Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-host interactions: a map of viral perturbation of the host system.

Since the 1980s, the rapid progression of the HIV/AIDS pandemic has prompted a major international research effort. As a result, the current knowledge on HIV biology, its evolution, and origins [1–5] exceeds that of many, if not all, other viruses. One of the most important areas of HIV research is the detailed understanding of HIV replication. As with all viruses, HIV must exploit the host’s cellular machinery and metabolism to copy its genetic material, synthesize viral proteins, and assemble new virions. The viral replication cycle is thus dependent on an intricate network of direct and indirect protein interactions: between the viral proteins, between the virus and the host, and ultimately between the various host proteins that constitute the subverted cellular systems. When we also take into account the host’s immune response and intrinsic antiviral factors, there are clearly a large number of host–pathogen relationships that are important to our full understanding of HIV biology. However, until recently [6], this valuable information has remained ‘locked’ in the published literature, making it time-consuming to study by individual researchers and inaccessible to computational analysis, thus hindering the progress of research. Here we highlight new developments in the area of host–pathogen systems biology that in our opinion will provide helpful insights to the HIVresearch community.
Ingestion of monosodium glutamate (MSG) in adult male rats reduces sperm count, testosterone, and disrupts testicular histology

Objective: Monosodium glutamate (MSG) is a widely used food additive with controversial side effects. Though neonatal administration of MSG has been shown to affect fertility via arcuate nucleus ablation, the body of work involving the effects of adult MSG administration on male rat fertility has yet to be collectively assessed.Design: Systematic review.Methods: A PubMed search using terms “monosodium glutamate” in addition to “male fertility” or “male reproduction” or “sperm” or “testes” was performed. Inclusion criteria included: English language, adult administration of MSG, male reproductive outcomes, and control groups. Additional studies were identified via reference lists of relevant articles.Results: Of 167 records originally identified, six studies remained after removal of duplicates and studies not meeting inclusion criteria. Data ranges included: cohort sizes of 24 – 32 animals, dosing from 0 to 4 g/kg, MSG administration duration of 10 – 56 days, and weight 75 – 200g. In MSG fed rats compared to controls: Sperm count was lower in three of four studies, serum testosterone concentration was lower in two of two studies, testicular component weights or size was decreased in two of three studies, and abnormal testicular and sperm histology was observed in five of six studies.Conclusion: Adult intake of MSG can negatively impact sperm count and serum testosterone concentrations as well as testicular morphology and histology in rats. Further investigation of this effect should be evaluated in humans for such a popular flavor enhancer.
Proteome-wide analysis of neural stem cell differentiation to facilitate transition to cell replacement therapies

Neurodegenerative diseases are devastating disorders and the demands on their treatment are set to rise in connection with higher disease incidence. Knowledge of the spatiotemporal profile of cellular protein expression during neural differentiation and definition of a set of markers highly specific for targeted neural populations is a key challenge. Intracellular proteins may be utilized as a readout for follow-up transplantation and cell surface proteins may facilitate isolation of the cell subpopulations, while secreted proteins could help unravel intercellular communication and immunomodulation. This review summarizes the potential of proteomics in revealing molecular mechanisms underlying neural differentiation of stem cells and presents novel candidate proteins of neural subpopulations, where understanding of their functionality may accelerate transition to cell replacement therapies.
Phyllochron of Paspalum notatum FL. and Coelorhachis selloana (Hack.) camus in natural pasture

Leaf appearance rate and phyllochron are related variables which play a central role in forage production. Phyllochron is the time interval between the appearance of successive leaves and varies according to a number of environmental factors, among which temperature is the most important. The experiment was conducted in natural pasture with the aim of testing phyllochron variation under different seasons, herbage allowances, and topographic positions. Marked tillers were used to define the phyllochron, establishing a relationship between the number of leaves produced against thermal time during the sampling period. The time (expressed in °C) needed for the emergence of a leaf is equal to 1/b, where b is the slope coefficient of the regression. The lines for the season combinations, herbage allowances and topographic positions sampled were compared. Under Spring and Summer conditions, the phyllochrons for P. notatum and C. selloana were 156°C and 238°C respectively, regardless of treatment.
Nonclonal Emergence of Colistin-Resistant Klebsiella pneumoniae Isolates from Blood Samples in South Korea

ABSTRACT In vitro activities of colistin and other drugs were tested against 221 Klebsiella pneumoniae isolates that were collected between 2006 and 2007 in nine tertiary care South Korean hospitals from patients with bacteremia. The clonality of colistin-resistant K. pneumoniae (CRKP) isolates was assessed by multilocus sequence typing (MLST). We found that 15 isolates (6.8%) were resistant to colistin. MLST showed that CRKP isolates were nonclonal, with colistin resistance in K. pneumoniae occurring independently and not by clonal spreading.
Bone density and other possible predictors of fracture risk in children and adolescents with spastic quadriplegia

Forty‐three patients with spastic quadriplegia (mean age 7.9 years, range 3.3 to 17.2 years) underwent bone mineral density (BMD) measurement of the lumbar spine and were evaluated between 2.6 and 5.5 years (mean 3.8) later to determine whether this measurement had predicted risk of fracture over the subsequent period of observation. Other potential risk factors that were evaluated include body weight z score, serum vitamin D levels, previous fracture, and hip spica casting. The baseline measurements showed that BUD falls further below normal with increasing age and was more than one standard deviation below age‐matched normal mean in 38 of the 43 patients. Fracture rate did not differ between those with low and those with very low spinal BMD. Similarly, serum vitamin D levels and body weight z scores were not predictive of fracture. However, fracture rate was over fourfold greater following spica casting and more than threefold greater following an initial fracture. Fracture rates in the study group were similar to those reported for age‐ and sex‐matched normal children, though generally the location of the fractures and mechanisms of injury differed.
Pre- and Perinatal Hazards and Family Background in Children with Specific Language Impairments: A Study of Twins

A clinical group composed of 84 twin pairs where one or both twins met stringent psychometric criteria for specific speech-language impairment was compared with 36 twin pairs with no history of speech-language difficulties. Twins with speech-language impairment tended to have more siblings than control twins and were significantly more likely to have an affected parent. Groups were closely similar in terms of length of gestation and mother's antenatal condition, except that maternal toxemia was unusually frequent in the clinical group. Children from the two groups did not differ in terms of Apgar scores or on a composite measure of perinatal hazards. Within the clinical group, MZ pairs with substantial differences in neonatal status did not differ in language outcome. It is suggested that if an association with toxemia can be replicated, this might reflect a common genetic basis for immune disorders and developmental language delay. Perinatal hazard was unrelated to subtype of speech-language impairment.
Direct Measurement of trans-Golgi pH in Living Cells and Regulation by Second Messengers (*)

In the endocytic compartment, an acidic pH plays a key role in receptor and ligand sorting, vesicular transport, and protein degradation. In the secretory compartment, indirect estimates of trans-Golgi pH based on partitioning of weak bases and following viral infection suggest a mildly acidic pH of >6.0. We developed a liposome microinjection method to introduce fluorescent indicators into the aqueous compartment of trans-Golgi in living cells. In the presence of ATP and at 37°C, 70-nm diameter liposomes delivered their fluid-phase contents selectively into the trans-Golgi compartment as assessed by colocalization with the trans-Golgi stain N- {6-[(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]caproyl}-sphingosine (C6-NBD-ceramide). Liposome fusion was ATP- and temperature-dependent and blocked by N-ethylmaleimide but not by guanosine 5′-O-(3-thiotriphosphate) (GTPγS). trans-Golgi pH in skin fibroblasts was 6.17 ± 0.02 (S.E., n = 174) as measured by ratio imaging confocal microscopy using fluorescein and rhodamine-based indicators and an in vivo calibration procedure. trans-Golgi pH increased to 6.8 ± 0.1 by cAMP agonists and to 6.5 ± 0.1 by protein kinase C activation. These results provide the first direct measurement of trans-Golgi pH in living cells and demonstrate pH regulation by second messengers.
Gastrointestinal Mechanisms Activated by Electrical Stimulation to Treat Motility Dysfunctions in the Digestive Tract: A Review

Studies performed to date have shown that electrical stimulation of the stomach and intestines can create or modulate motility functions in the gastrointestinal (GI) tract. Therefore, electrical stimulation of GI organs may become a valuable alternative to medication and surgical approaches in the treatment of GI motor dysfunctions. However, the mechanisms underlying the effects induced by electrical stimulation of the gut wall are not totally understood, and such knowledge is important for further development of stimulation methods and devices. Presently, it is known that electrical stimulation of GI organs triggers complex reactions comprising excitatory and inhibitory responses of the excitable components performing or controlling motility in the GI tract. I present here a review of what is known of the mechanisms of GI organ stimulation.
METHODOLOGICAL ISSUES IN NURSING RESEARCH 2 Focus groups as a research method : a critique of some aspects of their use in nursing research

Focus groups as a method of data collection seem to have grown in popularity in nursing in recent years, as evidenced by the number of publications reporting their use. In the process of reviewing the method as part of the planning process for several empirical research projects, it emerged that focus groups were being used in nursing not solely for qualitative research but for a number of other purposes perhaps more closely related to their earlier uses in political and marketing programmes. Furthermore, many articles were `theoretical discussion' papers not based on actual experience
Increasing incidence of gram-negative rod bacteremia in a newborn intensive care unit.

OBJECTIVES To determine whether there has been an increase in the incidence or a change in the epidemiology of gram-negative rod (GNR) bacteremia in patients in a newborn special care unit. METHODS Retrospective review of GNR bacteremia in patients hospitalized in the NBSCU at Yale-New Haven Hospital during a 10-year period. RESULTS There were 120 isolates from 113 episodes of GNR bacteremia during the study period. The incidence of GNR bacteremia increased from a mean of 10.2 to 25.5 (P = 0.017) episodes of GNR bacteremia per 1000 admissions per year between the time periods 1988 to 1994 and 1995 to 1997, respectively, paralleling an increase in the overall incidence of bacteremia. The increase in GNR bacteremia in these two groups was not related to changes in the patient population, the number of admissions or duration of hospitalization. Stepwise multivariate analysis identified two independent variables associated with infants who had GNR bacteremia during the period 1995 to 1997 as compared with 1988 to 1994, maternal intrapartum antibiotics (odds ratio, 4.9; 95% confidence interval, 1.9 to 12.6) and the presence of a percutaneous central venous catheter (odds ratio, 4.6; 95% confidence interval, 1.8 to 11.8). CONCLUSIONS We observed changes in clinical obstetric and neonatal care that paralleled the increase in GNR bacteremia at our institution. A prospective study is needed to elucidate the impact of these changes on the incidence of GNR bacteremia in this population.
Adjuvant therapy for gallbladder and bile duct cancers: retrospective comparative study.

PURPOSE To study the efficacy of adjuvant therapy (chemotherapy and radiotherapy) in early stages (I-III) of gallbladder and bile duct cancers. METHODS The clinical and pathological characteristics, treatment details and survival data of patients operated with early stages (I-III) of gallbladder and bile duct cancers and followed up in our clinic between August 2002 - November 2009 were retrospectively evaluated. RESULTS 52 patients (median age 64 years) with early stages of gallbladder (n=36) and bile duct (n=16) cancers were analysed. Twenty-three (44.2%) patients had stage I, 23 (44.2%) stage II, and 6 (11.5%) stage III cancers. Approximately half of the patients (n=25; 48.1%) received postoperative adjuvant chemotherapy and/or radiotherapy. Patients with adjuvant treatment were younger than those without (62 vs. 71 years, p=0.06). Eighteen patients received chemotherapy alone, 2 chemotherapy followed by radiotherapy, 1 chemotherapy concurrently with radiotherapy, and 4 radiotherapy alone as adjuvant therapy. The regimen most frequently used (57.1%) was CFF (cisplatin 50 mg/m(2), day 1; folinic acid 200 mg/m(2), day 1; 5-fluorouracil [5-FU] 400 mg/m(2) bolus day 1 and 1600 mg/m(2) 48h continuous infusion). Some poor prognostic factors like high tumor grade and vascular invasion were more frequent in patients who received adjuvant therapy. The median disease free survival (DFS) was 11.4 months for the patients that received adjuvant therapy vs. 8.2 months for those without adjuvant therapy (p=0.67). During follow up 11 patients (44.0%) with adjuvant therapy and 12 (44.4%) without have died (p=0.97). The estimated median survival was 29 months. CONCLUSION Although previous studies had shown that 5-FU-based adjuvant chemotherapy may provide a small survival advantage, this was not confirmed in the present study. Prospective adjuvant trials with a standard chemotherapy regimen and larger numbers of patients are required.
Methicillin-resistant Staphylococcus aureus (MRSA): a community-based prevalence survey

A prevalence survey of nasal methicillin-resistant Staphylococcus aureus (MRSA) carriage was undertaken on a random sample of adults (aged over 16) resident in the community in Birmingham, UK during 1998. Microbiological samples were taken from the anterior nares at the subjects' general practice or in their home. Information about risk factors for the acquisition of MRSA was obtained via a self-completed questionnaire. A 58% response rate (280/483) was achieved. The prevalence of nasal MRSA colonization was 1.5% [4/274, 95% confidence interval (CI) 0.03–2.9%]. Twenty-three per cent (63/274) of subjects were nasal carriers of S. aureus. Six per cent (4/63) of S. aureus isolates were MRSA and 2 of the 4 MRSA carriers reported previous contact with health facilities. The prevalence of MRSA colonization in the general adult population in Birmingham appears to be low.
Determining Risk in Pediatric Research with No Prospect of Direct Benefit: Time for a National Consensus on the Interpretation of Federal Regulations

United States federal regulations for pediatric research with no prospect of direct benefit restrict institutional review board (IRB) approval to procedures presenting: 1) no more than “minimal risk” (§ 45CFR46.404); or 2) no more than a “minor increase over minimal risk” if the research is commensurate with the subjects' previous or expected experiences and intended to gain vitally important information about the child's disorder or condition (§ 45CFR46.406) (DHHS 2001). During the 25 years since their adoption, these regulations have helped IRBs balance subject protections with the pursuit of scientific knowledge to advance children's welfare. At the same time, inconsistency in IRB application of these regulations to pediatric protocols has been widespread, in part because of the ambiguity of the regulatory language. During the past decade, three federally-charged committees have addressed these ambiguities: 1) the National Human Research Protections Advisory Committee (NHRPAC) (Washington, DC), 2) the Institute of Medicine (IOM) Committee on the Ethical Conduct of Clinical Research Involving Children (Washington, DC); and 3) the United States Department of Health and Human Services Secretary's Advisory Committee for Human Research Protections (SACHRP) (Washington, DC). The committees have reached similar conclusions on interpretation of language within regulations § § 45CFR46.404 and 406; these conclusions are remarkably consistent with recent international recommendations and those of the original National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research (1977) report from which current regulations are based. Drawing on the committees' public reports, this article identifies the ethical issues posed by ambiguities in regulatory language, summarizes the committees' deliberations, and calls for a national consensus on recommended criteria.
Multimodal evoked potentials, EEG and electroretinography in patients with dystrophia myotonica

ABSTRACT‐ EEG, somatosensory (SEP) and visual evoked potentials (VEP) and electroretinography (ERG) were recorded from 16 patients with clinical and electromyographically verified dystrophia myotonica. The results were compared to an age‐ and sex‐ matched control group and revealed statistically significant differences between the group mean values for almost all records. Furthermore, abnormal individual electrophysiological tests were relatively frequent in the patient group. No correlation was found between abnormalities in one test compared to abnormalities in the other tests. Furthermore, no correlation was found between the number of electrophysiological abnormalities and the frequency of the disease in the nearest family. The number of abnormal electrophysiological tests increased, however, with age of the patients and duration of the disease.
Central core disease and malignant hyperthermia syndrome

In a detailed investigation of a family with musculoskeletal abnormalities obsesrved in four generations, the probad and his mother were found to have central cores and multicores on histochemical and electron microscopic studies of biopsied muscle. A male sibling experienced a malignant hyperthermic reaction during hand surgery, and although similar reactions had not been observed in other family members, unexplained ventricular dysrhythmias did occur in the proband during surgery. The proband and his mother were subsequently shown to be susceptible to malignant hyperthermia by abnormal in vitro muscle contractures in the presence of halothane or caffeine.
Observed Supervisory Behavior and Teacher Burnout in Special Education

A method for assessing the relationship between supervisory behavior and staff burnout was developed and tested in two schools for mentally retarded children. The method uses a new instrument, the Supervisor Behavior Observation Scale. The two schools involved in the study differed significantly in level of staff burnout, as measured by the Maslach Burnout Inventory, and in supervisory behavior. Specifically, the principal of the low burnout staff interacted less frequently with others and spent less time observing staff in their classrooms. Instead, she spent more time in her office engaged in planning and coordinating activities. She also interacted more with her own superior. The low burnout principal also talked more and listened less, and she spent more time discussing work-related problems but less time discussing administrative issues. She also gave staff more emotional support but spent less time in “small talk” with them.
Atrial fibrillation patients do not benefit from acetylsalicylic acid.

AIMS Oral anticoagulation is the recommended treatment for stroke prevention in patients with atrial fibrillation. Notwithstanding, many patients are treated with acetylsalicylic acid (ASA) as monotherapy. Our objective was to investigate if atrial fibrillation patients benefit from ASA as monotherapy for stroke prevention. METHODS AND RESULTS Retrospective study of patients with a clinical diagnosis of atrial fibrillation between 1 July 2005 and 1 January 2009 in the National Swedish Patient register, matched with data from the National Prescribed Drugs register. Endpoints were ischaemic stroke, thrombo-embolic event, intracranial haemorrhage, and major bleeding. The study population consisted of 115 185 patients with atrial fibrillation, of whom 58 671 were treated with ASA as monotherapy and 56 514 were without any antithrombotic treatment at baseline. Mean follow-up was 1.5 years. Treatment with ASA was associated with higher risk of ischaemic stroke and thrombo-embolic events compared with no antithrombotic treatment. CONCLUSION Acetylsalicylic acid as monotherapy in stroke prevention of atrial fibrillation has no discernable protective effect against stroke, and may even increase the risk of ischaemic stroke in elderly patients. Thus, our data support the new European guidelines recommendation that ASA as monotherapy should not be used as stroke prevention in atrial fibrillation.
Astrocytes drive cortical vasodilatory signaling by activating endothelial NMDA receptors

Astrocytes express neurotransmitter receptors that serve as sensors of synaptic activity and initiate signals leading to activity-dependent local vasodilation and increases in blood flow. We previously showed that arteriolar vasodilation produced by activation of cortical astrocytes is dependent on endothelial nitric oxide synthase (eNOS) and endogenous agonists of N-methyl-D-aspartate (NMDA) receptors. Here, we tested the hypothesis that these effects are mediated by NMDA receptors expressed by brain endothelial cells. Primary endothelial cultures expressed NMDA receptor subunits and produced nitric oxide in response to co-agonists, glutamate and D-serine. In cerebral cortex in situ, immunoelectron microscopy revealed that endothelial cells express the GluN1 NMDA receptor subunit at basolateral membrane surfaces in an orientation suitable for receiving intercellular messengers from brain cells. In cortical slices, activation of astrocytes by two-photon flash photolysis of a caged Ca2+ compound or application of a metabotropic glutamate receptor agonist caused endothelial NO generation and local vasodilation. These effects were mitigated by NMDA receptor antagonists and conditional gene silencing of endothelial GluN1, indicating at least partial dependence on endothelial NMDA receptors. Our observations identify a novel astrocyte-endothelial vasodilatory signaling axis that could contribute to endothelium-dependent vasodilation in brain functional hyperemia.