Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of mass spectrometric parameters on peptide and protein identification rates for shotgun proteomic experiments on an LTQ‐orbitrap mass analyzer

The success of a shotgun proteomic experiment relies heavily on the performance and optimization of both the LC and the MS systems. Despite this, little consideration has, so far, been given to the importance of evaluating and optimizing the MS instrument settings during data‐dependent acquisition mode. Moreover, during data‐dependent acquisition, the users have to decide and choose among various MS parameters and settings, making a successful analysis even more challenging. We have systematically investigated and evaluated the effect of enabling and disabling the preview mode for FTMS scan, the number of microscans per MS/MS scan, the number of MS/MS events, the maximum ion injection time for MS/MS, and the automatic gain control target value for MS and MS/MS events on protein and peptide identification rates on an LTQ‐Orbitrap using the Saccharomyces cerevisiae proteome. Our investigations aimed to assess the significance of each MS parameter to improve proteome analysis and coverage. We observed that higher identification rates were obtained at lower ion injection times i.e. 50–150 ms, by performing one microscan and 12–15 MS/MS events. In terms of ion population, optimal automatic gain control target values were at 5×105–1×106 ions for MS and 3×103–1×104 ions for MS/MS. The preview mode scan had a minimal effect on identification rates. Using optimized MS settings, we identified 1038 (±2.3%) protein groups with a minimum of two peptide identifications and an estimated false discovery rate of ∼1% at both peptide and protein level in a 160‐min LC‐MS/MS analysis.
Comparison of two strategies for the administration of injectable depot medroxyprogesterone acetate: among women who returned to a family planning clinic at three- or six-month intervals

Abstract Objectives: The aim of this study was to compare the clinical performance of depot medroxyprogesterone acetate (DMPA) in women who received injections every 3 months at the Family Planning Clinic, and those who received every other injection at a health care facility near their place of residence, only returning to the clinic every 6 months. Materials and methods: The medical charts of DMPA users from 2 January 1980 through 31 December 2012 were evaluated for this study. Two cohorts of women were created and compared: those who regularly received DMPA injections every 3 months (3-month group) at the clinic and those who received alternating 3-month injections at a health care facility near their residence house, returning to the clinic every 6 months for an injection (6-month group). In addition, effectiveness rates, reasons for discontinuation, and continuation rates were evaluated. Results: Overall, 2637 women received all injections at 3-month intervals at the clinic, and 1190 women received every other injection at a health care facility near their residence. The women in the 3-month group had higher pregnancy rates and higher discontinuation rates (with the exception of discontinuation due to the loss of libido). Conclusion: The women who received alternating injections near their homes were more likely to continue using DMPA as a contraception method and presented lower pregnancy and discontinuation rates (for the majority of reasons), when compared to those women who returned to the clinic every 3 months.
Establishing a standardized clinical assessment tool of pathologic and prosthetic hand function: normative data, reliability, and validity.

OBJECTIVE To develop a new assessment procedure, the Southampton Hand Assessment Procedure (SHAP), that allows contextual results of hand function to be obtained readily in a clinical environment. DESIGN Reliability (test-retest, interrater) and validity (criterion, content) of new assessment procedure against standard medical outcome measure techniques. SETTING Normative data collected in a university laboratory. PARTICIPANTS Twenty-four volunteers selected on the basis of optimum hand function using these criteria: age (range, 18-25 y), and no adverse hand trauma, neurologic condition, or disabling effects of the upper limb. INTERVENTIONS Not applicable. MAIN OUTCOME MEASURES The normative control group was assessed for variability, and the procedure measured in terms of interrater and test-retest reliability. The absence of a direct comparison prevents a criterion standard from being established; however, content validity was shown by expert peer review. RESULTS The control group data were shown to be multivariate gaussian; test-retest and interrater reliability were demonstrated at the 95% confidence level. The content validity was demonstrated by peer panel approval. CONCLUSIONS Results of the control group established the statistical integrity of SHAP. Clinical trials are underway, although more extensive use of the procedure is advocated in primary care and rehabilitation centers where physiotherapy and occupational therapy are actively used in hand rehabilitation.
Sesame Lignans and Vitamin E Supplementation Improve Subjective Statuses and Anti-Oxidative Capacity in Healthy Humans With Feelings of Daily Fatigue

Sesamin has anti-oxidative functions in vivo. Fatigue is caused in part by oxidative stress. We evaluated whether sesame lignans (sesamin/episesamin = 1/1, 10 mg) with vitamin E (55 mg of α-tocopherol) (SVE) could improve subjective statuses and anti-oxidative capacity in humans using questionnaires on fatigue, sleep and physical appearance, as well as low-density lipoprotein oxidation lag time. A placebo-controlled, double-blind, parallel-group study was conducted with subjects experiencing daily fatigue. After a run-in period, subjects were administered oral SVE or a placebo (P) for 8 weeks. A questionnaire regarding fatigue, sleep and physical appearance was conducted at 0, 4, and 8 weeks. Plasma low-density lipoprotein oxidation lag time was measured as an indicator of anti-oxidative capacity. The per-protocol analysis revealed significant improvements in fatigue status at 4 and 8 weeks compared to 0 weeks in both groups (p < 0.01), and sleep and physical appearance at 8 weeks compared to 0 weeks only in the SVE group (p < 0.01). There were no significant differences observed between the groups. According to the 72-subject subgroup analysis (aged 40 and over), the sleep and physical appearance significantly improved compared to the P group (p < 0.05), and fatigue status showed a tendency for improvement compared to the P group. Anti-oxidative capacity in the SVE group significantly increased compared to the P group (p < 0.01). No adverse events relating to SVE supplementation were confirmed. These results suggest SVE supplementation could safely alleviate daily fatigue and oxidative stress.
Injection Behavior of Brushite Bone Cement Prepared with Granulated β-Tricalcium Phosphate

The injection behavior of β-tricalcium phosphate (Ca3(PO4)2: β-TCP) based cement was improved through the granulation of β-TCP. Dense β-TCP granules were obtained by heat treatment after spray drying. The fraction of injected paste under loaded mass in the syringe was measured while varying the granular fraction of β-TCP and the heat treatment temperature. The increase in granular fraction and heating treatment temperature reduced the amount of setting agent required to wet the granules. As the surplus setting agent could be used in the powdery β-TCP to reduce the viscosity, improved injectability was achieved. Inappropriate setting by the excessive setting agent was not observed and the cements tested exhibited normal setting behavior by forming a brushite phase.
Currency Depreciations in Emerging Markets: Financial Transfers and Borrowers Heterogeneity

The present paper investigates from the perspective of individual firms the channel between currency depreciations, currency mismatch and profits. In particular, we use a dataset on publicly listed, non-financial firms operating in Argentina, Brazil and Mexico during the period 1992-2004. Our key interest hereby is to explain why most of the considered episodes of large currency depreciations have been contractionary to the economies as opposed to the implications of the traditional Mundell-Fleming model. We develop a stylized partial equilibrium model of an individual firm that faces an unexpected currency depreciation to highlight three main channels: (1) a positive competitiveness effect for exporting firms; (2) a negative balance sheet effect for firms indebted in foreign currency; and (3) an adverse impact on interest payments. Thereafter, we quantify the relative importance of these channels in explaining the firms’ profitability during the depreciation episodes as a function of the currency composition of firms’ income and finance. Using panel regressions, we find evidence that the match between the currency-denomination of income and liabilities has been significantly better in Brazil than in Mexico and, especially, than in Argentina. JEL classification: F31, F34, F43
Tree extension algebras: logics, automata, and query languages

We study relations on trees defined by first-order constraints over a vocabulary that includes the tree extension relation T<T', holding if and only if every branch of T extends to a branch of T', unary node-tests, and a binary relation checking if the domains of two trees are equal. We show that from such a formula one can generate a tree automaton that accepts the set of tuples of trees defined by the formula, and conversely that every automaton over tree-tuples is captured by such a formula. We look at the fragment with only extension inequalities and leaf tests, and show that it corresponds to a new class of automata on tree tuples, which is strictly weaker then general tree-tuple automata. We use the automata representations to show separation and expressibility results for formulae in the logic. We then turn to relational calculi over the logic defined here: that is, from constraints we extend to queries that have second-order parameters for a finite set of tree tuples. We give normal forms for queries, and use these to get bounds on the data complexity of query evaluation, showing that while general query evaluation is unbounded within the polynomial hierarchy, generic query evaluation has very low complexity giving strong bounds on the expressive power of relational calculi with tree extension constraints. We also give normal forms for safe queries in the calculus.
Three-dimensional helical computed tomographic evaluation of three obturation techniques: In vitro study

Aim: The purpose of this study was to evaluate the adequacy of three obturation techniques namely lateral condensation, EQ Fil (backfill obturation) and thermafil (core carrier obturation) techniques using three-dimensional (3D) helical computed tomography (CT) by volume rendering method. Materials and Methods: Thirty freshly extracted teeth were randomly divided into three groups of 10 teeth each. Biomechanical preparation was done in all the teeth using rotary instruments. All three sets of teeth were placed in helical CT slice scanner and were imaged before obturation. The three sets were then obturated by following methods: Group I: lateral condensation, Group II: EQ Fil (backfill) and Group III: thermafil (core carrier obturation). Volume of the pulp chamber and gutta-percha after obturation were calculated using volume rendering technique and adequacy of the obturation techniques were calculated. Statistical Analysis Used: One-way ANOVA and Multiple-Range Tukey Test by Tukey-HSD procedure Results: Mean change in lateral condensation (0.005±0.002) was significantly higher than that of thermafil obturation (0.002±0.001) [P<0.05]. Conclusions: Conventional lateral condensation technique showed maximal inadequacy of obturation and thermafil obturation technique showed the least inadequacy of obturation when the volume of the specimens were calculated and reconstructed
Soft Electronic Strain Sensor with Chipless Wireless Readout: Toward Real‐Time Monitoring of Bladder Volume

Sensing mechanical tissue deformation in vivo can provide detailed information on organ functionality and tissue states. To bridge the huge mechanical mismatch between conventional electronics and biological tissues, stretchable electronic systems have recently been developed for interfacing tissues in healthcare applications. A major challenge for wireless electronic implants is that they typically require microchips, which adds complexity and may compromise long‐term stability. Here, a chipless wireless strain sensor technology based on a novel soft conductor with high cyclic stability is reported. The composite material consists of gold‐coated titanium dioxide nanowires embedded in a soft silicone elastomer. The implantable strain sensor is based on an resonant circuit which consists of a stretchable plate capacitor and a coil for inductive readout of its resonance frequency. Successful continuous wireless readout during 50% strain cycles is demonstrated. The sensor element has a Young's modulus of 260 kPa, similar to that of the bladder in order to not impair physiological bladder expansion. A proof‐of‐principle measurement on an ex vivo porcine bladder is presented, which shows the feasibility of the presented materials and devices for continuous, wireless strain monitoring of various tissues and organs in vivo.
Intergeneric and interspecies gene exchange in gram-positive cocci

Gram-positive cocci are important causes of both community-acquired and nosocomial infections (1, 34, 59, 78). Antimicrobial resistance is an increasing problem, especially in nosocomial isolates of group D streptococci and staphylococci. Gram-positive microorganisms become resistant to antimicrobial agents by the same mechanisms as other bacteria, either by mutation or by the acquisition of new DNA, most often by resistance plasmid (R plasmid) acquisition (8, 38). The evolution of resistance in these organisms seems to parallel that in gram-negative rods, with strain dissemination, transposition, and plasmid exchange interacting to result in the development of resistance (57). Plasmid transfer between bacteria is a mechanism for the rapid and widespread dissemination of resistance. Transfer of resistance to multiple antibiotics can take place between different bacterial species and genera and was first demonstrated among gram-negative bacilli. Such transfer of conjugative resistance plasmids has contributed to outbreaks of serious infections in several hospital settings (57). Until recently, little attention has been paid to the interspecific and intergeneric exchange ofgenetic information which occurs in gram-positive bacteria. This review will focus on the evolution of antimicrobial resistance in gram-positive cocci. Particular attention is given to the host range and mechanism of acquisition of extrachromosomal genes responsible for the exchange of genetic information in these pathogens.
Age‐related decrease in proteasome expression contributes to defective nuclear factor‐κB activation during hepatic ischemia/reperfusion

Hepatic ischemia/reperfusion (I/R) leads to liver injury and dysfunction through the initiation of a biphasic inflammatory response that is regulated by the transcription factor nuclear factor κB (NF‐κB). We have previously shown that there is an age‐dependent difference in the injury response to hepatic I/R in mice that correlates with divergent activation of NF‐κB such that young mice have greater NF‐κB activation, but less injury than old mice. In this study, we investigated the mechanism by which age alters the activation of NF‐κB in the liver during I/R. Young (4‐5 weeks) and old (12‐14 months) mice underwent partial hepatic I/R. Livers were obtained for RNA microarray analysis and protein expression assays. Using microarray analysis, we identified age‐dependent differences in the expression of genes related to protein ubiquitinylation and the proteasome. In old mice, genes that are involved in the ubiquitin‐proteasome pathway were significantly down‐regulated during I/R. Consistent with these findings, expression of a critical proteasome subunit, non‐adenosine triphosphatase 4 (PSMD4), was reduced in old mice. Expression of the NF‐κB inhibitory protein, IκBα, was increased in old mice and was greatly phosphorylated and ubiquitinylated. The data provide strong evidence that the age‐related defect in hepatic NF‐κB signaling during I/R is a result of decreased expression of PSMD4, a proteasome subunit responsible for recognition and recruitment of ubiquitinylated substrates to the proteasome. It appears that decreased PSMD4 expression prevents recruitment of phosphorylated and ubiquitinylated IκBα to the proteasome, resulting in a defect in NF‐κB activation. (HEPATOLOGY 2009.)
Robotic Room-Level Localization Using Multiple Sets of Sonar Measurements

In this paper, we aim to achieve robust and cost-effective room-level localization for the indoor mobile robot. It is unrealistic to obtain precise localization information from the sonar sensors because of the sparseness and uncertainty. Our attempts show that the room-level localization can be achieved using sonar sensors by accumulating the sonar data to overcome the limitations of sensor performance. To this end, we formulate the room-level localization as a joint sparse coding problem, which encourages the coding vectors to share the common room sparsity, but different locations. We systematically evaluate the performance of the different coding strategies on the collected sonar measurement data set.
Low Intracellular Iron Increases the Stability of Matriptase-2*

Background: Matriptase-2 (MT2) is essential for iron homeostasis. The mechanism for its regulation is controversial. Results: The cytoplasmic domain of MT2 is necessary for its stabilization by iron depletion. MT2 expression is not regulated at either the transcriptional mRNA or translational level by iron. Conclusion: Depletion of cellular iron stabilizes MT2. Significance: Low iron levels in hepatocytes stabilize MT2 to suppress hepcidin expression. Matriptase-2 (MT2) is a type II transmembrane serine protease that is predominantly expressed in hepatocytes. It suppresses the expression of hepatic hepcidin, an iron regulatory hormone, by cleaving membrane hemojuvelin into an inactive form. Hemojuvelin is a bone morphogenetic protein (BMP) co-receptor. Here, we report that MT2 is up-regulated under iron deprivation. In HepG2 cells stably expressing the coding sequence of the MT2 gene, TMPRSS6, incubation with apo-transferrin or the membrane-impermeable iron chelator, deferoxamine mesylate salt, was able to increase MT2 levels. This increase did not result from the inhibition of MT2 shedding from the cells. Rather, studies using a membrane-permeable iron chelator, salicylaldehyde isonicotinoyl hydrazone, revealed that depletion of cellular iron was able to decrease the degradation of MT2 independently of internalization. We found that lack of the putative endocytosis motif in its cytoplasmic domain largely abolished the sensitivity of MT2 to iron depletion. Neither acute nor chronic iron deficiency was able to alter the association of Tmprss6 mRNA with polyribosomes in the liver of rats indicating a lack of translational regulation by low iron levels. Studies in mice showed that Tmprss6 mRNA was not regulated by iron nor the BMP-mediated signaling with no evident correlation with either Bmp6 mRNA or Id1 mRNA, a target of BMP signaling. These results suggest that regulation of MT2 occurs at the level of protein degradation rather than by changes in the rate of internalization and translational or transcriptional mechanisms and that the cytoplasmic domain of MT2 is necessary for its regulation.
Maturing Thalamocortical Functional Connectivity Across Development

Recent years have witnessed a surge of investigations examining functional brain organization using resting-state functional connectivity MRI (rs-fcMRI). To date, this method has been used to examine systems organization in typical and atypical developing populations. While the majority of these investigations have focused on cortical–cortical interactions, cortical–subcortical interactions also mature into adulthood. Innovative work by Zhang et al. (2008) in adults have identified methods that utilize rs-fcMRI and known thalamo-cortical topographic segregation to identify functional boundaries in the thalamus that are remarkably similar to known thalamic nuclear grouping. However, despite thalamic nuclei being well formed early in development, the developmental trajectory of functional thalamo-cortical relations remains unexplored. Thalamic maps generated by rs-fcMRI are based on functional relationships, and should modify with the dynamic thalamo-cortical changes that occur throughout maturation. To examine this possibility, we employed a strategy as previously described by Zhang et al. to a sample of healthy children, adolescents, and adults. We found strengthening functional connectivity of the cortex with dorsal/anterior subdivisions of the thalamus, with greater connectivity observed in adults versus children. Temporal lobe connectivity with ventral/midline/posterior subdivisions of the thalamus weakened with age. Changes in sensory and motor thalamo-cortical interactions were also identified but were limited. These findings are consistent with known anatomical and physiological cortical–subcortical changes over development. The methods and developmental context provided here will be important for understanding how cortical–subcortical interactions relate to models of typically developing behavior and developmental neuropsychiatric disorders.
Intracerebral Stem Cell Administration Inhibits Relapse-like Alcohol Drinking in Rats

Study describes the blockade of relapse-like alcohol drinking by mesenchymal stem cells (MSCs). High alcohol-intake bred rats consumed alcohol for 3 months and were subjected to repeated alcohol deprivations for 7–14 days, followed by alcohol reaccess. Upon reaccess, animals consumed 2.2 g alcohol/kg in 60 minutes. A single intra-cerebroventricular MSC administration inhibited relapse-like drinking up to 80–85% for 40 days (P < 0.001). An alcohol-use-disorder was prevented.
Directions in GIS Introduction

The purpose of this paper is to discuss research directions in GIS. In doing so I will deliberately broaden the meaning of "GIS" to include a wide range of activities within the broad rubric of digital geographic information, since it seems to me that "GIS" is now generally used in that broad sense, rather than in the narrower sense of a software system designed specifically to store, retrieve, and analyze existing geographic information (Maguire 1991). We seem to be reaching a point where digital technology is encountered in almost all aspects of the communication of information, and the same is true of geographic information. It no longer seems important to ask whether information is digital or not-rather, the important questions seem to concern the degree to which the digital format imposes itself on the information, forcing us to modify, transform, or otherwise alter the information in order that it can be handled and communicated in digital systems.
Neuroimaging biomarker based prediction of Alzheimer'S disease severity with optimized graph construction

The prediction of Alzheimer's disease (AD) severity is very important in AD diagnosis and patient care, especially for patients at early stage when clinical intervention is most effective and no irreversible damages have been formed to brains. To achieve accurate diagnosis of AD and identify the subjects who have higher risk to convert to AD, we proposed an AD severity prediction method based on the neuroimaging predictors evaluated by the region-wise atrophy patterns. The proposed method introduced a global cost function that encodes the empirical conversion rates for subjects at different progression stages from normal aging through mild cognitive impairment (MCI) to AD, based on the classic graph cut algorithm. Experimental results on ADNI baseline dataset of 758 subjects validated the efficacy of the proposed method.