Miracle-dz/UniFAR-FTUs huggingface dataset:
Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus

ABSTRACT Paenibacillus sp. P22 is a Gram-negative facultative anaerobic endospore-forming bacterium isolated from poplar hybrid 741 (♀[Populus alba × (P. davidiana + P. simonii) × P. tomentosa]). This bacterium shows strong similarities to Paenibacillus humicus, and important growth-promoting effects on in vitro grown explants of poplar hybrid 741 have been described.
Modulative effects of COMT haplotype on age‐related associations with brain morphology

Catechol‐O‐methyltransferase (COMT), located on chromosome 22q11.2, encodes an enzyme critical for dopamine flux in the prefrontal cortex. Genetic variants of COMT have been suggested to functionally manipulate prefrontal morphology and function in healthy adults. This study aims to investigate modulative roles of individuals COMT SNPs (rs737865, val158met, rs165599) and its haplotypes in age‐related brain morphology using an Asian sample with 174 adults aged from 21 to 80 years. We showed an age‐related decline in cortical thickness of the dorsal visual pathway, including the left dorsolateral prefrontal cortex, bilateral angular gyrus, right superior frontal cortex, and age‐related shape compression in the basal ganglia as a function of the genotypes of the individual COMT SNPs, especially COMT val158met. Using haplotype trend regression analysis, COMT haplotype probabilities were estimated and further revealed an age‐related decline in cortical thickness in the default mode network (DMN), including the posterior cingulate, precuneus, supramarginal and paracentral cortex, and the ventral visual system, including the occipital cortex and left inferior temporal cortex, as a function of the COMT haplotype. Our results provided new evidence on an antagonistic pleiotropic effect in COMT, suggesting that genetically programmed neural benefits in early life may have a potential bearing towards neural susceptibility in later life. Hum Brain Mapp 37:2068–2082, 2016. © 2016 Wiley Periodicals, Inc.
Sensitive enzyme immunoassay for detecting immunoglobulin M antibodies to Sindbis virus and further evidence that Pogosta disease is caused by a western equine encephalitis complex virus

An antibody capture enzyme immunoassay (EIA) was adapted for the detection of immunoglobulin M (IgM) antibody to Sindbis (SIN) virus. Sera from humans with a febrile illness characterized by rash and arthralgia in eastern Finland (Pogosta [POG] disease) and Sweden (Ockelbo disease) and from humans with western equine encephalitis (WEE) virus infection in the United States were tested for IgM antibodies by EIA. Seroconversions were documented in patients with POG disease and with WEE virus infections by using SIN virus as antigen and rabbit anti-SIN virus immunoglobulin; this confirms previous observations that POG disease is caused by a virus closely related to SIN virus and that IgM antibodies to WEE complex alphaviruses are not type specific. This IgM EIA provided a sensitive diagnostic and research tool applicable to epidemiologic problems posed by POG disease.
Impact of round trip delay self-similarity on TCP performance

Previous measurement showed that self-similar nature is found not only in network traffic volume but also round trip packet delay. In this paper, we discuss three issues of the self-similarity of round trip time (RTT), which is one of the most important parameters to determine TCP throughput performance. First, we discuss the origin of the packet delay self-similarity. One study anticipated that the queueing delay of self-similar traffic is the reason for packet delay self-similarity. With computer simulation, we evaluate the correlation between traffic and RTT self-similarity. Next, we investigate the impact of RTT self-similarity on TCP throughput performance. Computer simulation results show that RTT self-similarity gives high variability to file transfer time. Finally, we investigate the impact of RTT self-similarity on RTO (retransmission time out). We discover that the bigger the Hurst parameter of the RTT is, the more frequent unnecessary timeouts occurs. Furthermore, we propose a new RTO calculation algorithm to improve these unnecessary timeouts.
A critique of available scales and presentation of the non‐human primate dyskinesia rating scale

Levodopa‐induced dyskinesia (LID) is a major limitation of long‐term management of Parkinson's disease. The roadblocks that have hindered the development of new treatments for levodopa‐induced dyskinesia were discussed at a meeting organized by the Michael J. Fox Foundation for Parkinson's research (New York, NY, March 2011). Among these, the lack of consensus methodology and clinical applicability for eliciting and rating LID in 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP)–treated monkeys was highlighted as a particular concern. Here we present an update on the practical use of rating scales for evaluating LID in MPTP‐lesioned primate models of PD, with a focus on macaques, and present specifics on the Non‐Human Primate Dyskinesia Rating Scale. © 2012 Movement Disorder Society
Characterization CSMD1 in a large set of primary lung, head and neck, breast and skin cancer tissues

The Cub and Sushi Multiple Domains-1 (CSMD1) is a tumor suppressor gene on 8p23.2, where allelic loss is both frequent and associated with poor prognosis in head and neck squamous cell carcinoma (HNSCC). To understand the extent of CSMD1 aberrations in vivo, we characterized 184 primary tumors from the head and neck, lung, breast, and skin for gene copy number and analyzed expression in our HNSCCs and lung squamous cell carcinomas (SCCs). We detected loss of CSMD1 in a large proportion of HNSCCs (50%), lung (46%) and breast cancers (55%), and to a lesser extent in cutaneous SCCs (29%) and basal cell carcinomas (BCCs, 17%) using array-based comparative genomic hybridization (aCGH). Studying the region more closely with quantitative real-time PCR (qPCR), the loss of CSMD1 increased to 80% in HNSCCs and 93% in lung SCCs. CSMD1 expression was decreased in tumors compared to adjacent benign tissue (65%, 13/20) and was likely due to gene loss in 45% of cases (9/20). We also identified truncated transcripts lacking exons due to DNA copy number loss (30%, 5/17) or aberrant splicing (24%, 4/17). We show loss of CSMD1 in primary HNSCC tissues, and document for the first time that CSMD1 is lost in breast, lung and cutaneous SCCs. We also show that deletions of CSMD1 and aberrant splicing contribute to altered CSMD1 function in vivo.
Bevacizumab plus XELOX as first-line treatment of metastatic colorectal cancer: The OBELIX study.

AIM To confirm the efficacy and safety of bevacizumab/XELOX combination for the treatment of locally advanced or metastatic colorectal cancer (CRC) in Italy. METHODS This multicentric, prospective, open-label study included patients with CRC previously untreated with chemotherapy. Patients were administered bevacizumab in combination with XELOX. The primary efficacy end-point was progression-free survival (PFS). Secondary end-points included time to overall response (TOR), duration of response (DOR), time to treatment failure (TTF) and overall survival (OS). The incidence and type of adverse events AEs and severe AEs were evaluated. Also, the mutational status of BRAF and KRAS was assessed by high resolution melting and direct sequencing, and quality of life (QoL) was measured by the EuroQoL EQ-5D questionnaire at baseline and at the last visit. RESULTS The intention-to-treat population included 197 patients (mean age: 62.3 ± 9.9 years, 56.4% males). At baseline, 16/34 evaluable subjects (47.1%) harbored a KRAS and/or a BRAF mutation; the mean QoL index was 80.2 ± 14.3. First-line therapy was given for 223.7 ± 175.9 d, and after a mean follow-up of 387.7 ± 238.8 d all patients discontinued from the study mainly for disease progression (PD, 45.4%) and AEs (25.4%). Median PFS was 9.7 mo (95%CI: 8.4-10.5) and the median values for secondary end-points were: TOR = 3.9 mo (95%CI: 2.6-4.7), DOR = 8.5 mo (95%CI: 7.3-10.3), TTF = 6.7 mo (95%CI: 6.0-7.7) and OS = 23.2 mo (95%CI: 20.1-27.2). Patients carrying at least one lesion had a lower overall response rate (66.7% vs 88.9%) and a lower probability of achieving complete or partial response than those without mutations, but the difference in relative risk was not statistically significant (P = 0.2). Mean EQ-5D-3L raw index score significantly decreased to 74.9 ± 19.1 at the last visit (signed-rank test, P = 0.0076), but in general the evaluation on QoL perceived by patients was good. CONCLUSION The efficacy of bevacizumab in combination with XELOX in terms of PFS in patients with aCRC or mCRC in Italy was confirmed, with acceptable toxicity.
ERK2 Contributes to the Control of Social Behaviors in Mice

Signaling through extracellular signal-regulated kinase (ERK) is important in multiple signal transduction networks in the CNS. However, the specific role of ERK2 in in vivo brain functions is not fully understood. Here we show that ERK2 play a critical role in regulating social behaviors as well as cognitive and emotional behaviors in mice. To study the brain function of ERK2, we used a conditional, region-specific, genetic approach to target Erk2 using the Cre/loxP strategy with a nestin promoter-driven cre transgenic mouse line to induce recombination in the CNS. The resulting Erk2 conditional knock-out (CKO) mice, in which Erk2 was abrogated specifically in the CNS, were viable and fertile with a normal appearance. These mice, however, exhibited marked anomalies in multiple aspects of social behaviors related to facets of autism-spectrum disorders: elevated aggressive behaviors, deficits in maternal nurturing, poor nest-building, and lower levels of social familiarity and social interaction. Erk2 CKO mice also exhibited decreased anxiety-related behaviors and impaired long-term memory. Pharmacological inhibition of ERK1 phosphorylation in Erk2 CKO mice did not affect the impairments in social behaviors and learning disabilities, indicating that ERK2, but not ERK1 plays a critical role in these behaviors. Our findings suggest that ERK2 has complex and multiple roles in the CNS, with important implications for human psychiatric disorders characterized by deficits in social behaviors.
Cystatin C, β‐2‐microglobulin and β‐trace protein in pre‐eclampsia

Background. An altered renal function is an essential component of the patho‐physiology of pre‐eclampsia. The plasma levels of low molecular mass proteins, e.g. β‐trace protein, β‐2‐microglobulin and cystatin C, are increased in the third trimester of normal pregnancy. The plasma levels of cystatin C and β‐2‐microglobulin are further increased in pre‐eclampsia, and the cystatin C level has been reported to be a reliable marker for the disease. The aim of this investigation was to study the plasma levels of β‐trace protein, β‐2‐microglobulin and cystatin C in pre‐eclampsia, and to determine the diagnostic performance of these proteins compared to that of urate and creatinine. Methods. A case‐control study of 57 women diagnosed with pre‐eclampsia, and 218 healthy women with uncomplicated singleton pregnancies in the third trimester. Women in the catchment area of Lund, Sweden, were included during an 18‐month period from October 2003 to April 2005. Venous blood samples were drawn upon inclusion when diagnosis was made. The maternal plasma concentrations of the 3proteins were analysed by automated particle‐enhanced immunoturbidimetric assays. Results. The plasma levels of the 3 proteins were significantly higher in the third trimester of pre‐eclamptic patients compared to healthy pregnant women in the third trimester. The upper reference limits (parametric 97.5 percentile) were 2.57mg/l for β‐2‐microglobulin, 0.72mg/l for β‐trace protein and 1.37mg/l for cystatin C. ROC analysis showed similar diagnostic performance for the 3 proteins, with β‐trace protein displaying the best diagnostic performance of all the analytes. Conclusions. In this study, the maternal plasma levels of β2‐microglobulin, β‐trace protein and cystatin C were all significantly elevated in pre‐eclampsia compared to those of healthy pregnant women, and displayed similar diagnostic performance for diagnosing pre‐eclampsia. The results indicate that low molecular mass proteins are useful as markers of renal impairment in pre‐eclampsia.
Accounting for the climate–carbon feedback in emission metrics

Abstract. Most emission metrics have previously been inconsistently estimated by including the climate–carbon feedback for the reference gas (i.e. CO2) but not the other species (e.g. CH4). In the fifth assessment report of the IPCC, a first attempt was made to consistently account for the climate–carbon feedback in emission metrics. This attempt was based on only one study, and therefore the IPCC concluded that more research was needed. Here, we carry out this research. First, using the simple Earth system model OSCAR v2.2, we establish a new impulse response function for the climate–carbon feedback. Second, we use this impulse response function to provide new estimates for the two most common metrics: global warming potential (GWP) and global temperature-change potential (GTP). We find that, when the climate–carbon feedback is correctly accounted for, the emission metrics of non-CO2 species increase, but in most cases not as much as initially indicated by IPCC. We also find that, when the feedback is removed for both the reference and studied species, these relative metric values only have modest changes compared to when the feedback is included (absolute metrics change more markedly). Including or excluding the climate–carbon feedback ultimately depends on the user's goal, but consistency should be ensured in either case.
The American Academy of Orthopaedic Surgeons evidence-based guideline on: treatment of osteoarthritis of the knee, 2nd edition.

The AAOS Evidence-Based Guideline on Treatment of Osteoarthritis of the Knee, 2nd Edition, includes only less-invasive alternatives to knee replacement. This brief summary of the AAOS Clinical Practice Guideline contains a list of the recommendations and the rating of strength based on the quality of the supporting evidence. Discussion of how each recommendation was developed and the complete evidence report are contained in the full guideline at www.aaos. org/guidelines. ### Conservative Treatments: Recommendations 1-6 #### RECOMMENDATION 1 We recommend that patients with symptomatic osteoarthritis of the knee participate in self-management programs, strengthening, low-impact aerobic exercises, and neuromuscular education; and engage in physical activity consistent with national guidelines. Strength of Recommendation: Strong #### RECOMMENDATION 2 We suggest weight loss for patients with symptomatic osteoarthritis of the knee and a BMI ≥25. Strength of Recommendation: Moderate #### RECOMMENDATION 3A We cannot recommend using acupuncture in patients with symptomatic osteoarthritis of …
Rare association of congenital penile urethrocutaneous fistula with Y-type urethral duplication

A 24-year-old man presented with symptoms of difficulty in passage of urine, mixed with gas and stool from penoscrotal junction since birth. He had a history of surgery (posterior sagittal anorectoplasty) for imperforate anus in first week of his life. On physical examination, external meatus was adequate with small 5×5 mm fistulous opening noted at penoscrotal junction with normal anal tone and opening. On evaluation with retrograde urethrography, voiding cystourethrogram, cystoscopy and barium enema, he was found to have penile urethrocutaneous fistula of 0.5×0.5 cm with Y-type incomplete urethral duplication. Urethroanal fistula (Y-type urethral duplication) was of small size (<5 mm), so closed primarily through perineal route with interposition of ischiorectal fat. Penile urethrocutaneous fistula (4 mm) too was closed primarily and covered with tunica vaginalis flap in single sitting. It has been 6 months since surgery and the patient is fully continent and voiding well with no urinary or faecal leak.
The CamPaIGN study of Parkinson's disease: 10-year outlook in an incident population-based cohort

Background Prognosis in Parkinson's disease (PD) remains poorly understood due to a lack of unbiased data on the natural history of treated PD. The CamPaIGN study has been the first to prospectively track disease evolution from diagnosis in an unselected population-representative incident cohort. We now report the 10-year follow-up data, focusing on three key irreversible milestones: postural instability (Hoehn and Yahr 3), dementia and death. Methods The cohort was collected between December 2000 and 2002. Those meeting diagnostic criteria (n=142) were followed-up until 1 January 2012. Clinical, neuropsychological and genetic testing were performed. Progression to key milestones was evaluated using Kaplan–Meier and Cox regression survival analyses. Results At 10 years, 55% had died, 68% had postural instability and 46% dementia. 23% had a good outcome at 10 years (surviving free of dementia/postural instability). Death rate was comparable with the UK population (standardised mortality ratio 1.29 (0.97–1.61)). Death certificates indicated PD was a substantial contributor in only 20%, with pneumonia being the commonest cause of death. Age, non-tremor-dominant motor phenotype and comorbidity predicted earlier postural instability. Baseline predictors of dementia were age, motor impairment, ‘posterior-cortical’ cognitive deficits and MAPT genotype. Conclusions (1) outlook in PD is heterogeneous, with most dying or developing dementia or postural instability by 10 years from diagnosis, but a quarter still doing well, with preserved mobility and intact cognition; (2) death is not directly related to PD in the majority; (3) baseline clinical and genetic variables are predictive of outcome and may be helpful in selecting patients for clinical trials.
Expression and characterization of UDPGlc dehydrogenase (KfiD), which is encoded in the type-specific region 2 of the Escherichia coli K5 capsule genes

Region 2 of the Escherichia coli K5 capsule gene cluster contains four genes (kfiA through -D) which encode proteins involved in the synthesis of the K5 polysaccharide. A DNA fragment containing kfiD was amplified by PCR and cloned into the gene fusion vector pGEX-2T to generate a GST-KfiD fusion protein. The fusion protein was isolated from the cytoplasms of IPTG (isopropyl-beta-D-thiogalactopyranoside)-induced recombinant bacteria by affinity chromatography and cleaved with thrombin. The N-terminal amino acid sequence of the cleavage product KfiD' corresponded to the predicted amino acid sequence of KfiD with an N-terminal glycyl-seryl extension from the cleavage site of the fusion protein. Anti-KfiD antibodies obtained with KfiD' were used to isolate the intact KfiD protein from the cytoplasms of E. coli organisms overexpressing the kfiD gene. The fusion protein, its cleavage product (KfiD'), and overexpressed KfiD converted UDPGlc to UDPGlcA. The KfiD protein could thus be characterized as a UDPglucose dehydrogenase.
Acute Kidney Injury After Intravenous Versus Intra-Arterial Contrast Material Administration in a Paired Cohort

ObjectivesThe aim of this study was to determine whether intra-arterial administration of contrast material is associated with a higher risk of acute kidney injury (AKI) compared with that of intravenous (IV) administration in a cohort of patients that received both routes of administration. Materials and MethodsAll patients who received both a contrast-enhanced computed tomography (CT) and a diagnostic or interventional cardiac catheterization between 2000 and 2014 were identified. Patients who lacked sufficient preprocedure and postprocedure serum creatinine results, who were on preexisting renal dialysis, or who underwent additional contrast-enhanced procedures within 7 days of either procedure were excluded. The rate of AKI (serum creatinine ≥0.3 mg/dL or 50% above baseline) was compared after CT scan and cardiac catheterization using McNemar test. ResultsA total of 1969 patients met all study inclusion criteria. The rate of AKI after CT scan was similar to the rate after catheterization when examining all patients (9.9% CT vs 11% catheterization, P = 0.12). A similar rate of AKI after both procedures was observed regardless of procedure order, catheterization type, and patient baseline estimated glomerular filtration rate. ConclusionsIntra-arterial administration of contrast material during cardiac catheterization had a similar risk of AKI as compared with that of CT scanning involving IV administration in a cohort of patients who underwent both procedures. These findings suggest that previously reported much higher rates of AKI after cardiac catheterization compared with that of IV contrast administration reflect higher baseline clinical risk factors for AKI in the former cohort compared with that in the latter.
Using co-training to empower active learning

Active Learning and co-training are cases of semi-supervised learning both are used when labeled data is scarce. Active learning attempts to improve learning model by querying over unlabeled data and the main challenge there, is to find the optimum instance query. And co-training tries to exploit two different feature sets to enlarge number of labeled data without any need to get external information. Several researches tried to couple these two methods and get best out of them and they achieve noteworthy results. But we have witnessed that using co-training and active learning in sequence architecture outperforms when they are working in parallel. Using them in sequence means we have used co-training techniques to just find the best queries for active learning, and not in learning process itself. We will demonstrate that it has better results than plain active learning and co-training and even current parallel architectures. For this work we have used different techniques to split data into two distinct datasets; we will also discuss about it alongside our query selection method.
IDENTIFYING HAND GESTURES USING SEMG FOR HUMAN MACHINE INTERACTION

Surface Electromyographic signals (sEMG) have emerged as a normal gadget for rehabilitation functions, medical analysis, and likewise as a source for manipulate of prosthetic and assistive instruments. It can be determined that EMG alerts showcase certain patterns for specified hobbies of the muscle. The right recognizance of the sample helps in greater manipulate of assistive gadgets for helping movement. This paper offers the growth of a neural networks classifier for classifying the one-of-a-variety hand moves of human forearm. Experiments are performed on the extensor digitorum and flexor digitorum superficial muscle of the right hand. Ten subjects are asked to participate in voluntary contractions with admire to the concerned muscle. From the obtained sEMG data, six parametric feature extraction techniques are used as function extracted and cascade forward back propagation neural network (CFBPNN), pattern recognizance network are utilized to gestures identifications. The classifier is learned to discriminate the patterns with an average classification accuracy of 95.13% for pattern recognizance network using auto regressive burg. The offline results showed that bit transfer rate (BTR) achieved highest value of 37.71 bits/sec.