Miracle-dz/UniFAR-FTUs huggingface dataset:
Appropriateness of some resampling‐based inference procedures for assessing performance of prognostic classifiers derived from microarray data

The goal of many gene‐expression microarray profiling clinical studies is to develop a multivariate classifier to predict patient disease outcome from a gene‐expression profile measured on some biological specimen from the patient. Often some preliminary validation of the predictive power of a profile‐based classifier is carried out using the same data set that was used to derive the classifier. Techniques such as cross‐validation or bootstrapping can be used in this setting to assess predictive power, and if applied correctly, can result in a less biased estimate of predictive accuracy of a classifier. However, some investigators have attempted to apply standard statistical inference procedures to assess the statistical significance of associations between true and cross‐validated predicted outcomes. We demonstrate in this paper that naïve application of standard statistical inference procedures to these measures of association under null situations can result in greatly inflated testing type I error rates. Under alternatives of small to moderate associations, confidence interval coverage probabilities may be too low, although for very large associations coverage probabilities approach their intended values. Our results suggest that caution should be exercised in interpreting some of the claims of exceptional prognostic classifier performance that have been reported in prominent biomedical journals in the past few years. Copyright © 2006 John Wiley & Sons, Ltd.
Taking back the power: an analysis of Black women’s communicative resistance

ABSTRACT Black women are a structurally oppressed group in a subordinate position in the power hierarchy. Language is an important demonstration of group identity and is used to manage the day-to-day realities of being both Black and women. Scholars have devoted attention to explaining why Black women’s discursive practices are a function of their particular vantage point and can serve as a measure of protection against social and political hostilities. While there is a great deal of research acknowledging Black women’s ability to resist, the work can be extended by analyzing the specific resistance strategies Black women employ in common social environments. This essay uses Black/feminist standpoint and power and discourse frameworks to analyze Black women’s communicative resistance across three communication contexts: (1) education, (2) workplace, and (3) personal relationships.
Feedback Strategies for Interactive Learning Tasks

Modern information technologies increase the range of feedback strategies that can be implemented in computer based learning environments; however, the design and implementation of feedback strategies are very complex tasks that are often based more on intuition than on psychologically sound design principles. The purpose of this chapter is to present theoretically and empirically based guidelines for the design and evaluation of feedback strategies. To this end, this chapter describes an interactive, two-feedback-loop model that explains core factors and effects of feedback in interactive instruction (Narciss, 2006). Based on these theoretical considerations, a multidimensional view of designing and evaluating multiples feedback strategies under multiple individual and situational conditions is presented. This multidimensional view integrates recommendations of prior research on elab-KEYWORDS Cybernetics: System theory concerned with the issues of regulation, order, and stability confronting us in the treatment of complex systems and processes. Feedback: Output of a system that is fed back to the controller of the system as an input signal to regulate the system with regard to a reference value (cybernetic definition); post-response information that is provided to learners to inform them of their actual state of learning or performance (instructional context). Informative tutoring feedback: Multiple-try feedback strategies providing elaborated feedback components that guide the learner toward successful task completion without offering immediately the correct response. Interactive learning task: Tasks providing multiple response steps or tries and instructional components such as feedback, guiding questions, prompts, simulation facilities, and so on.
Autoreactive T cells induce neurotrophin production by immune and neural cells in injured rat optic nerve: Implications for protective autoimmunity

Accumulating evidence suggests that activation of the immune system in the central nervous system (CNS) after trauma protects the CNS from damage propagation and facilitates regeneration. Studies by our group have shown that passive transfer of autoimmune T cells specific to myelin basic protein (TMBP) can protect injured neurons in the rat CNS from secondary degeneration. In this study, we investigated the effects of TMBP treatment on the local immune response (by B cells and macrophages) and on the expression of neurotrophic factors after crush injury of the rat optic nerve. Systemic injection of activated TMBP caused an increase in the accumulation of macrophages/microglia and B cells in the injured nerve, which was greater than that seen in the injured optic nerves of untreated animals. This accumulation was accompanied by a transient, but massive, increase in the expression of neurotrophic factors. Immunocytochemical analysis demonstrated differential expression of neurotrophins by resident astrocytes and by infiltrating B cells, T cells, and macrophages. Because postinjury neuronal survival and maintenance are known to be affected by neurotrophins, our findings point to a possible contribution of a neurotrophin‐related mechanism to the protective effect conferred by T cell‐mediated autoimmunity on injured neurons.
The development of adaptive behavior in typically developing and special needs preschoolers: Relationship to selected parenting and child characteristics /

The purpose of this research was first to determine if selected parenting characteristics, previously demonstrated to be predictive of child cognitive and emotional developmental levels, were also related to adaptive behavior in preschool children both with and without special needs. Secondly, this study sought to demonstrate whether or not there were differences between the parents of typically developing children and those with special needs as to which characteristics were significant predictors of child outcomes. Multiple regression analyses, which included the four parental characteristics (parent/child attachment, degree of parental support, cognitive stimulation provided through the home environment and parental expectations), child IQ and interactions between child IQ and each parental characteristic were conducted to clarify these relationships. As anticipated, different parenting behaviors and beliefs emerged as significant predictors of child adaptive behavior levels in the domains of communication, independence and socialization for each group. In addition, the amount of variance predicted by the regression model for each of the three domains of adaptive behavior differed according to group membership.
Intermittent Fasting Modulation of the Diabetic Syndrome in Streptozotocin- Injected Rats: Post-Mortem Investigations

Intermittent fasting was previously reported to exert beneficial effects in sand rats, an animal model of diabetes. The present report complements recent comparable findings recorded in streptozotocin-induced diabetic rats (STZ rats). Intermittent fasting minimized the increase in pancreatic, hepatic and renal weight otherwise observed in the STZ rats. The glycogen content of the liver was higher in the STZ rats than in the control animals. It was positively correlated, at the individual level, with the hepatic glucose content. Significant positive correlations also prevailed between the plasma glucose concentration at sacrifice, which was lower in intermittently fasting or calorie-restricted STZ rats than in non- fasting STZ rats, and either the liver glucose content or liver total carbohydrate content. The kidney PCNA (proliferating cell nuclear antigen) index, as well as the plasma creatinine and urea concentrations, were also lower in intermittently fast- ing or calorie-restricted STZ rats than in non-fasting diabetic animals. These findings reinforce the view that intermittent fasting may exert a favourable effect, in terms of glucose homeostasis and the undesirable consequences of its perturba- tion, in diabetic animals.
Seroprevalence of dengue infection: A hospital based study from Udaipur, Rajasthan

Dengue is one of the most important arthropod- borne viral infections, widely distributed throughout the tropics and subtropics. It is endemic to the Indian subcontinent and associated with explosive urban epidemics and has become a major public health problem in India. The present study was conducted to detect prevalence of Dengue virus infection in Udaipur, Rajasthan. Materials and Methods: Serum samples from 640 patients clinically suspected of having dengue infection visiting a tertiary care hospital during the period of August 2016 to February 2018 were screened for the presence of Dengue NS1 antigen and IgM and IgG antibodies using one-step immune-chromatographic assay (Dengue Rapid IgM/IgG test and NS1 test by SD BIOLINE). Result: Out of 640 samples 62 samples (9.68%) were positive for Dengue virus infection. Out of total positive Sample for dengue virus infection, 61% samples were of male patients and 39% samples were from female patients. Among them 28% positive samples were from paediatric age group (Age 1- 14 years) and rest were from Adult age group. Seasonal trend showed a gradual increase in Dengue positives starting from August with a peak in October. Most common presentation was fever (98%). Conclusion: Number of dengue cases is on increase in the region and continued surveillance is essential to determine epidemiological and seasonal trend.
HISTOPATHOLOGICALEVALUATION OF COLORECTAL CARCINOMA

Background: Colorectal cancer is the most common gastrointestinal tract cancer worldwide. In Iraq, colorectal cancer was the seventh top cancers, whereas in Kurdistan, it was the fourth most common cancer for both males and females. Although the methods of the diagnosis and therapy have been improved, only about 50% of the patients who resected the tumor died from disease within 5 years, due to distant metastasis. The study was carried out to determine the frequency of histopathological types of colorectal cancer, and to evaluate the correlation between colorectal cancer regarding the grade, stage, with different histological finding which include desmoplastic reaction, lymphocytic infiltration, foamy macrophages, necrosis, intraglandular necrosis, and calcification. Subject and Methods: This study includes (108) patients diagnosed with colorectal cancer. Cases were collected during the period January 2015 December 2017 from the histopathological department at Central Public Health Laboratory and other private labs in Duhok city. Clinical information were obtained from the available histopathological reports. Paraffin embedded blocks were sectioned and stained with immunohistochemistry markers; Ki67 and VEGF then processed automatically according to protocols supplied by the antibody manufacturer. Results: Patients age ranged from18-83 years with a mean of 54.42 years. The peak ages of the patients were between 60-69 years. Male: female ratio was 1.5:1. The commonest tumor location was (recto-sigmoidal region); rectum was (42.6 %) and sigmoid colon was(22.2%). Conventional adenocarcinoma was the predominant type 86(79.6%), majority of cases were moderately differentiated adenocarcinoma constituting85.2%. Stage III was the highest stage constituting 56(51.9%), followed by stage II which constitute 37(34.3%). The local invasion of the mucosa and other layers of colonic wall were associated with desmoplasia and collagen fiber remodeling. Infiltration of foamy macrophages decreased in number in relation to higher grade. Intraglandular necrosis showed significant correlation with tumor invasiveness, lymph node metastasis and grade. The frequency of both markers Ki67 and VEGF were 77 and 75 respectively. Ki67 immunoreactivity revealed significant relationship with tumor grade (P=0.014), whereas VEGF had significant relationship with TNM stage (P = 0.019), as well as the local invasion to the colorectal wall (P 0.009). Conclusions: Moderate differentiated adenocarcinoma (85.2%) and stage III (51.9%) were the most frequent diagnosed cases with colorectal cancer. Macrophages infiltration was conversely related with grading of colorectal cancer. Histopathological changes like desmoplastic reaction and intraglandular necrosis were common findings in colorectal cancer and they were in concordance correlation with stage and grade.Ki67 had relationship with tumor grade, whereas VEGF correlate with tumor invasion. Duhok Med J 2018; 12 (2): 45-67.
The Ultrastructural Changes of the Sertoli and Leydig Cells Following Streptozotocin Induced Diabetes

Objective(s) This investigation was conducted to evaluate the effects of diabetes on the structure and function of testicular tissue. Materials and Methods Diabetes was induced in male adult rats by a single intraperitoneal injection of streptozotocin. Body and testicular weight, hormonal analyses, histological and ultrastructural analyses were measured. Results The body and testicular weights were dropped significantly (P< 0.05) in diabetic rats in comparison with control rats. On the other hand, in diabetic rats, the blood glucose level increased significantly (P< 0.05). The blood plasma levels of testosterone, 17-β estradiol, progesterone, FSH and LH were reduced in diabetic rats. Histomorphological studies were revealed reduction in diameter of seminiferous tubules and germinal epithelium height, edema in interstitial tissue, germ cell depletion, decrease in cellular population and activity with disruption of spermatogenesis in diabetic rats. Ultrastructural study showed the mitochondrial change and reduction of smooth endoplasmic reticulum in Sertoli and presence of lipid droplets in Leydig cells of diabetic rat’s testes. Conclusion The results of the present study confirmed that, the ultrastructural changes of Sertoli and Leydig cells, brought about by streptozotocin induced diabetes, because of the alterations in pituitary gonadotropins, and these changes influence the normal spermatogenesis in rats.
Prevalence, clinical characteristics, and predictors of obesity hypoventilation syndrome in a large sample of Saudi patients with obstructive sleep apnea

Objectives: To assess the prevalence, clinical characteristics, and predictors of obesity hypoventilation syndrome (OHS) in a large sample of Saudi patients with obstructive sleep apnea (OSA). Methods: This prospective observational study consisted of 1693 patients who were diagnosed to have sleep-disordered breathing using type I attended polysomnography (PSG) between January 2002 and December 2012 in the University Sleep Disorders Center (USDC) at King Saud University Hospital, Riyadh, Kingdom of Saudi Arabia. Results: Out of 1693 OSA patients, OHS was identified in 144 (8.5%) (women 66.7%). Compared with the pure OSA patients, the OHS patients were significantly older (57.4±13.4 years versus 46.8±13.7 years), had a higher body mass index (44.6±10.8 versus 35.7±9.2 kg/m2), a higher daytime partial pressure of carbon dioxide (PaCO2) (56.5±12.7 versus 41.6±6.7 mmHg), a longer duration of nocturnal oxygen saturation (nSaO2) <90% (71.0±34.3 versus 10.5±20.5 minutes), and a higher apnea hypopnea index (68.2±47.1 versus 46.5±34.1 events/hour). A multivariate logistic regression analysis showed that serum bicarbonate (odds ratio [OR]=1.17, p=0.0001, confidence interval [CI]=1.10-1.25), and duration of nSaO2 <90% (OR=1.05, p=0.0001, CI=1.04-1.06) were predictors of OHS. Conclusion: Obesity hypoventilation syndrome is common among Saudi OSA patients referred to the Sleep Disorders Center. Serum bicarbonate and duration of nSaO2 <90% are independent predictors of OHS among patients with OSA.
A Class III PDZ Binding Motif in the Myotilin and FATZ Families Binds Enigma Family Proteins: a Common Link for Z-Disc Myopathies

ABSTRACT Interactions between Z-disc proteins regulate muscle functions and disruption of these interactions results in muscle disorders. Mutations in Z-disc components myotilin, ZASP/Cypher, and FATZ-2 (calsarcin-1/myozenin-2) are associated with myopathies. We report here that the myotilin and the FATZ (calsarcin/myozenin) families share high homology at their final C-terminal five amino acids. This C-terminal E[ST][DE][DE]L motif is present almost exclusively in these families and is evolutionary conserved. We show by in vitro and in vivo studies that proteins from the myotilin and FATZ (calsarcin/myozenin) families interact via this novel type of class III PDZ binding motif with the PDZ domains of ZASP/Cypher and other Enigma family members: ALP, CLP-36, and RIL. We show that the interactions can be modulated by phosphorylation. Calmodulin-dependent kinase II phosphorylates the C terminus of FATZ-3 (calsarcin-3/myozenin-3) and myotilin, whereas PKA phosphorylates that of FATZ-1 (calsarcin-2/myozenin-1) and FATZ-2 (calsarcin-1/myozenin-1). This is the first report of a binding motif common to both the myotilin and the FATZ (calsarcin/myozenin) families that is specific for interactions with Enigma family members.
Using Eye Tracking to Identify Cognitive Differences: A Brief Literature Review

Being the windows to the soul, eyes reveal information about individuals' feelings, emotions and behaviour, affecting various cognitive tasks, such as focus of attention, spatial cognition and navigation, cognitive load, etc. With the increased use of computer systems, complex information is visualized and communicated through visual interfaces as a mean of information presentation to and processing by the users. However, people differ regarding the way they seek, retrieve, process, comprehend, organize and recall information, based on their individual perceptual characteristics, cognitive skills, abilities and styles. Therefore, the point and the motion of the eye gaze could reveal behavioural patterns related to individual cognitive differences; patterns that are extracted using eye tracking tools which quantify and provide compelling data regarding eye gaze movement. In this paper we review the current literature regarding the effect between the FD-I cognitive style of users in visual exploration and search activities and to correlate these with objective measures gathered through eye-tracking.
Skill and knowledge requirements of entry-level logistics and supply chain management professionals: A comparative study of Ireland and Spain

Abstract The authors examine the educational and training requirements of entry-level graduates employed in the freight transport, distribution, and logistics sector. Five skill and knowledge categories are considered. By comparing the perceived importance of certain skills for companies and the performance of graduates, education and training gaps are identified. These gaps are compared for Ireland and Spain, two countries with different industrial and managerial contexts. Descriptive analysis of a sample of 108 firms reveals major gaps. The country comparison shows that Spanish graduates have more skill and knowledge deficiencies than Irish graduates. Despite the smaller gaps for Irish graduates, data variability is greater than for Spanish graduates.
Stability Loss in Quasilinear DAEs by Divergence of a Pencil Eigenvalue

The divergence through infinity of certain eigenvalues of a linearized differential-algebraic equation (DAE) may result in a stability change along an equilibrium branch. This behavior cannot be exhibited by explicit ODEs, and its analysis in index one contexts has been so far unduly restricted to semiexplicit systems. By means of a geometric reduction framework we extend the characterization of this phenomenon to quasilinear DAEs, which comprise semiexplicit problems as a particular case. Our approach clarifies the nature of the singularities which are responsible for the stability change and also accommodates rank deficiencies in the leading system matrix. We show how to address this problem in a matrix pencil setting, an issue which leads to certain results of independent interest involving the geometric index of a quasilinear DAE and the Kronecker index of its linearization. The results are shown to be of interest in electrical circuit theory, since the differential-algebraic network models actually u.
Ascending projections to the medial geniculate body of the cat: evidence for multiple, parallel auditory pathways through thalamus

The sources of ascending input to the medial geniculate body (MGB) of the cat were studied using the retrograde transport of horseradish peroxidase (HRP). HRP injections were made iontophoretically through micropipettes which were also used to record physiological properties at the injection sites. This technique produced small injections which appeared to be restricted to single subnuclei. The tectothalamic projection of the auditory system was found to consist of at least four distinct and separate pathways. The ventral division of the MGB receives a topographical projection from the central nucleus of the inferior colliculus (ICC) which preserves tonotopicity and provides short latency, sharply frequency-tuned responses. The medial part of the ICC projects to the deep dorsal nucleus, which contains only units tuned to high frequencies. The major inputs to the caudodorsal nucleus (DC) stem from nucleus sagulum and the pericentral nucleus of the inferior colliculus (ICP). Units in DC and the ventrolateral nucleus, which also receive input from ICP, have very broad tuning properties and late, habituating responses. Injections of HRP into the medial division (MGM) produced labeled cells scattered throughout the external nucleus of the inferior colliculus and the ventral part of ICC. This widespread input is reflected in the wide range of auditory responses found in MGM. Auditory responses in the suprageniculate nucleus were poorly defined and many units did not respond to tonal stimuli; following HRP injections no filled cells were found in the inferior colliculus, but labeled cells were found in the deeper layers of the superior colliculus and in the interstitial nucleus of the brachium of the inferior colliculus. Together with recent findings on the auditory thalamocortical projection, these results provide evidence for multiple parallel auditory pathways through the thalamus.
Evolutionary conservation of excision repair in Schizosaccharomyces pombe: evidence for a family of sequences related to the Saccharomyces cerevisiae RAD2 gene.

Cells mutated at the rad13 locus in the fission yeast, Schizosaccharomyces pombe are deficient in excision-repair of UV damage. We have cloned the S.pombe rad13 gene by its ability to complement the UV sensitivity of a rad13 mutant. The gene is not essential for cell proliferation. Sequence analysis of the cloned gene revealed an open reading-frame of 1113 amino acids with structural homology to the RAD2 gene of the distantly related Saccharomyces cerevisiae. The sequence similarity is confined to three domains, two close to the N-terminus of the encoded protein, the third being close to the C-terminus. The central region of about 500 amino acids shows little similarity between the two organisms. The first and third domains are also found in a related yet distinct pair of homologous S.pombe/S.cerevisiae DNA repair genes (rad2/YKL510), which have only a very short region between these two conserved domains. Using the polymerase chain reaction with degenerate primers, we have isolated fragments from a gene homologous to rad13/RAD2 from Aspergillus nidulans. These findings define new functional domains involved in excision-repair, as well as identifying a conserved family of genes related to RAD2.