBD and intestinal lymphoma. IBD was diagnosed in 48 dogs; small cell intestinal lymphoma was diagnosed in 46 dogs; large cell intestinal lymphoma was diagnosed in 30 dogs; and 25 healthy beagles were used as normal controls. Foxp3-positive Tregs in the duodenal mucosa were examined by immunohistochemistry and immunofluorescence. Duodenal expression of interleukin-10 mRNA was quantified by real-time reverse transcription polymerase chain reaction. The number of Foxp3-positive lamina propria cells and the expression of interleukin-10 mRNA were significantly lower in dogs with IBD than in healthy dogs and dogs with intestinal lymphoma. The number of Foxp3-positive intraepithelial cells was higher in dogs with small cell intestinal lymphoma. Some large cell intestinal lymphoma cases had high numbers of Foxp3-positive cells, but the increase was not statistically significant. Double-labeling immunofluorescence showed that CD3-positive granzyme B–negative helper T cells expressed Foxp3. In small cell intestinal lymphoma cases, the overall survival of dogs with a high Treg density was significantly worse than that of dogs with a normal Treg density. These results suggest that a change in the number of Foxp3-positive Tregs contributes to the pathogenesis of canine IBD and intestinal lymphoma by disrupting mucosal tolerance and suppressing antitumor immunity, respectively.
Short-term exposure to physiological levels of 17 beta-estradiol enhances endothelium-independent relaxation in porcine coronary artery.

OBJECTIVES While alterations in cholesterol and lipoprotein profiles partly account for menopause being a risk factor for coronary heart disease, recent studies have suggested that 17 beta-estradiol may have vascular effects. Our aims were to study the short-term effects of 17 beta-estradiol on vascular function in isolated porcine coronary artery rings. Concomitantly, we sought to determine if physiological concentrations of 17 beta-estradiol could acutely potentiate relaxation RESULTS 17 alpha- and 17 beta-estradiol at pharmacological (> 1 microM) concentrations produced relaxation in U46619-pre-contracted porcine coronary artery rings. Relaxation evoked by 17 beta-estradiol was not reversed by the estrogen receptor antagonists tamoxifen and ICI 182780. Following 20 min exposure to a physiological concentration of 17 beta-estradiol (1 nM), which on its own had no effect, relaxation elicited by cromakalim, levcromakalim and sodium nitroprusside, but not bradykinin or calcium ionophore A23187, were significantly enhanced. This potentiating action was also insensitive to tamoxifen and ICI 182780. Our data provide evidence for an acute indirect relaxant action of 17 beta-estradiol and suggest that it may be via a tamoxifen- and ICI 182780-insensitive estrogen receptor. While this response was only observed at pharmacological concentrations, the potentiation of cromakalim, levcromakalim and sodium nitroprusside relaxation was evident in the presence of a physiological concentration (1 nM) of 17 beta-estradiol. CONCLUSIONS These results demonstrate that short-term exposure to 17 beta-estradiol, at concentrations that have no effect on their own, can enhance vasorelaxation. These vascular effects may partly account for some of the acute effects of 17 beta-estradiol on blood flow.
Perioperative hypothermia in patients undergoing major colorectal surgery

Perioperative hypothermia occurs frequently and can have serious health‐related and financial consequences. Despite multiple warming methods available, perioperative hypothermia remains prevalent. To be effective, preventative measures must be timely and target patients most at risk. The aim of this retrospective review was to document the incidence and patterns of hypothermia in patients undergoing major colorectal surgery.
Understanding Bring Your Own Device (BYOD) and Employee Information Security Behaviors from A Work-Life Domain Perspective

Bring your own device (BYOD) is no longer the exception, it is the norm. Almost every employee today brings his or her own devices to the work environment. This has introduced new challenges to the current efforts to understand the mechanisms that can influence employee’s compliance behavior with regard to information security rules and policies. The key challenges relate to the creation of gray areas by the phenomenon of BYOD through diminishment of the boundaries between work and life domains. In this article, we define a framework of BYOD contextual factors, and the impact of each contextual factor on employees’ compliance behaviors relating to information security policy is presented from a work/life perspective. Accordingly, we have reviewed current information security studies in order to illustrate the current gap in the literature. Finally, we put forward a set of propositions and recommendations for future research.
Iso-orientation areas in the foveal cone mosaic

Abstract The quality of the foveal cone mosaic in human and primate retinas is a basic parameter of spatial vision function. The present study uses digital-texture analysis procedures to analyze the crystalline order of inner segment sections containing the rod-free portions of foveal cone mosaics. Definition of the cone cross-sectional centers made possible by adequate preprocessing allows precise mapping of lattice vertices and differentiation of hexagonal positions by procedures for direct neighbor recongnition. In a further step, the existence of subunits within the hexagonal areas is revealed by the determination of axial orientation. The lattice of the subunits is characterized by similar orientation and high positional correlation of its hexagonal units. The axial orientation of the areas differs from that of neighboring subunits by angular shifts of 10–15 deg and linear series of nonhexagonal irregularities demarcate the borders. Although larger patches with continuous hexagonal order occur in the surrounding rod-free regions, elevated degrees of disorder (30%) are found within the foveolar center (ca. 300 cones). Analysis of a mosaic showing labeled B cones (Szél et al., 1988) demonstrates that lattice disorder is in part associated with the blue cone subpopulation. The foveal mosaic from a glaucomatuous eye reveals severe lattice degradation throughout the rod-free zone, presumably due to extensive receptor loss. The low-frequency superstructure results in local sets of sampling grids (5'–8') with differing orientational bias. Besides a horizontal/vertical difference of mosaic compression (ca. 1:1.15), the present analysis gives no hints for the existence of systematic meridional anisotropies at the receptor mosaic level. The study reveals a discontinuous organization of the foveal mosaic and points to possible sources for the induction and location of lattice disorder.
Dissemination of gastroenteric viruses in the production of lettuce in developing countries: a public health concern

Abstract Investigation of major viruses responsible for acute viral gastroenteritis, such as norovirus (NoV), rotavirus species A (RVA) and human adenovirus (HAdV), was conducted in the mountainous region of the state of Rio de Janeiro in a lettuce‐producing area. Irrigation water and lettuce samples were collected at different production stages. Viruses were concentrated using an adsorption‐elution method and detected by quantitative polymerase chain reaction (qPCR). We detected HAdV in all collection points, although no virus infectivity was shown. The RVA was the most prevalent virus from both water (16.7% [10/60]) and lettuce samples (11.1% [4/36]), with loads ranging from 2.97 × 102 to 6.88 × 103 genomic copies per litre (gc L‐1) and 6.24 × 102 to 1.30 × 104 gc per 25 g, respectively. NoV was detected in 8.33% [8/96] in water and lettuce samples, with concentrations ranging from 7.29 × 101 to 1.92 × 103 gc L‐1 and from 4.29 × 101 to 2.98 × 103 gc 25 g‐1, respectively. Escherichia coli values also demonstrated poor quality of the irrigation and washing water. The presence of at least two different virus strains in all sites reveals the need to improve basic sanitation measures in order to increase food safety.
Remediating organizational functioning in children with ADHD: immediate and long-term effects from a randomized controlled trial.

OBJECTIVE The study compared the efficacy of 2 behavioral interventions to ameliorate organization, time management, and planning (OTMP) difficulties in 3rd- to 5th-grade children with attention-deficit/hyperactivity disorder (ADHD). METHOD In a dual-site randomized controlled trial, 158 children were assigned to organizational skills training (OST; N = 64); PATHKO, a performance-based intervention that precluded skills training (N = 61); or a wait-list control (WL, N = 33). Treatments were 20 individual clinic-based sessions over 10-12 weeks. OST involved skills building provided primarily to the child. PATHKO trained parents and teachers to reinforce children contingently for meeting end-point target goals. Primary outcomes were the Children's Organizational Skills Scales (COSS-Parent, COSS-Teacher). Other relevant functional outcomes were assessed. Percentage of participants no longer meeting inclusion criteria for OTMP impairments informed on clinical significance. Assessments occurred at post-treatment, 1-month post-treatment, and twice in the following school year. RESULTS OST was superior to WL on the COSS-P (Cohen's d = 2.77; p < .0001), COSS-T (d = 1.18; p < .0001), children's COSS self-ratings, academic performance and proficiency, homework, and family functioning. OST was significantly better than PATHKO only on the COSS-P (d = 0.63; p < .005). PATHKO was superior to WL on most outcomes but not on academic proficiency. Sixty percent of OST and PATHKO participants versus 3% of controls no longer met OTMP inclusion criteria. Significant maintenance effects were found for both treatments. CONCLUSIONS Two distinct treatments targeting OTMP problems in children with ADHD generated robust, sustained functional improvements. The interventions show promise of clinical utility in children with ADHD and organizational deficits.
A Common Haplotype Associated with the Basque 2362AG-TCATCT Mutation in the Muscular Calpain-3 Gene

Limb-girdle muscular dystrophy type 2A (LGMD2A) is caused by any of over 150 mutations in the calpain-3 (CAPN3) gene. Of those, 2362AG → TCATCT is particularly prevalent in Basque patients, and this mutation was hypothesized to have arisen in the Basque Country. To explore the natural history of this mutation, we genotyped 65 Basque and non-Basque patients with LGMD2A who carry the 2362AG → TCATCT mutation for four microsatellites within or flanking the gene. A particular haplotype was found in three-fourths of the patients and was assumed to be ancestral. From the average number of recombinations and mutations accumulated from this ancestral haplotype, the age of the 2362AG → TCATCT mutation was estimated to be 50 generations (i.e., 1,250 years), which is more recent than the Paleolithic Basque heritage. The subsequent spread of the 2362AG → TCATCT mutation can be related to gene flow out of the Basque Country, even across a cultural border.
Molecular Characterization of Nontypeable Group B Streptococcus

ABSTRACT Traditionally, the capsular polysaccharide (CPS) antigen has been used to distinguish between the nine known serotypes of group B streptococcus (GBS) by classical antibody-antigen reactions. In this study, we used PCR for all CPSs and selected protein antigens, multilocus sequencing typing (MLST), and pulsed-field gel electrophoresis (PFGE) to molecularly characterize 92 clinical isolates identified as nontypeable (NT) by CPS-specific antibody-antigen reactivity. The PCR and MLST were performed on blinded, randomly numbered isolates. All isolates contained the cfb gene coding for CAMP factor. While most (56.5%) contained a single CPS-specific gene, 40 isolates contained either two or three CPS-specific genes. Type V CPS-specific gene was present in 66% of the isolates, and all serotypes except types IV, VII, and VIII were represented. Most (44.5%) of the isolates contained a single protein antigen gene (bca, bac, rib, alp1, or alp3), and the remaining isolates had multiple protein antigen genes. Of the 61 isolates that had the V CPS-specific gene, 48 (78.6%) had the alp3 gene. PFGE analysis classified the isolates into 21 profile groups, while MLST analysis divided the isolates into 16 sequence types. Forty-two (69%) of 61 isolates with the V CPS-specific gene were in PFGE profile group 4; 41 of these 42 were sequence type 1 by MLST. These data shed new light on the antigenic complexity of NT GBS isolates, information that can be valuable in the formulation of an effective GBS vaccine.
COSTS AND LENGTH OF STAY ASSOCIATED WITH ANTIMICROBIAL RESISTANCE IN ACUTE KIDNEY INJURY PATIENTS WITH BLOODSTREAM INFECTION

Abstract Introduction: Antimicrobial resistance negatively impacts on prognosis. Intensive care unit (ICU) patients, and particularly those with acute kidney injury (AKI), are at high risk for developing nosocomial bloodstream infections (BSI) due to multi-drug-resistant strains. Economic implications in terms of costs and length of stay (LOS) attributable to antimicrobial resistance are underevaluated. This study aimed to assess whether microbial susceptibility patterns affect costs and LOS in a well-defined cohort of ICU patients with AKI undergoing renal replacement therapy (RRT) who developed nosocomial BSI. Methods: Historical study (1995-2004) enrolling all adult RRT-dependent ICU patients with AKI and nosocomial BSI. Costs were considered as invoiced in the Belgian reimbursement system, and LOS was used as a surrogate marker for hospital resource allocation. Results: Of the 1330 patients with AKI undergoing RRT, 92 had microbiologic evidence of nosocomial BSI (57/92, 62% due to a multi-drug-resistant microorganism). Main patient characteristics were equal in both groups. As compared to patients with antimicrobial- susceptible BSI, patients with antimicrobialresistant BSI were more likely to acquire Grampositive infection (72.6% vs 25.5%, P<0.001). No differences were found neither in LOS (ICU before BSI, ICU, hospital before BSI, hospital, hospital after BSI, and time on RRT; all P>0.05) or hospital costs (all P>0.05) when comparing patients with antimicrobial-resistant vs antimicrobial-susceptible BSI. However, although not statistically significant, patients with BSI caused by resistant Gram-negative-, Candida-, or anaerobic bacteria incurred substantial higher costs than those without. Conclusion: In a cohort of ICU patients with AKI and nosocomial BSI undergoing RRT, patients with antimicrobial-resistant vs antimicrobial-susceptible Gram-positive BSI did not have longer hospital stays, or higher hospital costs. Patients with resistant “other” (i.e. Gram-negative, Candida, or anaerobic) BSI were found to have a distinct trend towards increased resources use as compared to patients with susceptible “other” BSI, respectively.
Logic and the organization of information

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Molecular specificities of monoclonal antibodies directed against virulent Treponema pallidum

Radioimmunoprecipitation (RIP) and Western blot analyses with specific anti-Treponema pallidum subsp. pallidum monoclonal antibodies were used to identify antigens with apparent masses of 102, 84, 54, 53, 52, 47, 32, 29, and 24 kilodaltons (kDa). Cross-reactivity of these antibodies with T. pallidum subsp. pertenue antigens and lack of cross-reactivity with T. phagedenis biotype Reiter, T. vincentii, T. refringens, T. scoliodontum, and T. denticola were also demonstrated by RIP and Western blot analyses. Reactivities in the T. pallidum immobilization test, along with the RIP of lactoperoxidase-catalyzed iodination products, suggested that the identified antigens were surface associated. The abundance and surface association of the 47- and 84-kDa antigens were supported by reactivity in the microhemagglutination test for T. pallidum and by strong reactivity of monoclonal antibodies upon indirect immunofluorescence assays with rabbit-cultivated T. pallidum subsp. pallidum, respectively, but not with T. phagedenis biotype Reiter. Anti-47-kDa and anti-84-kDa monoclonal antibodies were also reactive in indirect immunofluorescence assays using treponemes found in dark-field-positive smears of human genital ulcers.
The Environmental Impacts of Reuse: A Review

The fear that human consumption is causing climate change, biodiversity loss, and mineral scarcity has recently prompted interest in reuse because of the intuitive belief that it reduces new production and waste. The environmental impacts of reuse have, however, received little attention—the benefits typically assumed rather than understood—and consequently the overall effects remain unclear. In this article, we structure the current work on the topic, reviewing the potential benefits and pitfalls described in the literature and providing a framework for future research.
[Clinical analysis of the patients with burning mouth syndrome].

OBJECTIVE Clinical data of burning mouth syndrome were investigated in detail and the relation to pain was analyzed in order to find a clue to clinical treatment. METHODS 78 patients with burning mouth syndrome were examined carefully and 7 factors that related to the degree of pain were analyzed with multivariate stepwise regression. RESULTS The study demonstrated that the psychological disorder, autonomic nerves system abnormity, oral dryness and high-extravasated blood level were positively related to the degree of pain. CONCLUSION The study suggested that psychotherapy, improvement of autonomic nerves system, treatment for oral dryness and Chinese traditional therapy of invigoration of blood circulation were of great importance in curing burning mouth syndrome.