Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Affymetrix GeneChip expression measures

MOTIVATION In the Affymetrix GeneChip system, preprocessing occurs before one obtains expression level measurements. Because the number of competing preprocessing methods was large and growing we developed a benchmark to help users identify the best method for their application. A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted. RESULTS We benchmarked 31 probe set algorithms using a U95A dataset of spike in controls. Using this dataset, we found that background correction, one of the main steps in preprocessing, has the largest effect on performance. In particular, background correction appears to improve accuracy but, in general, worsen precision. The benchmark results put this balance in perspective. Furthermore, we have improved some of the original benchmark metrics to provide more detailed information regarding precision and accuracy. A handful of methods stand out as providing the best balance using spike-in data with the older U95A array, although different experiments on more current arrays may benchmark differently. AVAILABILITY The affycomp package, now version 1.5. 2, continues to be available as part of the Bioconductor project (http://www.bioconductor.org). The webtool continues to be available at http://affycomp.biostat. jhsph.edu CONTACT rafa@jhu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
The Wages Fund Controversy Revisited

“The wages fund theory is the crowning instance of an untrue abstraction … and it has probably done more injury to the reputation of economic theory than any other generalization ever received into economics textbooks and then expunged from them. ” These words, by James Bonar, fairly well express the view that has dominated economic thought on the wages fund doctrine for the past century. Writing forty years after Bonar, Paul Samuelson claims he has been impressed by the “falseness and emptiness of the wage fund doctrine,” stating that the controversy it inspired “constitutes one of the most sterile chapters in that dreary gap between the classical age and the revolutionary neoclassical discoveries of that last third of the nineteenth century. ”
Exploring the E-Learning Experiences of Academic Staff at a South African University

While there is evidence of a burgeoning research output on academic staff’s e-learning acceptance and usage in universities, there is a paucity of studies that seek to understand the South African experience. Thus, the purpose of this study was to explore the experiences of academic staff with the uptake and use of e-learning innovations in teaching and learning in the context of a university in South Africa. Theoretically, the study was underpinned by activity theory. The study was qualitative in nature and an exploratory single case study design was employed. The participants comprised six purposively selected academic staff at a South African university. In the study, we used semi-structured interviews to gather the data required to answer the research questions. We analysed data using an inductive thematic framework following Braun and Clarke’s (2006) approach. The following themes emerged from the analysis: challenges with technology infrastructure and internet accessibility on campus, technical support for students and staff, staff development and training, difficulty in creating e-learning content, and challenges with non-resident students. Based on the findings we recommend an increased interactive and context-dependent e-learning support system for academic staff. In addition, to accelerate the acceptance and effective use of e-learning technologies there is a need for collaborative and peer-oriented activities that develop the knowledge of academic staff.
Robust human detection and localization in security applications

Human detection and localization has attracted much attention in security applications because of the increasing demand of safety and security in different environments, including surveillance systems, secure access control, person recognition, border monitoring, preventing criminal acts, intrusion detection, alarm monitoring, and so on. This article proposes a robust approach for human detection and localization by analyzing and matching corresponding facial features extracted from video sequences. The proposed technique captures the video scenes using a stereo system consisting of two cameras: left and right cameras with similar intrinsic parameters. The system first tracks the human by detecting the face area from the video scenes using an efficient fuzzy face detection algorithm. To localize the human position, the depth information is computed from the extracted face images by using a robust stereo matching algorithm. A neural network is used to match the correspondence pixels between the left and the right face images. Experimental evaluation demonstrates the competence and robustness of the proposed method. The low computation time required for the detection and localization of human objects compared with other methods raises its suitability toward its use in real‐time applications. Copyright © 2016 John Wiley & Sons, Ltd.
A study of the use of clozapine in old age psychiatry

The aim of this study was to review the use of clozapine in a Sydney area old age psychiatry service. Data were extracted from case files of all people who were treated in a health area's old age psychiatry units with clozapine during a 15-year period. Additional details were obtained from clinicians who provided ongoing care after discharge from the hospital. Note was made of psychiatric diagnoses, length of time taking clozapine, dosage, side effects and outcome. Sixteen patients aged over 65 years commenced or continued taking clozapine while inpatients of the service. Of the 13 patients who had a history of schizophrenia or schizoaffective disorder, four patients (all female) developed neutropenia and therefore clozapine was stopped. In one case, neutropenia was first diagnosed 6 years after commencing the medication. Two women died; the nine other women, and one of the deceased, stopped taking clozapine, usually because of side effects. The mean daily dose at cessation was 236 mg. All five men were still taking clozapine (mean 260 mg daily) when followed at a mean age of 72 years, having taken it for an average of 10 years. This case review adds to evidence of the risk of neutropenia when older people are prescribed clozapine.
Major depression in temporal lobe epilepsy with hippocampal sclerosis: clinical and imaging correlates

Purpose: Refractory temporal lobe epilepsy (TLE) is often associated with hippocampal sclerosis (HS). Patients with major depression (MD) may also show structural abnormalities in the limbic system. Co-occurrence of TLE with HS and MD is not uncommon. We have investigated the clinical and morphological characteristics of TLE patients in relation to MD. Methods: 34 TLE patients with HS were assessed at a Comprehensive Epilepsy Programme. All relevant clinical data were obtained, including the history of antecedent events to epilepsy. MD was diagnosed based on detailed psychiatric investigation. MRI was used to measure the volume and tissue signal (T2 relaxometry) of the hippocampus and amygdala. The imaging data were expressed as a percentage of the values obtained in a series of 55 controls. Results: A history of MD was present in 15 (44%) of 34 patients. Patients with MD had a longer duration of their epilepsy (p<0.05) and a lower frequency of antecedent events (13% with MD, 58% without MD, p<0.05). Both groups had a similar degree of ipsilateral HS (small hippocampal volume, increased hippocampal T2 relaxation time) and demonstrated bilateral amygdaloid atrophy. However, the contralateral amygdala showed lower signal in the presence of MD (97 (9) ms; no MD 103 (8) ms; ANCOVA, p = 0.02). Conclusion: The integrity of the amygdala may influence mood disturbances in TLE patients with HS, as depression was associated with a relative preservation of the contralateral amygdala. In contrast, hippocampal abnormalities were not related to the presence of depression.
Use of Intraoperative Botulinum Toxin in Facial Reconstruction

BACKGROUND Botulinum toxin is a potent neuromodulator that temporarily relaxes muscles and can improve wound healing. OBJECTIVE This retrospective analysis assessed the use of intraoperative botulinum toxin type A or B in patients undergoing surgical reconstruction after Mohs micrographic surgery for treatment of skin cancer. The primary effect of intradermal botulinum toxin on wound healing was also studied. METHODS & MATERIALS Charts of patients who received intraoperative botulinum toxin type A (n=9) or B (n=9) in conjunction with reconstructive surgery after Mohs micrographic surgery were reviewed. Three volunteers also underwent dermal injections of botulinum toxin type A followed by erbium laser resurfacing. RESULTS Outcomes did not differ in patients treated with botulinum toxin type A and type B. Patients had excellent apposition of wound edges and smooth skin overlying soft tissue; no significant complications were noted. Healing of erbium laser ablation did not differ between botulinum toxin type A—treated skin and control skin. CONCLUSIONS Administration of botulinum toxin type A or B after reconstruction after Mohs micrographic surgery aided wound healing; botulinum toxin type A and botulinum toxin type B were equally effective. Intradermal botulinum toxin type A demonstrated no primary effect on healing of erbium laser—resurfaced skin. The author owns common stock in Allergan and consults for Allergan, Solstice, and Merz, manufacturers of botulinum toxin. Elan Pharmaceuticals donated the botulinum toxin type B.
The information content of management sales forecasts

Abstract We investigate the information content of management sales forecasts by developing an incremental accruals measure. We examine whether market efficiently prices this incremental accrual component. We further relate the incremental accrual measure with management earnings forecast errors testing its effect on manager’s forecast accuracy. Our findings indicate sales forecasts to contain valuable information. We find a significant association between our incremental accruals measure and future stock returns, implying that market participants can benefit by utilizing information released through sales forecasts. Finally, we find a significant negative association between the incremental accrual component and management forecast errors, above historical accruals.
Italian Politics in an Era of Recession: The End of Bipolarism?

Abstract Italian politics have undergone momentous change in the 2007–2017 decade under the impact of the eurozone crisis, whose peak in 2011–2013 could be equated to the earlier watershed years of 1992–1994. The lasting impact of the upheaval in Italian politics in the early 1990s could still be felt in the decade of economic recession, but there were also new challenges prompted by a crisis that had its roots in international financial contagion and which unravelled under the shadow of both recession and austerity. The changes were of an economic, social, cultural, institutional, policy-oriented and political nature. If one central quintessentially political theme stands out by the end of this decade it is the apparent exhaustion of the quest for bipolarisation that was initiated in the early 1990s.
Operative Treatment of Syndesmotic Disruptions Without Use of a Syndesmotic Screw: A Prospective Clinical Study

A new protocol for the selected omission of transsyndesmotic fixation in Weber class C ankle fractures was prospectively evaluated in 21 consecutive patients. As proposed in a previous cadaveric study (J. Bone Joint Surg., 71A:1548–1555, 1989), the protocol suggested that transsyndesmotic fixation was not required if (1) rigid bimalleolar fracture fixation was achieved or (2) lateral without medial fixation was obtained (i.e., with accompanying deltoid tears) if the fibular fracture was within 4.5 cm of the joint. According to this protocol, only 3 of 21 patients (14%) required transsyndesmotic fixation. Ten of the patients who did not receive transsyndesmotic fixation underwent pronation-external rotation stress radiographs in a fashion analogous to the previous cadaveric study. At 1- to 3-year follow-up, no stress (N = 10) or static view (N = 18) widening of the mortise or syndesmosis was seen in any patient, which supports (with the above guidelines) a limited, rather than routine, use of supplemental transsyndesmotic fixation. Clinical results from this prospective study seem to substantiate previously proposed biomechanical guidelines for the selected omission of transsyndesmotic fixation. Given these guidelines, transsyndesmotic fixation was unnecessary in many cases and the need can be determined before surgery by assessing the integrity of the deltoid ligament and level of the fibular fracture.
Bovine WC1+ and WC1neg γδ T Lymphocytes Influence Monocyte Differentiation and Monocyte-Derived Dendritic Cell Maturation during In Vitro Mycobacterium avium Subspecies paratuberculosis Infection

During early Mycobacterium avium subspecies paratuberculosis (Map) infection, complex interactions occur between the bacteria, cells from the mononuclear phagocyte system (MPS) including both resident (macrophages and dendritic cells) and recruited (monocytes) cells, and other mucosal sentinel cells such as γδ T lymphocytes. Though the details of early host–pathogen interactions in cattle remain largely underexplored, our hypothesis is that these significantly influence development of host immunity and ultimate success or failure of the host to respond to Map infection. The aims of the present study were to first characterize monocyte-derived MPS cells from young calves with respect to their immunophenotype and function. Then, we set out to investigate the effects of WC1+ and WC1neg γδ T lymphocytes on (1) the differentiation of autologous monocytes and (2) the maturation of autologous monocyte-derived dendritic cells (MDDCs). To achieve this, peripheral blood WC1+ or WC1neg γδ T lymphocytes were cocultured with either autologous freshly isolated peripheral blood-derived monocytes or autologous immature MDDCs (iMDDCs). We began by measuring several markers of interest on MPS cells. Useful markers to distinguish monocyte-derived macrophages (MDMs) from MDDCs include CD11b, CD163, and CD172a, which are expressed significantly higher on MDMs compared with MDDCs. Function, but not phenotype, was influenced by WC1neg γδ T lymphocytes: viability of Map harvested from monocytes differentiated in the presence of WC1neg γδ T lymphocytes (dMonWC1neg) was significantly lower compared to MDMs and MDDCs. With respect to DC maturation, we first showed that mature MDDCs (mMDDCs) have significantly higher expression of CD11c, CD80, and CD86 compared with iMDDCs, and the phagocytic capacity of mMDDCs is significantly reduced compared to iMDDCs. We then showed that γδ T lymphocyte subsets induce functional (reduced phagocytosis) but not phenotypic (surface marker expression) iMDDC maturation. These data collectively show that γδ T lymphocytes influence differentiation, maturation, and ultimately the function of monocytes during Map infection, which has significant implications on survival of Map and success of host defense during early Map infection.
Natural Helicobacter infection modulates mouse intestinal muscularis macrophage responses

Helicobacter species are common laboratory pathogens which induce intestinal inflammation and disease in susceptible mice. Since in vitro studies indicate that Helicobacter products activate macrophages, we hypothesized that in vivo Helicobacter infection regulates the inflammatory response of intestinal muscularis macrophages from C57Bl/6 mice. Helicobacter hepaticus infection increased surface expression of macrophage markers F4/80, CD11b and MHC‐II within whole intestinal muscle mounts. However, constitutive cytokine and chemokine production by macrophages isolated from infected mice significantly decreased compared to macrophages from uninfected mice despite no detectable bacterial products in the cultures. In addition, muscularis macrophages from infected mice up‐regulated FIZZ‐1 and SK‐1 gene expression, suggesting the macrophages had an anti‐inflammatory phenotype. Corresponding with increased anti‐inflammatory gene expression, macrophages from infected mice were more phagocytic but did not produce cytokines after stimulation with LPS and IFN‐γ or immune complexes and IL‐4. Therefore, the presence of Helicobacter infection matures intestinal muscularis macrophages, modulating the constitutive macrophage response to become more anti‐inflammatory and resistant to secondary stimulation. Copyright © 2010 John Wiley & Sons, Ltd.
Seed dormancy, after-ripening and light requirements of four annual Asteraceae in south-western Australia.

The role of dormancy, temperature and light in the regulation of seed germination of four annual Asteraceae from south-western Australia was investigated. The experiments aimed to identify after-ripening patterns, and to relate these to climatic conditions of the habitat in which the species occur. Seeds of all species were strongly dormant at maturity and maintained high levels of dormancy for time periods corresponding to the duration of summer in south-western Australia. Dry after-ripening was promoted best by temperatures lower than those prevailing in the dry season, although differences among storage temperatures were mostly insignificant. Germination percentages were highest at average winter temperatures (15 degrees C). A logistic model revealed significant differences in germinability among species, but not between incubation temperatures or light and dark treatments across species. Three species with seeds >0.5 mg germinated better in darkness than in light, whereas germination in darkness was almost inhibited in the species with the smallest seeds (0.14 mg). The course of dormancy loss, tested over a range of fluctuating incubation temperatures (7-30 degrees C), showed that seeds of three species came out of dormancy first at temperatures that prevail in south-western Australia during the winter (10-15 degrees C). Seeds from one species, introduced from South Africa, first lost dormancy at the lowest temperature (7 degrees C). All species showed after-ripening patterns of Type 1, typical of species growing in Mediterranean climates. The germination characteristics of the investigated species can be interpreted as ensuring that initial growth and establishment occur during the winter growing season, thereby avoiding the hot and dry summer conditions that follow seed dispersal.
Mutagenic Stabilization and/or Disruption of a CD4-Bound State Reveals Distinct Conformations of the Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) gp120 exterior envelope glycoprotein is conformationally flexible. Upon binding to the host cell receptor CD4, gp120 assumes a conformation that is recognized by the second receptor, CCR5 and/or CXCR4, and by the CD4-induced (CD4i) antibodies. Guided by the X-ray crystal structure of a gp120-CD4-CD4i antibody complex, we introduced changes into gp120 that were designed to stabilize or disrupt this conformation. One mutant, 375 S/W, in which the tryptophan indole group is predicted to occupy the Phe 43 cavity in the gp120 interior, apparently favors a gp120 conformation closer to that of the CD4-bound state. The 375 S/W mutant was recognized as well as or better than wild-type gp120 by CD4 and CD4i antibodies, and the large decrease in entropy observed when wild-type gp120 bound CD4 was reduced for the 375 S/W mutant. The recognition of the 375 S/W mutant by CD4BS antibodies, which are directed against the CD4-binding region of gp120, was markedly reduced compared with that of the wild-type gp120. Compared with the wild-type virus, viruses with the 375 S/W envelope glycoproteins were resistant to neutralization by IgG1b12, a CD4BS antibody, were slightly more sensitive to soluble CD4 neutralization and were neutralized more efficiently by the 2G12 antibody. Another mutant, 423 I/P, in which the gp120 bridging sheet was disrupted, did not bind CD4, CCR5, or CD4i antibodies, even though recognition by CD4BS antibodies was efficient. These results indicate that CD4BS antibodies recognize conformations of gp120 different from that recognized by CD4 and CD4i antibodies.
Migrate to invest? An Event-History Analysis of Direct and Indirect Effects of International Migration on Investments in Senegal

In line with policy concerns, this paper investigates the impact of international migration on investments in origin countries in the African context. More specifically, the objective is to study the personal investments of Senegalese in their home country in three sectors that are commonly described as migrants’ investment targets: land, housing and businesses. The discrete-time event history analyses will allow us to assess (1) to what extent current migrants and return migrants show a specific behaviour regarding their investment choices and practices as compared to non-migrants; and (2) to what extent non-migrants’ investments are influenced by the fact that members of their social network are abroad (e.g. through material support, knowledge transfer or cultural influence). The quantitative data for this study comes from the MAFE survey (Migration between AFrica and Europe) implemented in 2008, which collected life-histories both at origin (Senegal) and in European destination countries (France, Spain, and Italy).
Soil Heating around the Ground Electrode of a HVDC System by Interaction of Electrical, Thermal, and Electro-Osmotic Phenomena

This article evaluates the influence of several parameters interacting in the electrical, thermal, and electro-osmotics phenomena that rule the transient/dynamic behavior of the soil temperature rising process. The aim is to provide a safe design of ground electrodes concerning the risk of soil collapse ("vitrification") as a consequence of thermal instability. An objective electro-osmosis modeling rather accurate, applicable to generic geometries of ground electrodes, not only for homogeneous but also for nonhomogeneous soils has been developed. Sensitivity analysis correlating design parameters and the grounding behavior for a basic geometry of a toroidal ground electrode is shown herein. The inadequacy of the simplified methodologies available in the technical literature leads to inconclusive results in terms of installation safety, taking into account the omissions of the electro-osmosis phenomenon.
Diversifying Science

Stereotypes influence academic interests, performance, and ultimately career goals. The long-standing National Institutes of Health Research Initiative for Scientific Enhancement (RISE) training program has been shown to be effective at retaining underrepresented minorities in science. We argue that programs such as RISE may alter the experience and impact of stereotype threat on academic achievement goals and future engagement in a scientific career. We report analyses of a national sample comparing RISE students with a propensity score-matched control group over a 6-year period. Mediation analyses revealed that while RISE program membership did not buffer students from stereotype threat, it changed students’ downstream responses and ultimately their academic outcomes. Nonprogram students were less likely than RISE students to persist in the sciences, partially because feelings of stereotype threat diminished their adoption of mastery goals. We discuss how these findings inform stereotype threat and goal orientation theories and provide insight into the success of intervention programs.