Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro development and gene expression of frozen-thawed 8-cell stage mouse embryos following slow freezing or vitrification

Objective This study was performed to compare the efficiency of slow freezing and vitrification based on survival, development to blastocysts, and cell numbers of blastocysts. Changes in embryonic gene expression in fresh and frozen-thawed embryos were also examined. Methods Eight-cell stage embryos were collected from superovulated female BDF1 mice. The collected embryos were randomly divided into three groups. One group was maintained as fresh controls (n=42), one was frozen by slow freezing (n=43), and one was cooled by vitrification (n=43). After thawing or cooling, survival rates, development to blastocyst, and cell numbers and inner cell mass (ICM) cell numbers of blastocysts were compared with those of the control group. The expressions of eight genes (Rbm3, Birc5, Sod1, Sod2, Cirbp, Caspase3, Trp53, Hsp70.1) were examined by real time-quantitative polymerase chain reaction in the fresh and frozen-thawed embryos. Results There were no significant differences in the slow freezing and vitrification groups' survival rate after thawing (88.4% vs. 88.4%), development to blastocyst (100% vs. 97.4%), cell numbers (107.0±21.0 vs. 115.0±19.7), or ICM cell numbers of blastocysts (11.3±5.2 vs. 11.1±3.7). Cell numbers of blastocysts were significantly (p<0.05) lower in the frozen-thawed embryos than the fresh embryos. There were no significant differences in the slow freezing and the vitrification groups' expressions of the eight genes. The expressions of CirbP and Hsp70.1 were higher in the frozen-thawed embryos than in the fresh embryos but there were no significant differences. Conclusion These results suggest that there were no significant differences between embryos that underwent slow freezing and vitrification.
Do Gender and Race/Ethnicity Influence Acute Myocardial Infarction Quality of Care in a Hospital with a Large Hispanic Patient and Provider Representation?

Background. Disparities in acute myocardial infarction (AMI) care for women and minorities have been extensively reported in United States but with limited information on Hispanics. Methods. Medical records of 287 (62%) Hispanic and 176 (38%) non-Hispanic white (NHW) patients and 245 women (53%) admitted with suspected AMI to a southern California nonprofit community hospital with a large Hispanic patient and provider representation were reviewed. Baseline characteristics, outcomes (mortality, CATH, PCI, CABG, and use of pertinent drug therapy), and medical insurance were analyzed according to gender, Hispanic and NHW race/ethnicity when AMI was confirmed. For categorical variables, 2 × 2 chi-square analysis was conducted. Odds ratio and 95% confidence interval for outcomes adjusted for gender, race/ethnicity, cardiovascular risk factors, and insurance were obtained. Results. Women and Hispanics had similar drug therapy, CATH, PCI, and mortality as men and NHW when AMI was confirmed (n = 387). Hispanics had less private insurance than NHW (31.4% versus 56.3%, P < 0.001); no significant differences were found according to gender. Conclusions. No differences in quality measures and outcomes were found for women and between Hispanic and NHW in AMI patients admitted to a facility with a large Hispanic representation. Disparities in medical insurance showed no influence on these findings.
Pareto efficient resource matching for LTE-A system

Carrier Aggregation (CA) is one of the main technologies used in Long Term Evolution Advanced (LTE-A) networks. It helps to increase bandwidth up to 100 MHz and downlink speed up to 3Gbps. Research work for CA based LTE-A network have focused on component carrier (CC) selection and packet scheduling. Most of the earlier work on resource scheduling has considered CC selection, resource allocation and link adaption as separate problems. In this paper we model the problem as a matching game and propose a Game theory based sub-optimal solution. This paper introduces concept of using two sided matching game for resource matching in CA based LTE-A 4G networks to find a Pareto optimal stable matching. Simulation result shows that the proposed scheme performs better than existing method.
Prognostic factors for thrombosis, myelofibrosis, and leukemia in essential thrombocythemia: a study of 605 patients

The findings from this study on a large series of patients treated according to current clinical practice provide reassurance that essential thrombocythemia is an indolent disorder and affected patients have a long survival. Background Essential thrombocythemia is a chronic myeloproliferative disorder; patients with this disorder have a propensity to develop thrombosis, myelofibrosis, and leukemia. Design and Methods We studied 605 patients with essential thrombocythemia (follow-up 4596 person-years) with the aim of defining prognostic factors for thrombosis, myelofibrosis, and leukemia during follow-up. Results Sixty-six patients (11%) developed thrombosis with a 10-year risk of 14%. Age >60 years (p<0.001) and a history of thrombosis (p=0.03) were independent risk factors for thrombosis. Progression to myelofibrosis occurred in 17 patients (2.8%) with a 10-year risk of 3.9%. Anemia at diagnosis of essential thrombocythemia was significantly correlated (p<0.001) with progression to myelofibrosis. Leukemia occurred in 14 patients (2.3%) at a median time of 11 years after the diagnosis of essential thrombocythemia; the risk was 2.6% at 10 years. Age >60 years (p=0.02) was significantly correlated with the development of leukemia. Cytotoxic treatment did not imply a higher risk of leukemia. At the time of the analysis, 64 of the 605 patients (10.6%) had died. The 10-year probability of survival was 88%, with a median survival of 22.3 years. Age >60 years (p<0.001) and history of thrombosis (p=0.001) were independent risk factors for survival. Conclusions The findings from this study on a large series of patients treated according to current clinical practice provide reassurance that essential thrombocythemia is an indolent disorder and affected patients have a long survival. The main risk is thrombosis, while myelofibrosis and leukemia are rare and late complications.
Antioxidant, Cytotoxic, and Antiproliferative Activities and Total Polyphenol Contents of the Extracts of Geissospermum reticulatum Bark

Geissospermum species are medically important plants due to their health-promoting effects. The objective of this study was to determine the antioxidant ability and antiproliferative and cytotoxic effects of infusions, tinctures, and ethanolic extracts of Geissospermum reticulatum barks in relation to the contents of total phenolics and flavonoids. Seven samples of barks were collected in various regions of Peruvian Amazonia. We found that the amount of total phenolics in the studied products varied from 212.40 ± 0.69 to 1253.92 ± 11.20 mg GAE/kg. In our study there is a correlation (R 2 = 0.7947) between the results of antioxidants assays: FRAP and ORAC for tinctures, infusions, and ethanolic extracts of G. reticulatum barks. We have also observed antiproliferative activities of the ethanolic extracts on normal T-cells. These extracts have caused death on malignant cell lines (THP-1 and HL-60) and this data correlates well with their antioxidant capacity measured by ORAC method. Interestingly, the highest concentration of the ethanolic extract was not toxic in the zebrafish embryo developmental assay. Our results indicate that G. reticulatum is rich in antioxidants and have cytotoxic and antiproliferative properties. The data suggests potential immunosuppressive role of the extracts. This is the first study presenting the results of chemical and biological analysis of multiple preparations from G. reticulatum.
Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery

Esophageal squamous cell carcinoma (ESCC) is among the top ten most frequent malignancies worldwide. In this study, our objective was to identify potential biomarkers for ESCC through a quantitative proteomic approach using the isobaric tags for relative and absolute quantitation (iTRAQ) approach. We compared the protein expression profiles of ESCC tumor tissues with the corresponding adjacent normal tissue from ten patients. LC-MS/MS analysis of strong cation exchange chromatography fractions was carried out on an Accurate Mass QTOF mass spectrometer, which led to the identification of 687 proteins. In all, 257 proteins were identified as differentially expressed in ESCC as compared to normal. We found several previously known protein biomarkers to be upregulated in ESCC including thrombospondin 1 (THBS1), periostin 1 (POSTN) and heat shock 70 kDa protein 9 (HSPA9) confirming the validity of our approach. In addition, several novel proteins that had not been reported previously were identified in our screen. These novel biomarker candidates included prosaposin (PSAP), plectin 1 (PLEC1) and protein disulfide isomerase A 4 (PDIA4) that were further validated to be overexpressed by immunohistochemical labeling using tissue microarrays. The success of our study shows that this mass spectrometric strategy can be applied to cancers in general to develop a panel of candidate biomarkers, which can then be validated by other techniques.
Fast Computation of Moore-Penrose Inverse Matrices

Many neural learning algorithms require to solve large least square systems in order to obtain synaptic weights. Moore-Penrose inverse matrices allow for solving such systems, even with rank deficiency, and they provide minimum-norm vectors of synaptic weights, which contribute to the regularization of the input-output mapping. It is thus of interest to develop fast and accurate algorithms for computing Moore-Penrose inverse matrices. In this paper, an algorithm based on a full rank Cholesky factorization is proposed. The resulting pseudoinverse matrices are similar to those provided by other algorithms. However the computation time is substantially shorter, particularly for large systems.
Human T lymphocytes bioactivate heterocyclic aromatic amines by forming DNA adducts

Heterocyclic aromatic amines (HAA) are formed in cooked meat, poultry and fish but also arise in tobacco smoke and exhaust gases. HAA are potential human carcinogens, which require metabolic activation to exert their genotoxicity. Human tissues can bioactivate HAA to produce reactive intermediates that bind to DNA. HAA DNA adduct formation occurs in human hepatocytes; however, the potential of HAA to form DNA adducts has not been investigated in human T lymphocytes. In this study, we investigated the ability of human T lymphocytes activated with PMA/Ionomycin or CD3/CD28 to express functional CYP1 activity and bioactivate three major HAA: 2‐amino‐1‐methyl‐6‐phenylimidazo[4,5‐b]pyridine (PhIP), 2‐amino‐3,8‐dimethylimidazo[4,5‐f]quinoxaline (MeIQx), and 2‐amino‐9H‐pyrido[2,3‐b]indole (AαC) to form DNA adducts. Adducts were measured by ultraperformance liquid chromatography‐electrospray ionization/multistage scan mass spectrometry. The highest level of DNA adducts occurred for AαC (16 adducts per 109 nucleotides), followed by PhIP (9 adducts per 109 nucleotides). In contrast, DNA adducts formed from MeIQx and the structurally related aromatic amine 4‐aminobiphenyl, a known human carcinogen, were below the limit of detection (< 3 adducts per 109 nucleotides). Moreover, we demonstrate that AαC is a potent inducer of CYP1A1 and CYP1B1 activity through a transcriptional mechanism involving the AhR pathway. Overall, our results highlight the capacity of activated human T lymphocytes to more efficiently bioactivate AαC to form DNA adducts than other prominent HAA or 4‐ABP. Environ. Mol. Mutagen. 57:656–667, 2016. © 2016 Wiley Periodicals, Inc.
Amphotericin B refractory aspergillosis after itraconazole: evidence for significant antagonism

Summary. Failure of amphotericin B to halt aspergillosis in a patient previously treated with itraconazole raised the question of whether amphotericin B lost its activity as a result of antagonism between the two antifungal drugs. Azoles exhaust the target of amphotericin B on the fungal cell membrane. Accordingly amphotericin B in vitro lost its activity against six isolates of Aspergillus fumigatus after exposure to subfungici‐dal concentrations of itraconazole. Prior treatment of mice with itraconazole abolished the protective effect of amphotericin B, even when itraconazole was stopped before starting amphotericin B therapy. These observations raise concern about sequential therapy of aspergillosis with itraconazole followed by amphotericin B.
Protein Expression Regulation under Oxidative Stress*

Oxidative stress is known to affect both translation and protein turnover, but very few large scale studies describe protein expression under stress. We measure protein concentrations in Saccharomyces cerevisiae over the course of 2 h in response to a mild oxidative stress induced by diamide, providing detailed time-resolved information for 815 proteins, with additional data for another ∼1,100 proteins. For the majority of proteins, we discover major differences between the global transcript and protein response. Although mRNA levels often return to baseline 1 h after treatment, protein concentrations continue to change. Integrating our data with features of translation and protein degradation, we are able to predict expression patterns for 41% of the proteins in the core data set. Predictive features include, among others, targeting by RNA-binding proteins (Lhp1 and Khd1), RNA secondary structures, RNA half-life, and translation efficiency under unperturbed conditions and in response to oxidative reagents, but not chaperone binding. We are able to both describe general dynamics of protein concentration changes and suggest possible regulatory mechanisms for individual proteins.
A quantitative comparison of interval type-2 and type-1 fuzzy logic systems: First results

The question “When will an IT2 FLS outperform a T1 FLS? ” has been asked by many, and is acknowledged by many experts to be arguably the most important unanswered question in the T2 field. As a research problem, this question turns into: Establish when and by how much a type-2 fuzzy logic system (T2 FLS) will outperform a type-1 (T1) FLS. This paper provides first results on solving this problem. Its approach is novel because it does not focus immediately on a specific application, but instead focuses on the common component to all performance analyses, thereby providing results that can be used by others in their application-based performance comparisons. The Wu-Mendel minimax uncertainty bounds [16], which in the past have been used to approximate the type-reduced set, and to also act as a starting point for designs of IT2 FLSs, play the key role in this paper. Although comparing an IT2 FLS to a T1 FLS seems like a daunting task, because of the complicated nature of the equations that describe them, this paper shows that when an IT2 FLS is expanded about a T1 FLS-itself a new concept-, surprisingly, very simple first results are obtained.
Convergence in law in the second Wiener/Wigner chaos

Let L be the class of limiting laws associated with sequences in the second Wiener chaos. We exhibit a large subset $L_0$ of $L$ satisfying that, for any $F_\infty$ in $L_0$, the convergence of only a finite number of cumulants suffices to imply the convergence in law of any sequence in the second Wiener chaos to $F_\infty$. This result is in the spirit of the seminal paper by Nualart and Peccati, in which the authors discovered the surprising fact that convergence in law for sequences of multiple Wiener-Ito integrals to the Gaussian is equivalent to convergence of just the fourth cumulant. Also, we offer analogues of this result in the case of free Brownian motion and double Wigner integrals, in the context of free probability. An Erratum is available in ECP volume 17 paper number 54 .
Validation of the San Francisco Syncope Rule in two hospital emergency departments in an Asian population.

OBJECTIVES The objective was to externally validate the ability of the San Francisco Syncope Rule (SFSR) to accurately identify patients who will experience a 7-day serious clinical event in an Asian population. METHODS This was a prospective cohort study, with a sample of adult patients with syncope and near-syncope enrolled. Patients 12 years old and below and patients with loss of consciousness after head trauma, a witnessed seizure, with known alcohol or illicit drug ingestion, and altered level of consciousness or persistent new neurologic deficits were excluded. The patients were evaluated for the presence of one or more of the five SFSR variables: shortness of breath, history of heart failure, hematocrit <30%, systolic blood pressure <90 mm Hg, and abnormal electrocardiogram (ECG). The patients were followed up by medical record review or telephone interview. Seven-day outcomes were death, arrhythmia, myocardial infarction, acute pulmonary edema, significant structural heart disease, pulmonary embolism, major cardiac procedure, stroke, subarachnoid hemorrhage, major bleeding, and anemia. RESULTS A total of 1,250 patients from two centers were recruited. Fifty-six patients were excluded from primary analysis because of incomplete data (n = 55) and/or they were noncontactable for follow-up (n = 32). Of the 1,194 patients analyzed, 138 patients (11.6%) experienced adverse outcomes at 7 days. The rule performed with a sensitivity of 94.2% (95% confidence interval [CI] = 89.0% to 97.0%) and a specificity of 50.8% (95% CI = 47.7% to 53.8%). CONCLUSIONS In this study, SFSR rule had a sensitivity of 94.2%. This suggests caution on the strict application of the rule to all patients presenting with syncope. It should only be used as an aide in clinical decision-making in this population.
Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (FST = 0.35), and FST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.
A study of longitudinal data examining concomitance of pain and cognition in an elderly long-term care population

Purpose To examine if a concomitant relationship exists between cognition and pain in an elderly population residing in long-term care. Background/significance Prior research has found that cognitive load mediates interpretation of a stimulus. In the presence of decreased cognitive capacity as with dementia, the relationship between cognition and increasing pain is unknown in the elderly. Patients and methods Longitudinal cohort design. Data collected from the Minimum Data Set-Resident Assessment Instrument (MDS-RAI) from the 2001–2003 annual assessments of nursing home residents. A covariance model was used to evaluate the relationship between cognition and pain at three intervals. Results The sample included 56,494 subjects from nursing homes across the United States, with an average age of 83 ± 8.2 years. Analysis of variance scores (ANOVAs) indicated a significant effect (P < 0.01) for pain and cognition, with protected t test revealing scores decreasing significantly with these two measures. Relative stability was found for pain and cognition over time. Greater stability was found in the cognitive measure than the pain measure. Cross-legged effects observed between cognition and pain measures were inconsistent. A concomitant relationship was not found between cognition and pain. Even though the relationship was significant at the 0.01 level, the correlations were low (r ≤ 0.08), indicating a weak association between cognition and pain. Conclusion Understanding the concomitance of pain and cognition aids in defining additional frameworks to extend models to include secondary needs, contextual factors, and resident outcomes. Cognitive decline, as with organic brain diseases, is progressive. Pain is a symptom that can be treated and reduced to improve resident quality of life. However, cognition can be used to determine the most appropriate method to assess pain in the elderly, thereby improving accuracy of pain detection in this population.
The distance between successive lightning flashes

The distribution of the distance between successive cloud-ta-ground (CG) flashes has been studied for storms in several regions of the United States. This information is useful for the understanding of several aspects of lightning phenomenology. It is particularly important for personal safety strategies, so that a person can estimate the likelihood that the next flash could be a personal threat. The study concentrates en this application. Use was made of the National Lightning Detection System (NLDN) database.
THE DISTRIBUTION OF LIFE‐HISTORY VARIATION IN THE DAPHNIA PULEX COMPLEX

In the midwestern United States the Daphnia pulex complex consists of a mosaic of sexual and asexual populations, providing a useful model system for studying the evolutionary forces underlying the maintenance of sex. One asexual and two sexual populations were surveyed for genetic variation for isozymes, mitochondrial DNA, and life‐history characters. While the sexual populations exhibited substantial levels of genetic variance for fitness characters, no variation was detected in the asexual population at any level. However, a parallel survey among asexual clones derived from other ponds revealed large amounts of quantitative variation among clones, even among those with the same molecular profile. As a group, the asexuals are more variable for life histories than are the sexual populations. The molecular data indicate a relatively recent origin for the extant asexual D. pulex. The polyphyletic origin of these clones, combined with their microevolutionary potential, provides an explanation for their broad geographic distribution. The distribution of sex in the complex cannot be explained with the standard models that assume an invariant asexual population in reproductive isolation from the parental species. Although the frequency of asexuality may be driven by the spread of a sex‐limited meiosis suppressor through sexual populations, the complete displacement of sexuality may be prevented by ecological distinctions between the two classes of individuals. On average, the asexuals are larger but produce smaller clutches than the sexuals.