Miracle-dz/UniFAR-FTUs huggingface dataset:
Error estimates for the analysis of differential expression from RNA-seq count data

Background. A number of algorithms exist for analysing RNA-sequencing data to infer profiles of differential gene expression. Problems inherent in building algorithms around statistical models of over dispersed count data are formidable and frequently lead to non-uniform p-value distributions for null-hypothesis data and to inaccurate estimates of false discovery rates (FDRs). This can lead to an inaccurate measure of significance and loss of power to detect differential expression. Results. We use synthetic and real biological data to assess the ability of several available R packages to accurately estimate FDRs. The packages surveyed are based on statistical models of overdispersed Poisson data and include edgeR, DESeq, DESeq2, PoissonSeq and QuasiSeq. Also tested is an add-on package to edgeR and DESeq which we introduce called Polyfit. Polyfit aims to address the problem of a non-uniform null p-value distribution for two-class datasets by adapting the Storey–Tibshirani procedure. Conclusions. We find the best performing package in the sense that it achieves a low FDR which is accurately estimated over the full range of p-values, albeit with a very slow run time, is the QLSpline implementation of QuasiSeq. This finding holds provided the number of biological replicates in each condition is at least 4. The next best performing packages are edgeR and DESeq2. When the number of biological replicates is sufficiently high, and within a range accessible to multiplexed experimental designs, the Polyfit extension improves the performance DESeq (for approximately 6 or more replicates per condition), making its performance comparable with that of edgeR and DESeq2 in our tests with synthetic data.
Externalities and Corporate Investment

We show that investment patterns often associated with agency and information problems can emerge as rational responses to product-market rivalry. We establish this result using simultaneous and sequential models of innovative investment that balance two negative externalities. One externality arises when all competing firms invest, thus eroding the gains to innovation accruing to any one firm. Another externality arises when some firms do not invest and lose out to rivals who do innovate. The value of innovative investment therefore depends on the innovation's intrinsic value to each firm and the actions of all competitors. Our analysis can rationalize investment patterns that might appear suboptimal when these externalities are ignored. For instance, our simultaneous model can justify investment levels that might otherwise be interpreted as under or over-investment. Our sequential model shows that value-maximizing firms might optimally herd in their investment decisions. We present evidence supporting key aspects of both the simultaneous and sequential models.
Heightened intrathecal release of proinflammatory cytokines in Creutzfeldt–Jakob disease

Article abstract The authors report high intrathecal release of tumor necrosis factor alpha (TNF-α) and interleukin (IL)-1β in five patients with sporadic or new-variant Creutzfeldt–Jakob disease (CJD) without activation of the humoral or lymphocytic immune responses. Increased release of TNF-α and IL-1β was also detected in some patients with progressive dementias. CJD is associated with a local cerebral host response that involves the release of proinflammatory cytokines.
Facial nerve electromyography: a useful tool in detecting nonauditory side effects of cochlear implantation.

BACKGROUND Facial nerve stimulation is a known complication of cochlear implantation. Until recently, the assessment of facial nerve stimulation was primarily based on self reports which can be problematic in a pediatric setting. For children with facial nerve stimulation, the long-term implications implant use are unclear. OBJECTIVES To illustrate the clinical utility of facial electromyography (EMG) in avoiding nonauditory stimulation evoked by cochlear implant use and to assess the potential for change in these responses over time with chronic electrical stimulation. METHODS Midline evoked auditory brainstem responses and surface EMG of the facial musculature were performed in three children suspected clinically of having electrically evoked facial nerve stimulation. Each child had a different clinical presentation; the first complained of pain, the second experienced involuntary facial movements, and the third experienced nonspecific discomfort after sequential bilateral cochlear implantation. RESULTS All three children had EMG evidence of facial nerve stimulation. However, based on thresholds and patterns of responses in specific facial nerve branches, stimulation was responsible for the subjective and behavioural responses in only two of the three children. CONCLUSIONS Pediatric cochlear implant users are unreliable in their reports of facial nerve stimulation. Evoked surface EMG is an objective and useful clinical tool in patients with known or suspected facial nerve stimulation and can lead to improved implant use.
Characteristics of respondents and nonrespondents to a questionnaire for estimating community mood.

Comstock, G. W. (Training Center for Public Health Research, Johns Hopkins School of Hygiene and Public Health, Box 2067, Hagerstown, Md. 21740) and K. J. Helsing. Characteristics of respondents and nonrespondents to a questionnaire for estimating community mood. Am J Epidemiol 97: 233-239, 1973. —In a study of community mood in Washington County, Maryland, a representative sample of adult residents was selected for interviews. Among this sample, a total of 649 persons had participated in a previous nonofficial census and for this group, similar information was available both for the 571 who were interviewed and the 78 who refused. Characteristics associated with refusals were poor education, residential stability and small households. There was also suggestive evidence that young adults and males were more likely to refuse. Urbanrural residence, cigarette smoking and frequency of church attendance did not appear to be related to refusal.
The Effect of Entrepreneurial Orientation on the Organizational Performance: A Study on Banks in Libya

The present study aimed to examine the effect of the entrepreneurial orientation (EO) on organizational performance (OP). This study was motivated by the mixed findings in literature regarding the relationships between EO and organizational performance. Owing to the mixed results, a novel stream of research was created and this motivated further examining of the impact of other variables that may shed a light on the nature of the relationship. Several theories have been proposed in literature posit the direct relationships among strategies, resources and capabilities as antecedents of success. In this study, copies of questionnaires were distributed to 300 Libyan banks branches, where 200 copies of questionnaires were returned and analyzed. The proposed hypothesis was tested through PLS-SEM and the study results showed that EO positively predicted organizational performance.
Automatic generation of summarized driving video with music and captions

This paper provides a novel summarization method for driving data, including a driving video captured by car-mounted camera, vehicle behavior such as velocity, steering angle, and other information. While a large amount of the driving data have been gathered recently, looking back method, however, has not been well-considered. In this paper, we integrate various information from the driving data as a summarized video with a time stretched video based on the driving behavior, text annotations describing salient events and geo-location, and background music adapted with the driving behavior. This representation is generated automatically from driving data with symbolization process of driving behavior based on nonparametric Bayesian approach. Through subjective evaluations, we evaluated the efficiency of proposed method for understanding the driving data appropriately in short time.
Live Tumor-Promoting Effect of β-Naphthoflavone, a Strong CYP 1A1/2 Inducer, and the Relationship between CYP 1A1/2 Induction and Cx32 Decrease in Its Hepatocarcinogenesis in the Rat

Interrelationships among induction of cytochrome P-450 (CYP) 1A1/2, decrease in connexin 32 (Cx32), and liver tumor-promoting activity by β-naphthoflavone (BNF) in the promotion stage were examined in a 2-stage liver carcinogenesis model. A total of 20 male Fischer 344 rats were initiated with a single intraperitoneal injection of 150 mg/kg of diethylnitrosamine (DEN) or were given the saline vehicle alone. Starting 2 weeks later, they were fed a diet containing 2%, 1%, or 0% BNF for 6 weeks. All animals were subjected to a two-thirds partial hepatectomy at week 3 and were sacrificed at week 8. Absolute and relative liver weights were significantly increased in the DEN+BNF groups as compared to the DEN-alone group. Diffuse hepatocellular hypertrophy with cytoplasmic eosinophilia, sometimes accompanied by development of adenoma-like hepatic foci, was observed in the BNF-treated rats. Remarkable induction of cytochrome CYP 1A1/2 and significant increase in CYP 2E1 were noted in the DEN+BNF groups, and positive immunohistochemical staining for both was observed diffusely. The areas of Cx32-positive spots per hepatocyte in the centrilobular areas of livers of the BNF-treated rats were significantly decreased, but no changes were observed in periportal areas. The numbers and areas of foci positive for glutathione S-transferase placental form were increased in the BNF-treated groups. These results suggest that BNF is a liver tumor promoter that, unlike phenobarbital, does not induce CYP 2B1/2 isozymes, and there seems to be no direct relationship between CYP 1A1/2 induction and Cx32 reduction in BNF hepatocarcinogenesis.
The nature of the litter size loss in senescent hamsters

Young and senescent female hamsters were sacrificed on days 8, 10, 12, 14 and 15 of pregnancy, and the number of viable and resorbing conceptuses was determined. The ovulation rate for each group was also recorded. At each day, there was a reduction in the litter size in senescent animals as compared to the young, but the number of ovulations in each age group was equal. The results indicated that the litter size loss, in senescent hamsters, is not due to a reduction in the ovulation rate, but to a seven fold increase in preimplantation deaths and to a two fold increase in resorption.
South Africa's Health: New South Africa's mental health

The environment in South Africa has been characterised by a long history of abuse of human rights, repression, racial segregation, forced physical removal, pass laws, laws preventing interracial marriages, violence, alcohol related problems, malnutrition, and poverty. If environment is a major determinant of mental health, then the mental health of South Africans might be expected to be poorer than that of people elsewhere. Dr Brian Robertson, professor of psychiatry at the Groote Schuur Hospital in Cape Town, agreed: “A lot depends, however, on how mental health is defined, what indicators of mental health are used, and the effects of protective factors. If mental health is defined broadly as symptoms rather than categorical illnesses, there are clear indicators that the mental health of South Africans has been seriously damaged: I am referring to indicators such as the high levels of substance abuse, crime, and violence. “There is no evidence of a higher incidence of functional psychoses in South Africa than elsewhere. Functional psychoses, however, are generally regarded as being less influenced by environmental factors than ‘neurotic' disorders. ” Dr M B Magner is a psychiatrist attached to the Lentegeur Psychiatric Hospital in Cape Town and also in private practice. He felt that the range of psychiatric problems in South Africa was similar to those in other countries. “But the symptomatology may be different at ‘non pathologic' levels,” he added. “We lack, however, valid data on the mental health profile of South Africans. While most psychiatric services have analysed their own patient data, nationally or provincially coordinated data are lacking. ” Health Trends in South Africa (1993), published by the department of health and population development, makes no mention of psychiatric morbidity. Melwyn Freeman of the Centre for Health Policy in the University of Witwatersrand agreed that reliable data on the mental health of …
Explaining social exchanges in information-based online communities (IBOCs)

Purpose – The purpose of this paper is to scrutinize platforms for members to exchange information by information-based online communities (IBOCs, like LinkedIn or Facebook). Because member participation is vital for IBOCs, this research aims to identify and validate factors that drive member participation. Design/methodology/approach – With reference to social exchange theory the authors developed a model of antecedents of participation in IBOCs that was tested with survey data using PLS. Because some of the results contradicted the theory, the authors examined those results in a mainly qualitative study with online community providers. These experts offered explanations that inform the discussion and managerial implications. Findings – Role clarity, provider’s responsiveness, and enjoyment all influence member participation. Contrary to theory, the cooperation of other members affects member participation negatively while a member’s ability shows no effect. Practical implications – This research has sev.
Doxycycline-induced pancreatitis: a rare finding.

BACKGROUND Drug-induced pancreatitis (DIP) is a rare problem in medicine. A retrospective study from 45 German centers of gastroenterology concluded that only 22 of 1613 (1.4 percent) cases of acute pancreatitis in 1993 were DIP. Though DIP is a rare etiology of acute pancreatitis compared to other common etiologies like alcohol, gallstones, hypercalcemia, hypertriglyceridemia, infection, trauma or medical procedures like endoscopic retrograde cholangiopancreatography (ERCP), its incidence continues to rise. We report a case of a 21-year-old female with DIP following doxycycline treatment for an upper respiratory infection. CASE A 21-year-old, otherwise healthy female presented with severe abdominal discomfort associated with nausea and vomiting. She was hemodynamically stable with normal vital signs. Physical exam revealed a soft but tender to palpation epigastric area. Peritoneal signs were negative. Urinalysis was negative for acute infection. Urine human chorionic gonadotrophin was negative for pregnancy. Laboratory findings revealed a mildly elevated lipase level at 128 U/L (normal 13-60) but was otherwise normal. A computed tomography of abdomen and pelvis revealed evidence of fat stranding consistent with acute pancreatitis. A right upper quadrant ultrasound ruled out gallstones. A serum triglyceride was within normal limit at 80mg/dl. She denied any alcohol use. On further questioning, the patient admitted to previously being diagnosed with an upper respiratory infection two weeks earlier. She had consequently finished a 10-day course of doxycycline therapy, with her last dose five days before presentation. After a literature review of drugs implicated in DIP and ruling out other causes of acute pancreatitis, we concluded that our patient had doxycycline-induced pancreatitis. Follow-up visit three weeks post discharge revealed complete resolution of previous symptoms. CONCLUSION In our vastly evolving pharmacotherapy world, DIP should be entertained as a possible etiology of idiopathic pancreatitis, especially after other common causes have been ruled out.
Characteristics of a Circular Loop Antenna in the Presence of a Coaxial Conducting BOR Attached to a Planar Reflector

The performance of the circular loop antenna (CLA) largely improves in terms of impedance matching and directive gain when a body of revolution (BOR)-type of reflector is placed symmetrically relative to the loop. The input impedance, reflection coefficient, VSWR, directivity, and radiation patterns of a loop antenna for cases of a reflector-hemisphere and a reflector-cone are investigated in this letter. It is found that for a resonant loop, directivity over 9 dB and VSWR less than 2 over a bandwidth of 48.5 MHz can be obtained. The study also shows that the characteristics of the CLA depend mainly on the height of the loop over the reflector and the total surface area of the reflector-body irrespective of the body shape.
A Quantitative Review of Research Design Effects on Response Rates to Questionnaires

A comprehensive literature review of techniques used to increase response rates to questionnaires was conducted. Conclusions were based on arithmetic combination of 497 response rates found in 93 journal articles. Response rates were found to be increased by personal and telephone (versus mail) surveys, either prepaid or promised incentives, nonmonetary premiums and rewards, and increasing amounts of monetary reward. Other facilitators that increased responding were preliminary notification, foot-in-the-door techniques, personalization, and followup letters. Several facilitators were found to be ineffective. An estimated magnitude of effect was calculated for each design variation.
Beyond Crisis Care in Brain Injury Rehabilitation in Australia

Objective: The aim of this commentary was to bring together the various significant issues associated with delivering brain injury rehabilitation in Australia. Through observational critique, the authors aimed to identify gaps in practice and opportunities for change. Approach: In light of Australia’s national health reform process, it is necessary to consider rehabilitation practices and models for brain injury service delivery. There are lessons to be learned within the Australian system, but also opportunities to apply international reform. Conclusion: For those within the service delivery system, brain injury rehabilitation can often appear to be a crisis-driven response. Gaps in service provision persist, leaving individuals who have reduced cognitive and emotional capacity to self-navigate an unpredictable health system at a time in their lives when they are least prepared to do so. Deficiencies in the delivery of timely and appropriate psychosocial or behavioral rehabilitation services undoubtedly contribute to the current pressures on the health system created by increased length of stay in neurological and slow-to-recover rehabilitation units, repeat presentations to primary care, and frequent use of community mental health services. Implication: The experiences of people with acquired brain injury highlights the need for early and targeted interventions that can deal with emerging complexities and support needs, interorganizational approaches, and new accommodation options with a matched service philosophy. Rather than count on good fortune, individual outcomes, and the future of brain injury, rehabilitation ought to depend on deliberate and systemic design.
Nonsurgical Treatment of a Case With Skeletal Class III Malocclusion and Total Open - Bite: A Case Report

This case report presents an adult skeletal Class III and open-bite malocclusion case treated without surgical intervention using the fixed edgewise technique, an RME appliance and box elastics.The patient was an 18-year-old female who had completed her growth and development. She had a total openbite, maxillary retrognathia, a crossbite in the posterior, and hypoplasia of the maxillary centrals and first molars. In addition, the patient's left mandibular first molars had previously been extracted because of caries, and extraction spaces were present.We extracted the upper first premolars and right lower first molar for treatment. We then applied a RME appliance, Roth edgewise device and intermaxillary elastics. At the end of treatment, we obtained a Angle class I dental relationship in the canines, an ideal occlusion relationship and an esthetic dental and facial relationship. reatment was completed in 20 months.
Effects of dimensions of corporate social responsibility on organization performance

Most of organizations including busines enterprise or non-commercial (public-sector or private-sector) in competi ve environment trend to take place the corporate social responsibility as a strategy for achieving their goals. But there are several definitions of CSR (Dahlsrud, 2006) that every definition cover some dimensions of corporate social responsibility. Thus, organizations should determine their purpose and dimensions of CSR that efect on performance of organization.
Heart failure: evaluation of cardiopulmonary transit times with time-resolved MR angiography.

PURPOSE To measure cardiopulmonary transit times in patients with heart failure by using low-dose, time-resolved magnetic resonance (MR) angiography and to determine if transit curves reflect conventional MR indexes of cardiac function. MATERIALS AND METHODS Twenty-six patients with heart failure and left ventricular (LV) systolic dysfunction (17 men and nine women; age range, 22-78 years) and thirteen control subjects (eight men and five women; age range, 23-59 years) were examined with MR imaging. The examination consisted of rapid cine MR imaging throughout the heart, followed by contrast material-enhanced time-resolved three-dimensional MR angiography of the cardiac chambers and pulmonary vasculature. Time-intensity curves for the pulmonary artery and ascending aorta were derived from the MR angiography images. Cardiopulmonary transit times and dispersions (full widths at half maximum [FWHM]) were determined from the curves. Transit times and FWHM values for the patients with heart failure were compared with control values by using two-tailed t tests, and transit time was correlated with standard LV functional parameters calculated from the cine MR images. RESULTS Cardiopulmonary transit times and FWHM values were significantly prolonged in the patients with heart failure compared with those in the control patients (P <.001). Transit time correlated directly with LV end-diastolic and end-systolic volumes and inversely with LV ejection fraction (R > 0.60). However, transit time did not correlate strongly with age, body surface area, heart rate, LV mass, stroke volume, cardiac output, or sphericity index. CONCLUSION Time-resolved MR angiography allows determination of cardiopulmonary transit times that are significantly prolonged in heart failure and correlate directly with LV volumes and inversely with LV ejection fraction.
Lethal Infection of C3H/HeJ and C3H/SCID Mice with an Isolate of Leptospira interrogans Serovar Copenhageni

ABSTRACT Leptospira interrogans serovar Copenhageni strain RJ16441, a blood isolate from humans with the severe pulmonary form of leptospirosis, has previously been shown to cause fatal pulmonary hemorrhage in guinea pigs and asymptomatic chronic renal tubular colonization with urinary shedding in rats. In this study, RJ16441 caused lethal infection of both C3H/HeJ and C3H/SCID mice, but no hemorrhagic phenomena were observed.