Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of the Accelerate Pheno System for Identification and Antimicrobial Susceptibility Testing of Pathogens in Positive Blood Cultures and Impact on Time to Results and Workflow

ABSTRACT The Accelerate Pheno system uses automated fluorescence in situ hybridization technology with morphokinetic cellular analysis to provide rapid species identification (ID) and antimicrobial susceptibility testing (AST) results for the most commonly identified organisms in bloodstream infections. The objective was to evaluate the accuracy and workflow of bacterial and yeast ID and bacterial AST using the Accelerate Pheno system in the clinical microbiology laboratory. The consecutive fresh blood cultures received in the laboratory were analyzed by the Accelerate Pheno system within 0 to 8 h of growth detection. ID/AST performance, the average times to results, and workflow were compared to those of the routine standard of care. Of the 232 blood cultures evaluated (223 monomicrobial and 9 polymicrobial) comprising 241 organisms, the overall sensitivity and specificity for the identification of organisms were 95.6% and 99.5%, respectively. For antimicrobial susceptibility, the overall essential agreement was 95.1% and categorical agreement was 95.5% compared to routine methods. There was one very major error and 3 major errors. The time to identification and the time to susceptibility using the Accelerate Pheno system were decreased by 23.47 and 41.86 h, respectively, compared to those for the standard of care. The reduction in hands on time was 25.5 min per culture. The Accelerate Pheno system provides rapid and accurate ID/AST results for most of the organisms found routinely in blood cultures. It is easy to use, reduces hands on time for ID/AST of common blood pathogens, and enables clinically actionable results to be released much earlier than with the current standard of care.
Heparinase 1 selectivity for the 3 , 6-diO-sulfo-2-deoxy-2-sulfamido-α-D-glucopyranose ( 1 , 4 ) 2O-sulfo-α-L-idopyranosyluronic acid ( GlcNS 3 S 6 S-IdoA 2 S ) linkages

Zhongping Xiao2,3, Wenjing Zhao4, Bo Yang3, Zhenqing Zhang3, Huashi Guan1,2, and Robert J Linhardt1,3,4,5 Key Laboratory of Marine Drugs, Chinese Ministry of Education, Institute of Marine Drug and Food, Ocean University of China, Qingdao 266003, China; Department of Chemistry and Chemical Biology, Department of Biology, and Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
Sequence and organization of genes encoding enzymes involved in pyruvate metabolism in mycoplasma capricolum

The region of the genome of Mycoplasma capricolum upstream of the portion encompassing the genes for Enzymes I and IIAglc of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) was cloned and sequenced. Examination of the sequence revealed open reading frames corresponding to numerous genes involved with the oxidation of pyruvate. The deduced gene organization is naox (encoding NADH oxidase)‐lplA (encoding lipoate‐protein ligase)‐odpA (encoding pyruvate dehydrogenase EIα)‐odpB (encoding pyruvate dehydrogenase EIβ)‐odp2 (encoding pyruvate dehydrogenase EII)‐dldH (encoding dihydrolipoamide dehydrogenase)‐pta (encoding phosphotransacetylase)‐ack: (encoding acetate kinase)‐orfA (an unknown open reading frame)‐kdtB‐ptsI‐crr. Analysis of the DNA sequence suggests that the naox and IplA genes are part of a single operon, odpA and odpB constitute an additional operon, odp2 and dldH a third operon, and pta and ack an additional transcription unit. Phylogenetic analyses of the protein products of the odpA and odpB genes indicate that they are most similar to the corresponding proteins from Mycoplasma genitalium, Acholeplasma laidlawii, and Gram‐positive organisms. The product of the odp2 gene contains a single lipoyl domain, as is the case with the corresponding proteins from M. genitalium and numerous other organisms. An evolutionary tree places the M. capricolum odp2 gene product in close relationship to the corresponding proteins from A. laidlawii and M. genitalium. The dldH gene encodes an unusual form of dihydrolipoamide dehydrogenase that contains an aminoterminal extension corresponding to a lipoyl domain, a property shared by the corresponding proteins from Alcaligenes eutrophus and Clostridium magnum. Aside from that feature, the protein is related phylogenetically to the corresponding proteins from A. laidlawii and M. genitalium. The phosphotransacetylase from M. capricolum is related most closely to the corresponding protein from M. genitalium and is distinguished easily from the enzymes from Escherichia coli and Haemophilus influenzae by the absence of the characteristic amino‐terminal extension. The acetate kinase from M. capricolum is related evolutionarily to the homologous enzyme from M. genitalium. Map position comparisons of genes encoding proteins involved with pyruvate metabolism show that, whereas all the genes are clustered in M. capricolum, they are scattered in M. genitalium.
An Accurate Diagnosis of Myalgic Encephalomyelitis and Chronic Fatigue Syndrome requires strict Clinical Case definitions and Objective Test Methods

Myalgic Encephalomyelitis (ME) and Chronic Fatigue Syndrome (CFS) are subject to controversy. Although ME and CFS are often considered to be to be synonymous, the case criteria for ME and CFS define two distinct diseases with partial overlap. ME, recognized as a new clinical entity in the 1950’s, is characterized by distinctive muscular, neurological and autonomic symptoms. In contrast the core feature of CFS, introduced in 1988 and redefined in 1994, is chronic fatigue. Some researchers consider CFS to be equivalent to (incapacitating) chronic fatigue (CF). After the introduction of CFS, other criteria for ME, ME/CFS, CFS and CF were introduced and used in research studies, creating obfuscation and controversy. The use of various diagnostic criteria has hampered effective research into ME and CFS. Next to the various diagnostic criteria, the assessment of symptoms is almost always based on questionnaires and subjective measures, e.g. physical functioning. Due to their nature subjective measures are incomparable over time and between patients. Moreover subjective measures introduce a significant risk of bias, for example due to researcher allegiance, the Hawthorne effect, and buy-in effects. Despite the fact that ME and CFS (subclasses) lack a clear etiological explanation (yet), the symptoms can and should be assessed by objective test measures, since subjective measures are ambiguous, incomparable and minimize the risk of bias. Objective test measures can also confirm the seriousness of both ME and CFS. To resolve the diagnostic issues in research studies and clinical practice, a clear distinction between ME and CFS (not ME), based on the original criteria, is crucial. Although the use of objective test methods is more expensive and time-consuming and severe cases cannot be subjected to these tests, considering the (scientific) confusion originating from the use of subjective measures it is essential to assess the symptoms of patients objectively both in clinical practice and research settings.
The inactivating factor of glutamine synthetase, IF7, is a “natively unfolded” protein

Glutamine synthetase (GS) is the key enzyme responsible for the primary assimilation of ammonium in all living organisms, and it catalyses the synthesis of glutamine from glutamic acid, ATP, and ammonium. One of the recently discovered mechanisms of GS regulation involves protein‐protein interactions with a small 65‐residue‐long protein named IF7. Here, we study the structure and stability of IF7 and its binding properties to GS, by using several biophysical techniques (fluorescence, circular dichroism, Fourier transform infrared and nuclear magnetic resonance spectroscopies, and gel filtration chromatography) which provide complementary structural information. The findings show that IF7 has a small amount of residual secondary structure, but lacks a well defined tertiary structure, and is not compact. Thus, all of the studies indicate that IF7 is a “natively unfolded” protein. The binding of IF7 to GS, its natural binding partner, occurs with an apparent dissociation constant of KD = 0.3 ± 0.1 μM, as measured by fluorescence. We discuss the implications for the GS regulation mechanisms of IF7 being unfolded.
Differential Antianxiety Response to Caloric Intake between Normal and Obese Subjects

&NA; Obese subjects (N = 152) attending a weight reduction clinic and controls (N = 62) rated numerous aspects of their psychological state using analogue scales before and after a standard liquid meal. Prior to the meal, the only difference in psychological state between the groups was that the obese subjects had higher scores than controls on the questions relating to their self‐perception of “fatness. ” Following the meal, the obese subjects, including some previously obese (now normal weight) subjects, reported a decrease in “anxiety” as reflected by significant changes in premeal to postmeal scores on 5 anxiety‐related questions. Control subjects tested in two separate groups, one demographically matched and one nonmatched, did not experience this “antianxiety” effect, but reported postmeal increases in feelings of “fatness” and “sexual arousal” as compared with the obese subjects.
Unemployment, re-employment and the use of primary health care services.

OBJECTIVE To examine the association between re-employment and the use of primary health care services. DESIGN A cohort study of employed teenagers and a 'natural experiment' among adult long-term unemployed with an intervention group of re-employed, a control group of not re-employed, and a matched control group of permanently employed. SETTING An industrial town (pop. 25,000) in southwestern Finland. PARTICIPANTS 84 teenage and 143 adult long-term unemployed and 82 permanently employed individuals. MAIN OUTCOME MEASURE Frequency of primary health care visits. RESULTS Primary health care visits increased during re-employment among both teenage and adult re-employed (n = 82), but not in a control group of 61 long-term unemployed who were not employed under the re-employment scheme. A comparison with persons in regular wage employment indicated that visits increased from a low to a normal level. CONCLUSION To explain the results, reference is made to the need for sickness absence certificates and to epidemiological factors. The findings also raise serious questions with regard to the ability of the health care system to reach, let alone help, unemployed citizens.
TL ; DR : Learning Long Term Dependencies with Deep Logarithmic Residual LSTMs

We present logarithmically spaced residual connections, a modification to the existing encode-decode LSTM architecture for sequence to sequence learning problems that combats vanishing gradients and facilitates learning in otherwise unsolved long term seq-to-seq problems. Our scheme effectively allows backpropagation to train on length N sequences as if they were length logN ; our simplest scheme has negligible impact on speed and memory. We also present several natural modifications to our basic scheme that may yield increased performance at a potentially nontrivial cost in speed. Finally, we demonstrate correctness through several text summarization tests on the Gigaword corpus and suggest several future applications for our work.
Jewish and Arab ethnocentrism in Israel

Sumner (1906), in a classic essay, considers ethnocentrism as a universal syndrome of attitudes and behavior. The 'ingroup' sees itself as virtuous and superior and the 'outgroup' as contemptible and inferior, it sanctions association with its own members and dissociation with others, loves and trusts insiders and hates and distrusts outsiders, and so forth (LeVine and Campbell, 1972). Ethnocentrism is essential for the survival of the group and for keeping its distinct identity, culture, solidarity and ability to compete successfully with other groups. Although they simplify and distort reality, group preconceptions and prejudices provide the individual with a sense of direction and belonging. This perspective regards ethnocentrism as a permanent, functional, positive and universal group feature. It stands in contrast with the more common and critical approach which conceives of ethnocentrism as an antonym for cultural relativism and human equality, and identifies it with intolerance, chauvinism and racism. These competing conceptions emphasise different components of ethnocentrism, where a simple test of proportion and plausibility would produce more balanced and realistic appraisals. To be ethnocentric, attitudes must contain an excessive or unjustified element of superiority, rejection or hostility toward an outgroup. For instance, mistrust is not ethnocentric if it is firmly grounded in facts; objection to intermarriage is not prejudicial if minority and majority agree on separation. Judiciousness is therefore necessary for establishing a case of ethnocentrism. The task of examining each case is rather complex because ethnocentrism may manifest itself on individual and institutional levels. Spontaneous, personal ethnocentrism consists of an aggregate set of individual attitudes and behaviours, whereas organized, ideological ethnocentrism refers to public policies and institutional practices (Lanternari, 1980). Both forms should be explored. One should also look into the ethnocentrism of both sides of the ethnic divide. It is a long-standing tradition in the literature of intergroup relations to concentrate solely on the ethnocentrism of the dominant group because it is more freely expressed, entrenched and consequen-
Impaired activation of adenylyl cyclase in lung of the Basenjigreyhound model of airway hyperresponsiveness: decreased numbers of high affinity β‐adrenoceptors

1 To evaluate mechanisms involved in the impaired β‐adrenoceptor stimulation of adenylyl cyclase in tissues from the Basenji‐greyhound (BG) dog model of airway hyperresponsiveness, we compared agonist and antagonist binding affinity of β‐adrenoceptors, β‐adrenoceptor subtypes, percentage of β‐adrenoceptors sequestered, and coupling of the β‐adrenoceptor to Gsα in lung membranes from BG and control mongrel dogs. We found that lung membranes from the BG dog had higher total numbers of β‐adrenoceptors with a greater percentage of receptors of the β subtype as compared to mongrel lung membranes. 2 Agonist and antagonist binding affinity and the percentage of β‐adrenoceptors sequestered were not different in BG and mongrel dog lung membranes. However, the percentage of β‐adrenoceptors in the high affinity state for agonist was decreased in BG lung membranes suggesting an uncoupling of the receptor from Gsα. 3 Impaired coupling between the β‐adrenoceptor and G protein documented by the decreased numbers of β‐adrenoceptors in the high affinity state in BG lung membranes, is a plausible explanation for the reduced stimulation of adenylyl cyclase and the resultant reduction in airway smooth muscle relaxation in this model.
A Sociodemographic, Phenomenological, and Long-Term Follow-up Study of Patients with Body Dysmorphic Disorder in Brazil

Objective: The main characteristic of body dysmorphic disorder (BDD) is a preoccupation with an imagined defect in appearance in a normal-appearing person or an excessive preoccupation with appearance in a person with a small physical defect. In this non-controlled study, our objective was to describe the socio-demographic, phenomenological, and long-term outcome features of a Brazilian sample of patients with BDD. Methods: We performed a chart-review of the 166 patients who attended the Obsessions, Compulsions, and Impulsions Subprogram of the Institute of Psychiatry of the Federal University of Rio de Janeiro, Brazil, during the period between 1998 and 2005. Results: Twenty patients (12%) had clinically significant BDD. This sample was characterized by a predominance of female (n = 11; 55%), single or divorced (n = 18; 90%), and economically unproductive patients (n = 17; 85%). We found an average of 2.5 current imagined defects per patient. The most frequently reported body parts of excessive concern were the overall appearance, size or shape of the face (n = 7; 35%), the skin (n = 6; 30%), the hair (n = 6; 30%), the nose (n = 5; 25%), and the body build and weight (n = 5; 25%). Most individuals exhibited a chronic condition (n = 13; 65%) and kept the same concerns during the course of the disorder (n = 12; 60%). All patients displayed compulsive behaviors, including recurrent mirror checking (n = 14; 70%), camouflaging (n = 13; 65%), reassurance seeking by means of repetitive questioning of others (n = 9; 45%), and excessive use of cosmetics (n = 7; 35%). Two patients reported “do-it-yourself surgeries. Seven patients had current suicidal ideation (35%). Six patients (30%) showed no insight over their dysmorphic beliefs. Fifteen patients (95%) exhibited psychiatric comorbidities, mostly obsessive-compulsive disorder (OCD) (n = 14, 70%) and major depressive disorder (n = 11; 55%). The majority of patients were treated naturalistically with serotonin reuptake inhibitors (n = 15; 75%), either solo or in association with antipsychotics (n = 10; 50%). Nevertheless, only 5 (25%) responded favorably to treatment during the long-term follow-up (CGI < 2). Conclusions: BDD is a severe disorder that is frequently associated with other psychiatric conditions and responds poorly to treatment in the naturalistic setting. No significant trans-cultural variations were identified in the comparison between Brazilian, North American, and European samples.
A Scale for Measuring Internet Banking Service Quality: Literature Review and Validation with Indian Public Sector Banks

There have been many fragmented studies of Internet service quality which have resulted in several models with different combinations of constructs and items, some focusing on different perspectives, and many using different names for the same construct. Some of these models were developed for the specific context of Internet banking. This paper consolidates these fragmented studies of Internet service quality and Internet banking service quality and proposes a scale with nine constructs to measure Internet banking service quality. The scale compares expected service (E) with perceived service (P) across all nine constructs and measures perceived service quality based on P-E. The paper then validates the scale using exploratory and confirmatory factor analyses of 499 survey responses from Internet banking customers of five Indian public sector banks. The service quality scale was conceptualised as a nine-construct, 39-item scale. Through the purification process it was reduced to 34 items spread across nine constructs: availability, site aesthetics, ease of use, technical performance, reliability, privacy, trust, responsiveness, and customisation.
Determination of Sex of an Individual by Identifying SRY Gene through PCR Analysis of DNA Extracted From Incinerated Teeth-A Single Blind Pilot Study

Introduction: Sex determination using skeletal fragments presents a great difficulty to forensic investigators. The teeth are resistant to all conditions due to relatively high degree of physical and chemical resistance of the dental structure. With the development of Polymerised Chain Reaction (PCR), DNA analysis of teeth for sex determination could be performed in bodies that are severely mutilated. Aim and Objective: To determine the reliability of sex determination from incinerated teeth samples using Polymerised Chain Reaction. Materials and Methods: The study was carried on 10 maxillary and mandibular premolars and permanent molars (5 – male, 5-female). Ten samples were subjected to analysis after the storage period of 6 months. All samples were incinerated at 3000 C for 60 minutes to mimic the forensic scene. DNA extraction was done using Real Genomics YGB 100 DNA extraction kit. DNA quantification was performed using Nano-drop 100 spectrophotometer. SRY gene detection was done by the Real Plex Master Cycler. Results: Gender identification was done by amplification of sex determining region on Y chromosome gene using real time polymerase chain reaction. The prediction rate for males was 100 % and for females was 80% . The difference in the prediction of gender was found to be statistically significant (p value-0.04) . Conclusion: DNA extraction was successful in all the incinerated samples which were incinerated till 3000C . Hence, teeth are reliable source for sex determination with 100 % accuracy using Real time PCR.
Profile-based Data Base Scanning for Animal L-type Lectins and Characterization of VIPL, a Novel VIP36-like Endoplasmic Reticulum Protein*

Consensus profiles were established to screen data bases for novel animal L-type lectins. The profiles were generated from linear sequence motifs of the human L-type lectin-like membrane proteins ERGIC-53, ERGL, and VIP36 and by optimal alignment of the entire carbohydrate recognition domain of these proteins. The search revealed numerous orthologous and homologous L-type lectin-like proteins in animals, protozoans, and yeast, as well as the sequence of a novel family member related to VIP36, named VIPL for VIP36-like. Sequence analysis suggests that VIPL is a ubiquitously expressed protein and appeared earlier in evolution than VIP36. The cDNA of VIPL was cloned and expressed in cell culture. VIPL is a high-mannose type I membrane glycoprotein with similar domain organization as VIP36. Unlike VIP36 and ERGIC-53 that are predominantly associated with postendoplasmic reticulum (ER) membranes and cycle in the early secretory pathway, VIPL is a non-cycling resident protein of the ER. Mutagenesis experiments indicate that ER retention of VIPL involves a RKR di-arginine signal. Overexpression of VIPL redistributed ERGIC-53 to the ER without affecting the cycling of the KDEL-receptor and the overall morphology of the early secretory pathway. The results suggest that VIPL may function as a regulator of ERGIC-53.
Chromatin Remodeling and Transcriptional Activity of the Bone-specific Osteocalcin Gene Require CCAAT/Enhancer-binding Protein β-dependent Recruitment of SWI/SNF Activity*

Tissue-specific activation of the osteocalcin (OC) gene is associated with changes in chromatin structure at the promoter region. Two nuclease-hypersensitive sites span the key regulatory elements that control basal tissue-specific and vitamin D3-enhanced OC gene transcription. To gain understanding of the molecular mechanisms involved in chromatin remodeling of the OC gene, we have examined the requirement for SWI/SNF activity. We inducibly expressed an ATPase-defective BRG1 catalytic subunit that forms inactive SWI/SNF complexes that bind to the OC promoter. This interaction results in inhibition of both basal and vitamin D3-enhanced OC gene transcription and a marked decrease in nuclease hypersensitivity. We find that SWI/SNF is recruited to the OC promoter via the transcription factor CCAAT/enhancer-binding protein β, which together with Runx2 forms a stable complex to facilitate RNA polymerase II binding and activation of OC gene transcription. Together, our results indicate that the SWI/SNF complex is a key regulator of the chromatin-remodeling events that promote tissue-specific transcription in osteoblasts.