Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative analysis of differential gene expression tools for RNA sequencing time course data

Abstract RNA sequencing (RNA‐seq) has become a standard procedure to investigate transcriptional changes between conditions and is routinely used in research and clinics. While standard differential expression (DE) analysis between two conditions has been extensively studied, and improved over the past decades, RNA‐seq time course (TC) DE analysis algorithms are still in their early stages. In this study, we compare, for the first time, existing TC RNA‐seq tools on an extensive simulation data set and validated the best performing tools on published data. Surprisingly, TC tools were outperformed by the classical pairwise comparison approach on short time series (<8 time points) in terms of overall performance and robustness to noise, mostly because of high number of false positives, with the exception of ImpulseDE2. Overlapping of candidate lists between tools improved this shortcoming, as the majority of false‐positive, but not true‐positive, candidates were unique for each method. On longer time series, pairwise approach was less efficient on the overall performance compared with splineTC and maSigPro, which did not identify any false‐positive candidate.
Viability and fertility of stallion semen frozen with ethylene glycol and acetamide as a cryogenic agent

This study was designed to determine the effect of cooling at a rate of -0.13 o C/min or any slow cooling prior to freezing on stallion sperm and to determine the effect of two thawing temperatures on the viability of sperm frozen using a lactose-EDTA-egg yolk extender (LAC) with 3.5% ethylene glycol (LAC 3.5% EG) or a LAC with the additional incorporation of methyl cellulose, trehalose and acetamide (LAC+5% AC). No differences were observed in the post-thaw parameters of sperm frozen using either one of the cryogenic agents or frozen with or without previous slow cooling. Thawing at 75 o C was better than at 37 o C (P < 0.05). An interaction was observed between the cryoprotectant and the freezing protocol (P < 0.05). A conception rate of 23.3% was obtained after AI using equine semen frozen with LAC+5% AC.
Does the evidence support the implementation of lung cancer screening with low-dose computed tomography?

(1) Does evidence from randomized controlled trials (RCTs) show that LDCT screening reduces lung cancer mortality? (2) Does evidence from RCTs show that the benefits of LDCT screening outweigh the harms? (3) What direct or indirect evidence is there that LDCT screening performed in the U.S. as part of routine clinical care (and outside of a research setting) can attain the same benefits to harms ratio as seen in RCTs, or at least attain a minimally acceptable benefits to harms ratio?
Breast tumours following combined hormone replacement therapy express favourable prognostic factors

The aim of the present study was to evaluate the association between different types of hormone replacement therapy (HRT) and risk of specific breast cancer subgroups. A population‐based prospective cohort study including 12,583 peri‐ or postmenopausal women were followed using record‐linkage with national cancer registries. During an average follow‐up of 4.5 years, 332 cases of invasive breast cancer were diagnosed. Tumour samples were available from 283 cases. These tumours were re‐evaluated according to histological type, grade, and mitotic index. Evaluation of tumours included estrogen and progesterone receptor status (ERα, ERβ and PgR), as well as expression of Ki67, HER2, cyclin D1 and p27. The incidence of breast cancer in current users of combined HRT (CHRT) was significantly higher than in non‐users. The difference corresponded to an adjusted relative risk (95% confidence interval) of 3.01 (2.35–3.84) as obtained using a Cox's proportional hazards analysis. CHRT was associated with lobular tumours (3.48:1.99–6.10), grade 1 tumours (4.46:2.79–7.13) and tumours with a low mitotic index (4.35:2.99–6.34). CHRT was not related to any specific subgroup in terms of ERα‐, ERβ‐ or PgR‐expression. CHRT was associated with low proliferating tumours, defined by the Ki67 index (3.58:2.60–4.93), HER2 amplified tumours (4.40:1.93–10.06), low expression of the oncogene cyclin D1 (3.14:2.32–4.23) and high expression of the tumour suppressor gene p27 (3.47:2.40–5.01). Use of estrogen‐alone HRT (ERT) was not associated with any statistically significant risk of breast cancer. We conclude that the use of CHRT is associated with an increased incidence of breast tumours with comparatively favourable prognostic factors. © 2007 Wiley‐Liss, Inc.
Incidence of transient ischemic attack in Rochester, Minnesota, 1985-1989.

BACKGROUND AND PURPOSE There is scant information available on the incidence of transient ischemic attack (TIA) in a defined population. This study defines incidence rates of first TIA and subtypes of TIA during 1985-1989 and compares the incidence to that obtained from a 1960-1972 cohort study. METHODS Medical records of all residents of Rochester with potential diagnosis of TIA during 1985-1989 were screened to determine whether the case met the criteria for TIA. All available data were used to determine the vascular distribution of the TIA. Average annual age- and sex-adjusted incidence rates were calculated for 1985-1989, and results were compared with incidence rates determined in a Rochester-based 1960-1972 cohort study. RESILTS: Two hundred two cases of first TIA or amaurosis fugax occurred among Rochester residents during 1985-1989. The age- and sex-adjusted incidence rate for any TIA was 68/100 000 population. Incidence of amaurosis fugax was 13/100 000; anterior circulation (cerebral) TIA, 38/100 000; and vertebrobasilar distribution TIA, 14/100 000. Rates were similar to those determined from a 1960-1972 cohort study. CONCLUSIONS The incidence rate of TIA is 41% that of stroke incidence. TIA incidence in Rochester, Minn, is higher than has been previously reported for other sites throughout the world. Although comparison with prior time periods is difficult because of ascertainment issues, it appears that there has been no significant change in TIA incidence since the decade of the 1960s or earlier. This suggests that the most common mechanism for TIA (atherosclerosis) has not changed in prevalence, nor have risk factors leading to this mechanism.
Mycobacterium avium ssp. paratuberculosis and its potential survival tactics

Mycobacterium avium ssp. paratuberculosis (Map) is an important animal pathogen with a potential, but as yet unproven, role in human disease. This review briefly describes the characteristics of Map that distinguish it from other Mycobacterium spp. , presenting new information arising from completion of the sequencing of the Map genome. It then focuses on the potential mechanisms Map might employ to survive and disseminate in the environment, including interaction with protozoa and insects, dormancy, biofilm formation and aerosolization.
Lycopene Interferes With Cell Cycle Progression and Insulin-Like Growth Factor I Signaling in Mammary Cancer Cells

Recent studies have shown that high insulin-like growth factor I (IGF-I) blood level is a risk factor in breast and prostate cancer. The aim of this study was to determine whether the mitogenic activity of IGF-I in mammary cancer cells can be reduced by the dietary carotenoid lycopene. The anticancer activity of lycopene, the major tomato carotenoid, has been suggested by in vitro, in vivo, and epidemiological studies. Growth stimulation of MCF7 mammary cancer cells by IGF-I was markedly reduced by physiological concentrations of lycopene. The inhibitory effects of lycopene on MCF7 cell growth were not accompanied by apoptotic or necrotic cell death, as determined by annexin V binding to plasma membrane and propidium iodide staining of nuclei in unfixed cells. Lycopene treatment markedly reduced the IGF-I stimulation of tyrosine phosphorylation of insulin receptor substrate 1 and binding capacity of the AP-1 transcription complex. These effects were not associated with changes in the number or affinity of IGF-I receptors, but with an increase in membrane-associated IGF-binding proteins, which were previously shown in different cancer cells to negatively regulate IGF-I receptor activation. The inhibitory effect of lycopene on IGF signaling was associated with suppression of IGF-stimulated cell cycle progression of serum-starved, synchronized cells. Moreover, in cells synchronized by mimosine treatment, lycopene delayed cell cycle progression after release from the mimosine block. Collectively, the above data suggest that the inhibitory effects of lycopene on MCF7 cell growth are not due to the toxicity of the carotenoid but, rather, to interference in IGF-I receptor signaling and cell cycle progression.
Diagnosis and management of pleomorphic sarcomas (so‐called “MFH”) in adults

The existence of “malignant fibrous histiocytoma” (“MFH”) as a distinct entity is controversial. Previously accepted as the most common sarcoma affecting adults, it is now known to comprise a heterogeneous group of tumors without a specific known line of differentiation. Reclassification of many tumors in this group afforded better prognostication, but traditional treatments still apply. Pleomorphic soft tissue tumors for which a line of differentiation is debatable are presently categorized as undifferentiated pleomorphic sarcoma. J. Surg. Oncol. 2008;97:330–339. © 2008 Wiley‐Liss, Inc.
Tasting the difference: do multiple defence chemicals interact in Müllerian mimicry?

Müllerian mimicry, where two unpalatable species share a warning pattern, is classically believed to be a form of mutualism, where the species involved share the cost of predator education. The evolutionary dynamics of Müllerian mimicry have recently become a controversial subject, after mathematical models have shown that if minor alterations are made to assumptions about the way in which predators learn and forget about unpalatable prey, this textbook case of mutualism may not be mutualistic at all. An underlying assumption of these models is that Müllerian mimics possess the same defence chemical. However, some Müllerian mimics are known to possess different defence chemicals. Using domestic chicks as predators and coloured crumbs flavoured with either the same or different unpalatable chemicals as prey, we provide evidence that two defence chemicals can interact to enhance predator learning and memory. This indicates that Müllerian mimics that possess different defence chemicals are better protected than those that share a single defence chemical. These data provide insight into how multiple defence chemicals are perceived by birds, and how they influence the way birds learn and remember warningly coloured prey. They highlight the importance of considering how different toxins in mimicry rings can interact in the evolution and maintenance of Müllerian mimicry and could help to explain the remarkable variation in chemical defences found within and between species.
CARRY-OVER OF AFLATOXIN B1-FEED INTO AFLATOXIN M1-MILK IN DAIRY COWS TREATED WITH NATURAL SOURCES OF AFLATOXIN AND BENTONITE

High occurrence of aflatoxin contamination in feed stuffs implicates for a long time experience ofaflatoxin B1 (AFB1) exposure to dairy cattle in Indonesia. A latin square 4X4 research design wasadopted to study the characteristic of AFB1 carry-over rate (COR) of Indonesian crossbred FriesianHolstein (PFH) as effects of inclusions of AFB1-naturally contaminated feed and bentonite in the diet.Results showed a rapid aflatoxin M1 (AFM1) excretion in the milk, detected in the first milking sampleor 10 hours after AFB1 ingestion. The steady state of AFM1 concentration observed since the first dayof treatment period and AFM1 contamination was still detected until 5 days after AFB1 removed fromthe diet. The COR in this study was observed 0.1%. AFM1 concentration was highly significantly(P 0.05) of levels of AFB1and bentonite inclusions on the COR, nutrients intake, milk production, and milk composition. IIt isconcluded that AFM1 concentration was influenced by AFB1 intake and that transfer of AFB1-feed intoAFM1-milk (COR) in PFH cow was lower compare to reported COR value for dairy cow in sub tropicalregion.
Methane Found in Well Water Near Fracking Sites

In a study of 68 private drinking water wells in northeastern Pennsylvania and New York, methane contamination rose sharply with proximity to natural gas drilling and hydraulic fracturing (“fracking”) sites.1 The average methane concentration in shallow groundwater in active drilling areas fell within the defined action level (> 10 mg/L but < 28 mg/L) for hazard mitigation recommended by the U.S. Department of the Interior, and the maximum (64 mg/L) was well beyond that threshold, according to the report. However, the researchers found no evidence of fracturing fluids. Principal investigator Robert B. Jackson of Duke University says fracking has been conducted in the sampled region since about 2008. The team sampled the water supplies in 2010. The researchers measured concentrations of gases and certain isotopes of carbon in methane and other hydrocarbons to distinguish the ancient thermogenic gas stores sought in drilling operations from methane generated by microbial degradation of organic matter. The closer the well was to an active drilling site, the more likely it was the methane detected was thermogenic. Flammable levels of natural gas are common in water supplies, and explosions—even reports of flammable drinking water—have occurred near fracking sites, says Abrahm Lustgarten, a reporter for Propublica who has investigated gas drilling across the United States. But no peer-reviewed studies have investigated health effects of chronic ingestion of small amounts of methane, Jackson says.2 John Hanger, a former head of the Pennsylvania Department of Environmental Protection (DEP), blames poor gas well construction or design, not fracking, for methane contamination noted to date. He says repairs or plugging of gas wells eliminated contamination in 14 of 19 previously contaminated water wells tested in 2010 by the DEP. But Jackson maintains fracking cannot be ruled out as a cause, given the high pressures used in the practice. Just how likely are leaks? Based on a non-peer-reviewed survey of the five states that systematically report incidents at wells where fracking occurs and where complaints have spurred inspections, Ronald E. Bishop, a lecturer in chemistry and biochemistry at the State University of New York, Oneonta, estimates nearly 2% of such gas wells may end up contaminating groundwater with fracking fluids.3 Bishop says 50% of new natural gas wells recently inspected in Quebec leaked methane.4 Hanger says Pennsylvania has enacted strict standards for design, construction, and materials used in gas wells, which became effective in February 2011.5 The state also requires testing, monitoring, and disclosure of chemicals used in fracking. But Amy Mall, a senior policy analyst with the Natural Resources Defense Council, says state fracking regulations vary widely, and a federal law passed in 2005 exempts fracking from the Safe Drinking Water Act and companies from disclosing chemicals used during the process.
Helping Survivors of Human Trafficking: A Systematic Review of Exit and Postexit Interventions

Background: Human trafficking is a global problem and results in deleterious psychological, social, and physical effects on the lives of those who are trafficked; however, it is not clear how to best intervene with survivors. The purpose of this review was to synthesize the evidence of exit and postexit intervention programs for survivors of human trafficking to inform practice and research. Method: Systematic review methods were used to search, select, and extract data from published and unpublished experimental, quasi-experimental, and preexperimental studies that assessed the effects of any exit or postexit interventions for victims of human trafficking. The authors searched eight databases, reviewed bibliographies, and conducted forward citation searches from relevant reports and prior reviews to find studies authored between 2005 and 2015. Results: The search yielded six eligible studies that included 155 female and 6 male survivors from four countries. Interventions were diverse, with three using a trauma-informed approach. Authors measured a myriad of outcomes, including mental health, social network, community reintegration, and employment; however, the quality of most studies was poor. Discussion: Evidence of effects of exit and postexit interventions is sparse, and much of the research is poorly designed and executed; however, the needs of trafficking survivors are complex and effective interventions are desperately needed. Implications for practice and research are discussed.
Nonadherence to Antihypertensive Medication Among Hypertensive Adults in the United States─HealthStyles, 2010

Nonadherence, or not taking medications as prescribed, to antihypertensive medications has been associated with uncontrolled hypertension. The authors analyzed data from HealthStyles 2010 to assess medication nonadherence among adults with hypertension. The overall prevalence of hypertension was 27.4% and the prevalence of nonadherence was 30.5% among hypertensive adult respondents. Nonadherence rates were highest among younger adults (aged 18–44 years), Hispanics, those who reported lowest annual income (<$25,000), and those who reported depression. The most common reason stated for nonadherence was “I cannot afford the medication” (35.1%). A multivariate logistic regression model showed age, race, and household income to be associated with nonadherence. These findings suggest that certain subgroups are more likely to report barriers to adherence. Interventions to support the management of hypertension should consider the identification of certain at‐risk subgroups and utilize community and clinical evidenced‐based resources to improve long‐term control.
Age-period-cohort modelling of breast cancer incidence in the Nordic countries.

The Nordic countries have experienced a steady increase in breast cancer incidence throughout the past 35 years. We analysed the incidence in Denmark, Finland, Norway and Sweden during the period 1958 to 1992 using age-period-cohort models and taking the systematic mammography screening into account. Assuming the age dependency of the incidence pattern in old age to be common for the Nordic countries, an internal comparison could be made among the four countries of the cohort effects and the period effects. The study indicated that the period effects have been of importance for the increase in breast cancer incidence seen in the Nordic countries. The widespread practice of neglecting the period effects in age-period-cohort analysis of time trends in breast cancer incidence therefore probably needs reconsideration. A key finding was that Danish women born in the 20th century seem to have been exposed to an increasing load of cohort borne breast cancer risk factors not experienced to the same extent by Norwegian women, whereas they were seemingly subjected to the same period effects.
Application of PLISSIT Counseling Model for Women with Cervical Cancer Undergoing Treatment on Enhancing Sexuality

Background: Sexuality is an important part of normal human functioning. Gynecological cancer diagnosis and treatment has a devastating effect on Sexual issues. The study was conducted at Outpatient oncology, Helwan General hospital, Egypt. The study aim to evaluate the effect of application of PLISSIT Counseling Model for women with cervical cancer undergoing treatment on enhancing sexuality. A quasi –experimental design was used. A purposive sample of 80 women with cervical cancer was included. Four tools, a structured interview questionnaire, body image scale, female sexual function index (FSDI), and the revised dyadic adjustment scale. The study findings indicated that a significant relationship was found between treatment, side effect pre and post application regarding nausea & vomiting, diarrhea, and pain. The study and research hypothesis concluded that applying of PLISSIT counseling model for sexuality was effective in enhancing sexual functioning except in the area of sexual desire or libido, improvement in couple satisfaction and body image after application of PLISSIT counseling model post application compared to pre-application. The study recommended that dissemination of PLISSIT Counseling Model For Women with cervical cancer in addressing sexual dysfunction in a cancer treatment, Applying the evidence-based nursing intervention to address and manage the effects of cervical cancer on sexuality.
Effects of Pterygium Excision on Corneal Curvatures

Objective: To determine the difference in mean corneal curvatures before and after pterygium excision, by using automated refraction and keratometry. Methodology: This quasi-experimental study was conducted at Eye Unit-I, Bahawal Victoria Hospital, Bahawalpur, from March 2010 to August 2010. Thirty patients with primary pterygium were analyzed before and after pterygium surgery for corneal curvature changes. Automated refraction and Automated keratometry were used to calculate the cylindrical error and the corneal surface power respectively. The mean and standard deviation were calculated for the corneal curvatures and the refractive cylinder before and after the operation. Paired sample t-test was used to compare the corneal curvatures and refractive cylinder before and after pterygium excision. P-value<0.05 was considered significant. Results: The preoperative cylindrical error decreased from 4.32+ 1.88 D to 2.11 +1.96D postoperatively. Similarly, before surgery, the keratometry readings were 43.71 + 1.12 D in horizontal meridian and 44.94+ 1.41 D in vertical meridian. One week after the pterygium surgery these values were 44.45+0.85 D in horizontal meridian and 45.23 + 0.78 D in vertical meridian. Conclusion: Pterygium excision brings a statistically significant change in corneal curvatures which leads to a decrease in cylindrical correction needed. This causes an improvement in subjective visual acuity in patients who have undergone pterygium surgery.
PHYSIOLOGY OF THE INHIBITION BY GLUCOSE OF THE INDUCED SYNTHESIS OF THE β-GALACTOSIDE-ENZYME SYSTEM OF ESCHERICHIA COLI

In previous papers a model (Cohn, 1956, 1958; Cohn and Horibata, 1959a, b) was described which completely rationalized the kinetics of the induction by galactosides and the inhibition by glucose in terms of the properties of the galactoside-permease. However, little information was provided on the mechanism by which glucose acts as an inhibitor of induction. It is known (Cohn and Horibata, 1959a, b; Herzenberg, 1958) that glucose inhibits induced f-galactosidase synthesis in mutants which lack permease, and, conversely, induced permease synthesis is inhibited in mutants which lack f3-galactosidase. Therefore, it is clear that the inhibiting action of glucose is not at the level of the activity of either permease or galactosidase but at some other point in the series of reactions leading to the synthesis of either component. The experiments described here are best understood in terms of the hypothesis that induced enzymes are those whose synthesis can be repressed (Neidhardt and Magasanik, 1956a, b; 1957; Vogel, 1957) by some derivative of the carbon source. The inducer relieves the repression. Certain very inhibitory carbohydrates, such as glucose or mannitol, are metabolized to yield high internal levels of repressor, whereas less inhibitory substances such as succinate and lactate give lower levels of repressor. The repressor-hypothesis with some qualifications will be used as the basis for the description of the data.