Miracle-dz/UniFAR-FTUs huggingface dataset:
Frailty index and its associations with self‐neglect, social support and sociodemographic characteristics among older adults in rural China

The frailty index is used to measure the health status of older individuals. However, its association with self‐neglect, social support and sociodemographic characteristics of older adults is underexplored. The purpose of the present study was to explore such associations among the rural older adults in Anhui Province of China, and to provide scientific evidence for policy‐makers to improve the health and well‐being of older adults in rural China.
Membrane Transport Piece by Piece: Production of Transmembrane Peptides for Structural and Functional Studies

Membrane proteins are involved in all cellular processes from signaling cascades to nutrient uptake and waste disposal. Because of these essential functions, many membrane proteins are recognized as important, yet elusive, clinical targets. Recent advances in structural biology have answered many questions about how membrane proteins function, yet one of the major bottlenecks remains the ability to obtain sufficient quantities of pure and homogeneous protein. This is particularly true for human membrane proteins, where novel expression strategies and structural techniques are needed to better characterize their function and therapeutic potential. One way to approach this challenge is to determine the structure of smaller pieces of membrane proteins that can be assembled into models of the complete protein. This unit describes the rationale for working with single or multiple transmembrane segments and provides a description of strategies and methods to express and purify them for structural and functional studies using a maltose binding protein (MBP) fusion. The bulk of the unit outlines a detailed methodology and justification for producing these peptides under native‐like conditions. Curr. Protoc. Protein Sci. 75:29.8. 1‐29.8. 28 © 2014 by John Wiley & Sons, Inc.
Optimal staging of esophageal cancer

EUS and EUS-FNA represent the most accurate method for locoregional staging of esophageal carcinoma, and should be performed for local staging in those patients who are good surgical candidates and other imaging techniques (CT, PET) have demonstrated no distant metastases. The presence of EUS as an adjunct for staging is mandatory in buzy thoracic surgery practices.
Multiple sclerosis: diagnostic issues and modern management

Aim: To provide an insight into the current issues in the diagnosis and management of multiple sclerosis (MS). Methods: A literature-based review was undertaken to determine diagnostic criteria, differential diagnosis, and the use of disease-modifying medication and symptomatic treatments for MS. The main source of references was Medline via PubMed but standard major reference works on MS were also used. Results: The prevalence of MS may be increasing, especially in women, thereby increasing the need for resources for diagnosis and clinical management of the condition. Clinical diagnosis of MS has changed little since the descriptions of Charcot. However, new diagnostic techniques ranging from neurophysiology and spinal fluid analysis to increasingly sophisticated magnetic resonance imaging have allowed the condition to be diagnosed earlier and with more confidence. New insights in immunology and neuropathology allow differential diagnoses to be excluded and continue to lead to different approaches to managing the condition. New disease-modifying drugs are being used, with the realistic hope of altering the progression of disability. Equally important are new techniques and medications aimed at symptom management, ranging from multidisciplinary team working to drug treatment of pain, fatigue, spasticity, continence and nystagmus. Conclusions: There is continuing improvement in many aspects of the care of people with MS. Insights from epidemiology, genetics, pathology and clinical trials have all contributed to this.
Fission yeast IQGAP maintains F‐actin‐independent localization of myosin‐II in the contractile ring

During cytokinesis in many eukaryotic cells, myosin‐II concentrates at the equatorial cortex with actin filaments (F‐actin) and is supposed to generate forces to divide the cell into two, which is called the contractile ring (CR) hypothesis. Several lines of evidence indicate that the myosin‐II is recruited independently of F‐actin and interacts specifically with the equatorial F‐actin. Molecular details of these mechanisms are still unknown. We used the fission yeast Schizosaccharomyces pombe to investigate the regulation of myosin‐II localization. We demonstrate that the CR myosin‐II was composed of F‐actin‐dependent and ‐independent fractions by simultaneously observing F‐actin and myosin. The F‐actin‐independent fraction was visualized as cortical dots in the absence of F‐actin. IQGAP Rng2, an indispensable element of CR, was implicated in maintenance of the F‐actin‐independent fraction of myosin‐II, whereas anillin Mid1 was required for assembly but not for maintenance of the fraction. In the CR of the rng2 mutant, myosin‐II was less concentrated, unstable, and nonhomogeneous, which often resulted in cytokinesis failure. These results suggest that Rng2 tethers myosin‐II to the cortex along the CR independently of F‐actin to provide a sufficient concentration. The robust localization of myosin‐II would ensure successful cytokinesis.
A Review and Critique of the Touch Inventory for Elementary School-Aged Children (TIE)

The paper presents a review of the published literature about and a critique of the Touch Inventory for Elementary School-Aged Children (TIE), a screening tool for children to self-report on their emotional and behavioural responses to tactile stimuli, developed by Royeen (1985, 1986) and Royeen and Fortune (1990). The TIE is used as a screening tool for children aged 6–12 years who have an IQ of at least 80 and no history of physical disabilities. Psychometric properties based on previously published studies of the TIE are discussed and recommendations for further research are made.
Models of Inflammation: Carrageenan‐ or Complete Freund's Adjuvant (CFA)–Induced Edema and Hypersensitivity in the Rat

Animal models of inflammation are used to assess the production of inflammatory mediators at sites of inflammation, the anti‐inflammatory properties of agents such as nonsteroidal anti‐inflammatory drugs (NSAIDs), and the efficacy of putative analgesic compounds in reversing cutaneous hypersensitivity. This unit details methods to elicit and measure carrageenan‐ and complete Freund's adjuvant (CFA)–induced cutaneous inflammation. Due to possible differences between the dorsal root sensory system and the trigeminal sensory system, injections of either the footpad or vibrissal pad are described. In this manner, cutaneous inflammation can be assessed in tissue innervated by the lumbar dorsal root ganglion neurons (footpad) and by the trigeminal ganglion neurons (vibrissal pad). Curr. Protoc. Pharmacol. 56:5.4. 1‐5.4. 7. © 2012 by John Wiley & Sons, Inc.
FTY720 stimulated ROS generation and the Sty1/Atf1 signaling pathway in the fission yeast Schizosaccharomyces pombe

Fingolimod hydrochloride (FTY720) is the first‐in‐class immune modulator known as sphingosine 1‐phosphate (S1P) receptor agonists. FTY720 has also been reported to exert a variety of physiological functions such as antitumor effect, angiogenesis inhibition, and Ca2+ mobilization. Here, we show that FTY720 treatment induced reactive oxygen species (ROS) accumulation, and investigated the effect of FTY720 on the stress‐activated MAP kinase Spc1/Sty1, a functional homologue of p38 MAPK, using a Renilla luciferase reporter construct fused to the CRE, which gives an accurate measure of the transcriptional activity of Atf1 and thus serves as a faithful readout of the Spc1/Sty1 MAPK signaling in response to oxidative stresses. FTY720 stimulated the CRE responses in a concentration‐dependent manner, which was markedly reduced by deletion of the components of the Spc1/Sty1 MAPK pathway. The blockade of ROS production by NAC (N‐acetyl‐l‐cysteine) significantly reversed the FTY720‐induced ROS accumulation, subsequent activation of the Spc1/Sty1 MAPK pathway, and inhibition of cell proliferation. Cells lacking the components of the Spc1/Sty1 MAPK exhibited higher sensitivity to FTY720 and higher ROS levels upon FTY720 treatment than in wild‐type cells. Thus, our results demonstrate the usefulness of fission yeast for elucidating the FTY720‐mediated signaling pathways involving ROS.
Malnutrition and associated risk factors among elderly living in Lebanese community homes

Purpose – The purpose of this study is to explore the relationship between nutritional status and associated risk factors such as:, socio-economic, physical, pathological and psychological factors, among elderly residing in Lebanese nursing homes. Design/methodology/approach – This cross-sectional study was carried out in 36 elderly care nursing homes with 2,094 residents. Of these, only 221 (11 per cent) elderly met the inclusion criteria and successfully completed the interview question. Data on socio-demographic characteristics and health conditions: oral, nutritional, depression, chronic diseases and activities of daily living, were collected. The analysis used a chi-square test and a binary logistic regression. Findings – High levels of malnourishment were found among elderly who had no jobs (p = 0.012) and had oral health problems (p = 0.038), functional impairment (p < 0.001) and depression (p = 0.021). Comorbid illnesses, however, had no significant association with nutritional status. In addition.
Identification of novel target genes specifically activated by deregulated E2F in human normal fibroblasts

The transcription factor E2F is the principal target of the tumor suppressor pRB. E2F plays crucial roles not only in cell proliferation by activating growth‐related genes but also in tumor suppression by activating pro‐apoptotic and growth‐suppressive genes. We previously reported that, in human normal fibroblasts, the tumor suppressor genes ARF, p27Kip1 and TAp73 are activated by deregulated E2F activity induced by forced inactivation of pRB, but not by physiological E2F activity induced by growth stimulation. In contrast, growth‐related E2F targets are activated by both E2F activities, underscoring the roles of deregulated E2F in tumor suppression in the context of dysfunctional pRB. In this study, to further understand the roles of deregulated E2F, we explored new targets that are specifically activated by deregulated E2F using DNA microarray. The analysis identified nine novel targets (BIM, RASSF1, PPP1R13B, JMY, MOAP1, RBM38, ABTB1, RBBP4 and RBBP7), many of which are involved in the p53 and RB tumor suppressor pathways. Among these genes, the BIM gene was shown to be activated via atypical E2F‐responsive promoter elements and to contribute to E2F1‐mediated apoptosis. Our results underscore crucial roles of deregulated E2F in growth suppression to counteract loss of pRB function.
Short CCG repeat in huntingtin gene is an obstacle for replicative DNA polymerases, potentially hampering progression of replication fork

Trinucleotide repeats (TNRs) are highly unstable in genomes, and their expansions are linked to human disorders. DNA replication is reported to be involved in TNR instability, but the current models are insufficient in explaining TNR expansion is induced during replication. Here, we investigated replication fork progression across huntingtin (HTT)‐gene‐derived fragments using an Escherichia coli oriC plasmid DNA replication system. We found most of the forks to travel smoothly across the HTT fragments even when the fragments had a pathological length of CAG/CTG repeats (approximately 120 repeats). A little fork stalling in the fragments was observed, but it occurred within a short 3′‐flanking region downstream of the repeats. This region contains another short TNR, (CCG/CGG)7, and the sense strand containing CCG repeats appeared to impede the replicative DNA polymerase Pol III. Examining the behavior of the human leading and lagging replicative polymerases Pol epsilon (hPolε) and Pol delta (hPolδ) on this sequence, we found hPolδ replicating DNA across the CCG repeats but hPolε stalling at the CCG repeats even if the secondary structure is eliminated by a single‐stranded binding protein. These findings offer insights into the distinct behavior of leading and lagging polymerases at CCG/CGG repeats, which may be important for understanding the process of replication arrest and genome instability at the HTT gene.
Examinations into the Calcium Hypothesis of Alzheimer's Disease

Alzheimer's disease (AD) is devastating to the patient, their family and friends, and represents a significant fiscal burden to our society. Currently available therapeutics provide only mild symptomatic relief and do not alter the course of the disease. Developing the next generation of disease modifying therapies requires an understanding of the early cellular changes responsible for AD. A hindrance to progress is the fact that most patients develop AD sporadically. However, mutations in the presenilin (PS) homologs cause dominantly inherited, early-onset AD. These mutations provide an important tool for understanding the cellular changes that cause AD. One consequence of PS mutations is exaggerated intracellular Ca2+ ([Ca2+]i) signaling. However, the mechanisms underlying this phenomenon remain controversial and its role in AD pathogenesis is unknown. Presented here are data indicating that exaggerated [Ca2+]i signaling is dependent upon the inositol 1,4,5-trisphosphate receptor (InsP3R) and contributes to AD pathogenesis in vivo. We began our studies by testing multiple proposed mechanisms for exaggerated [Ca2+]i signaling. To do this we employed multiple Ca2+ imaging protocols and Ca2+ indicators to directly measure ER Ca2+ dynamics in several cell systems. We found that decreasing InsP3R protein level rescues exaggerated [Ca2+]i signaling in primary cortical neurons and hippocampal slices from mutant PS1 expressing mice. We then determined the contribution of exaggerated [Ca2+]i signaling to AD pathogenesis. Using a combination of genetic, biochemical, electrophysiological and behavioral techniques, we found that rescue of exaggerated [Ca2+]i signaling dramatically attenuates mild cognitive impairment and AD phenotypes in AD mouse models. Reduction of InsP3R1 protein level in PS1M146V-KIN mice rescued enhanced hippocampal ryanodine receptor protein level, enhanced hippocampal synaptic potentiation, and constitutive activation of the CaMKIV-CREB transcriptional pathway. In 3xTg mice, reduced InsP3R1 protein level attenuated Aβ and phospho-tau accumulation and hippocampal electrophysiology and memory impairments. Together, these results reveal that mutant PS-associated exaggerated [Ca2+]i signaling is InsP3R1-dependent, a proximal event, and contributes to the development of AD in vivo. These findings advance our understanding of the pathological role of exaggerated [Ca2+]i signaling in AD and identify several novel targets for the development of disease modifying therapeutics. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Neuroscience First Advisor J. K. Foskett Subject Categories Neuroscience and Neurobiology This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/697 EXAMINATIONS INTO THE CALCIUM HYPOTHESIS OF ALZHEIMER’S DISEASE
Autophagy is required for efficient meiosis progression and proper meiotic chromosome segregation in fission yeast

Autophagy is a conserved intracellular degradation system, which contributes to development and differentiation of various organisms. Yeast cells undergo meiosis under nitrogen‐starved conditions and require autophagy for meiosis initiation. However, the precise roles of autophagy in meiosis remain unclear. Here, we show that autophagy is required for efficient meiosis progression and proper meiotic chromosome segregation in fission yeast. Autophagy‐defective strains bearing a mutation in the autophagy core factor gene atg1, atg7, or atg14 exhibit deformed nuclear structures during meiosis. These mutant cells require an extracellular nitrogen supply for meiosis progression following their entry into meiosis and show delayed meiosis progression even with a nitrogen supply. In addition, they show frequent chromosome dissociation from the spindle together with spindle overextension, forming extra nuclei. Furthermore, Aurora kinase, which regulates chromosome segregation and spindle elongation, is significantly increased at the centromere and spindle in the mutant cells. Aurora kinase down‐regulation eliminated delayed initiation of meiosis I and II, chromosome dissociation, and spindle overextension, indicating that increased Aurora kinase activity may cause these aberrances in the mutant cells. Our findings show a hitherto unrecognized relationship of autophagy with the nuclear structure, regulation of cell cycle progression, and chromosome segregation in meiosis.
Increased systemic immune activation and inflammatory profile of long-term HIV-infected ART-controlled patients is related to personal factors, but not to markers of HIV infection severity.

OBJECTIVES The objective of this study was to analyse the respective roles of personal factors and HIV infection markers on the systemic immune activation/inflammatory profile of long-term antiretroviral treatment-controlled patients. PATIENTS AND METHODS A panel of soluble immune activation/inflammatory biomarkers was measured in 352 HIV-infected treatment-controlled patients from the APROCO-COPILOTE cohort, all of whom were started on a PI in 1997-99 and had a final evaluation 11 years later, and in 59 healthy controls. RESULTS A total of 81.5% of the patients were male, with the following characteristics: median age 49 years; 620 CD4 cells/mm(3); 756 CD8 cells/mm(3); CD4/CD8 ratio 0.81; BMI 23.0 kg/m(2); waist-to-hip ratio 0.95. Markers of inflammation-high-sensitivity (hs) IL-6 (median and IQR) (1.3 pg/L, 0.7-2.6), hs C-reactive protein (CRP) (2.1 mg/L, 0.9-4.5) and D-dimer (252 ng/mL, 177-374)-were elevated compared with healthy controls (P < 0.001) and strongly related to each other, as were markers of immune activation [soluble (s) CD14 (1356 ng/mL, 1027-1818), β2-microglobulin (2.4 mg/L, 2.0-3.1) and cystatin-C (0.93 mg/L, 0.82-1.1)]. Inflammatory and immune activation markers were also associated with each other. In HIV-infected patients: age was related to D-dimer, β2-microglobulin and cystatin-C levels; being a smoker was related to increased IL-6 and cystatin-C; and BMI and waist-to-hip ratio were related to CRP. Conversely, markers of HIV infection, current CD4 or CD8 values, CD4 nadir, CD4/CD8 ratio, AIDS stage at initiation of PIs, current viral load and duration of ART were not associated with immune activation/inflammation markers. CONCLUSIONS In these long-term treatment-controlled HIV-infected patients, all systemic markers of inflammation and immune activation were increased compared with healthy controls. This was related to demographic and behavioural factors, but not to markers of severity of the HIV infection. Intervention to decrease low-grade inflammation must thus prioritize modifiable personal factors.
Performance of EUCAST and CLSI approaches for co-amoxiclav susceptibility testing conditions for clinical categorization of a collection of Escherichia coli isolates with characterized resistance phenotypes.

OBJECTIVES There are different methodological recommendations for in vitro testing of the co-amoxiclav combination. Performance of co-amoxiclav MIC testing for Escherichia coli by the standard ISO microdilution method (ISO 20776-1) was compared using EUCAST (fixed 2 mg/L clavulanate concentration) and CLSI (2 : 1 ratio) interpretive criteria. METHODS MICs were determined by broth microdilution using a 2 : 1 ratio and fixed clavulanate concentrations (2 and 4 mg/L) for 160 clinical E. coli isolates with characterized resistance mechanisms. Essential agreements, categorical agreements and relative errors were determined. RESULTS For all isolates, essential agreement between microdilution using 2 mg/L clavulanate and a 2 : 1 ratio was 25.6%. For ESBL-producing isolates, considering EUCAST breakpoints, 55% of isolates tested with 2 mg/L clavulanate were classified as resistant; conversely, 95% of isolates tested with 4 mg/L clavulanate were susceptible. When using CLSI breakpoints and a 2 : 1 ratio, 90% of isolates were susceptible and 10% were intermediate. CONCLUSIONS Variation in the clavulanate concentration gave different susceptibility testing results, particularly among ESBL-producing E. coli isolates. The in vitro concentration of clavulanate that better correlates with clinical outcome is still under debate and should be established.
Folate‐/FAD‐dependent tRNA methyltransferase from Thermus thermophilus regulates other modifications in tRNA at low temperatures

TrmFO is a N5, N10‐methylenetetrahydrofolate (CH2THF)‐/FAD‐dependent tRNA methyltransferase, which synthesizes 5‐methyluridine at position 54 (m5U54) in tRNA. Thermus thermophilus is an extreme‐thermophilic eubacterium, which grows in a wide range of temperatures (50–83 °C). In T. thermophilus, modified nucleosides in tRNA and modification enzymes form a network, in which one modification regulates the degrees of other modifications and controls the flexibility of tRNA. To clarify the role of m5U54 and TrmFO in the network, we constructed the trmFO gene disruptant (∆trmFO) strain of T. thermophilus. Although this strain did not show any growth retardation at 70 °C, it showed a slow‐growth phenotype at 50 °C. Nucleoside analysis showed increase in 2′‐O‐methylguanosine at position 18 and decrease in N1‐methyladenosine at position 58 in the tRNA mixture from the ∆trmFO strain at 50 °C. These in vivo results were reproduced by in vitro experiments with purified enzymes. Thus, we concluded that the m5U54 modification have effects on the other modifications in tRNA through the network at 50 °C. 35S incorporations into proteins showed that the protein synthesis activity of ∆trmFO strain was inferior to the wild‐type strain at 50 °C, suggesting that the growth delay at 50 °C was caused by the inferior protein synthesis activity.
Bedaquiline susceptibility testing of Mycobacterium tuberculosis in an automated liquid culture system.

OBJECTIVES The objective of this study was to evaluate the performance of the BACTEC MGIT960 system to test the susceptibility to bedaquiline for Mycobacterium tuberculosis complex. METHODS We determined the quality control (QC) range of bedaquiline using the M. tuberculosis H37Rv reference strain and the epidemiological cut-off (ECOFF) in MGIT960 and on Middlebrook 7H11 agar (M7H11) using 47 strains from bedaquiline treatment-naive patients. The accuracy of MGIT960 was evaluated versus M7H11 using 74 'probably susceptible to bedaquiline' and 18 'probably resistant to bedaquiline' strains. Repeatability and reproducibility of MGIT960 were assessed using five strains showing different resistance levels. RESULTS The QC range for the H37Rv strain was between 0.125 and 0.50 mg/L. The WT MIC distribution ranged from ≤0.03 to 1.00 mg/L in MGIT960 and from ≤0.008 to 0.25 mg/L on M7H11 with suggested ECOFFs of 1.00 and 0.25 mg/L, respectively. Applying these ECOFFs, the probably susceptible and probably resistant strains were distinguishable by both methods, albeit with only a 2-fold increased MIC for one of the resistant strains compared with the ECOFF. Intermethod agreement to classify the isolates was excellent (100%). All replicates in the repeatability and reproducibility experiments fell within the normal range. CONCLUSIONS The MGIT960 system proved to be highly stable, reproducible and accurate relative to the M7H11 agar method for determining the bedaquiline MIC. The small margin between the suggested ECOFF and the lowest MIC for the mutant strains risks making both methods prone to discordant results. Further validation in clinical settings linked to treatment outcome data is needed.