Miracle-dz/UniFAR-FTUs huggingface dataset:
Transfer learning for object category detection

Object category detection, the task of determining if one or more instances of a category are present in an image with their corresponding locations, is one of the fundamental problems of computer vision. The task is very challenging because of the large variations in imaged object appearance, particularly due to the changes in viewpoint, illumination and intra-class variance. Although successful solutions exist for learning object category detectors, they require massive amounts of training data. Transfer learning builds upon previously acquired knowledge and thus reduces training requirements. The objective of this work is to develop and apply novel transfer learning techniques specific to the object category detection problem. This thesis proposes methods which not only address the challenges of performing transfer learning for object category detection such as finding relevant sources for transfer, handling aspect ratio mismatches and considering the geometric relations between the features; but also enable large scale object category detection by quickly learning from considerably fewer training samples and immediate evaluation of models on web scale data with the help of part-based indexing. Several novel transfer models are introduced such as: (a) rigid transfer for transferring knowledge between similar classes, (b) deformable transfer which tolerates small structural changes by deforming the source detector while performing the transfer, and (c) part level transfer particularly for the cases where full template transfer is not possible due to aspect ratio mismatches or not having adequately similar sources. Building upon the idea of using part-level transfer, instead of performing an exhaustive sliding window search, part-based indexing is proposed for efficient evaluation of templates enabling us to obtain immediate detection results in large scale image collections. Furthermore, easier and more robust optimization methods are developed with the help of feature maps defined between proposed transfer learning formulations and the “classical” SVM formulation. This thesis is submitted to the Department of Engineering Science, University of Oxford, in fulfillment of the requirements for the degree of Doctor of Philosophy. This thesis is entirely my own work, and except where otherwise stated, describes my own research. Yusuf Aytar, Brasenose College
Human immunodeficiency virus-associated squamous cell cancer of the anus: epidemiology and outcomes in the highly active antiretroviral therapy era.

PURPOSE To evaluate and determine predictors of squamous cell carcinoma of the anus (SCCA) outcomes in the highly active antiretroviral therapy (HAART) era for HIV-positive and -negative individuals using large national Veterans Affairs (VA) Administration databases. PATIENTS AND METHODS We used the VA administrative databases to perform a retrospective cohort study in 1,184 veterans diagnosed with SCCA between 1998 and 2004. We calculated HIV infection rates and used logistic regression to identify epidemiologic factors that were associated with HIV infection. Kaplan-Meier curves and Cox proportional hazards models were calculated to compare survival between HIV-positive and HIV-negative veterans. RESULTS In our cohort, 175 patients (15%) were HIV positive. The median age of the HIV-negative and -positive patients was 63 and 49 years, respectively (P < .001). Individuals with HIV were eight times more likely to be male (P = .01) and three times more likely to be African American (P < .001). There were no differences between HIV-positive and HIV-negative individuals in the receipt of treatment. The 2-year observed survival rates were 77% and 75% among HIV-positive and HIV-negative individuals, respectively. In multivariate Cox analysis, significant predictors of survival were age, sex, metastasis at diagnosis, and comorbidity score. HIV infection did not affect survival. CONCLUSION A noteworthy proportion of individuals with SCCA in the VA system are HIV positive. HIV-associated SCCA seems mainly to be a disease among younger men. Survival of SCCA is equivalent between HIV-positive and HIV-negative individuals in the HAART era. Treatment should not be withheld or deintensified based on HIV status.
Improving Test Interpretation for Detecting Executive Dysfunction in Adults and Older Adults: Prevalence of Low Scores on the Test of Verbal Conceptualization and Fluency

Knowing the prevalence of low scores on a battery of executive-functioning tests supplements clinical interpretation and can reduce the likelihood of misdiagnosing deficits in executive functioning. The purpose of this study is to examine the base rates of low scores on the Test of Verbal Conceptualization and Fluency (TVCF; Reynolds & Horton, 2006) in healthy adults (n = 332; M age = 33.0 years, SD = 10.5, range = 20–59) and older adults (n = 138; M age = 74.9 years, SD = 7.8, range = 60–89) from the TVCF standardization sample. The TVCF consists of four tests of executive functioning (i.e., Category Fluency, Letter Naming, Classification, and Trails C) that provide five age-adjusted T-scores. The prevalence of low scores was examined in the total sample and was stratified by educational level. When the five T-scores were considered simultaneously, having one or more scores that were 1 standard deviation (SD) below the mean was found in 28% of healthy adults and 38% of older adults. Education-based differences were also present with more lenient cutoff scores (e.g., 1 SD) but not with more conservative cutoffs. Consistent with the existing literature on other test batteries, at least one low subtest score on the TVCF is common in healthy adults and older adults.
Enhanced Immunogenicity of Heat Shock Protein 70 Peptide Complexes from Dendritic Cell-Tumor Fusion Cells1

We have developed a molecular chaperone-based tumor vaccine that reverses the immune tolerance of cancer cells. Heat shock protein (HSP) 70 extracted from fusions of dendritic (DC) and tumor cells (HSP70.PC-F) possess superior properties such as stimulation of DC maturation and T cell proliferation over its counterpart from tumor cells. More importantly, immunization of mice with HSP70.PC-F resulted in a T cell-mediated immune response including significant increase of CD8 T cells and induction of the effector and memory T cells that was able to break T cell unresponsiveness to a nonmutated tumor Ag and provide protection of mice against challenge with tumor cells. By contrast, the immune response to vaccination with HSP70-PC derived from tumor cells is muted against such nonmutated tumor Ag. HSP70.PC-F complexes differed from those derived from tumor cells in a number of key manners, most notably, enhanced association with immunologic peptides. In addition, the molecular chaperone HSP90 was found to be associated with HSP70.PC-F as indicated by coimmunoprecipitation, suggesting ability to carry an increased repertoire of antigenic peptides by the two chaperones. Significantly, activation of DC by HSP70.PC-F was dependent on the presence of an intact MyD88 gene, suggesting a role for TLR signaling in DC activation and T cell stimulation. These experiments indicate that HSP70-peptide complexes (PC) derived from DC-tumor fusion cells have increased their immunogenicity and therefore constitute an improved formulation of chaperone protein-based tumor vaccine.
Vascular Endothelial Growth Factor Enhances the Expression of Urokinase Receptor in Human Endothelial Cells via Protein Kinase C Activation

Summary Among other proteolytic enzymes, the urokinase-type plasminogen activator (u-PA)/plasmin cascade contributes to cell migration and the formation of capillary-like structures in a fibrinous exudate. The u-PA receptor (u-PAR) focuses proteolytical activity on the cell surface of the endothelial cell and hereby accelerates the pericellular matrix degradation. Vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF)-2 enhance u-PA receptor expression in human endothelial cells. In this paper we show that the protein kinase C (PKC) inhibitors Ro31-8220 and GF109203X inhibit VEGF165-induced u-PAR antigen expression in human endothelial cells, whereas PKC inhibition had no effect on FGF-2-induced u-PAR antigen enhancement. In addition, inhibition of PKC activity had no effect on VEGF165-or FGF-2-induced proliferation in human endothelial cells. We conclude that VEGF165 induces u-PAR via a PKC-dependent pathway, whereas proliferation is induced via a different pathway probably involving tyrosine phosphorylation of proteins downstream of the VEGF receptors.
Effects of a modified shoe on knee load in people with and those without knee osteoarthritis.

OBJECTIVE To evaluate the effects of a modified shoe that incorporates both lateral wedging and a variable-stiffness sole on knee joint loading in 3 populations: individuals with symptomatic and radiographic knee osteoarthritis (OA), asymptomatic overweight individuals, and asymptomatic healthy weight individuals. METHODS Ninety participants (30 per group) underwent a 3-dimensional gait analysis across 3 test conditions: modified shoes, standard control shoes, and barefoot. For each condition, the first peak knee adduction moment (KAM) and knee flexion moment (KFM) (both expressed as Nm/[body weight × height]%) as well as the KAM impulse (expressed as Nm.s/[body weight × height]%) were determined. RESULTS The modified shoes significantly reduced the peak KAM as compared to the control shoes in both the OA (P = 0.002) and the overweight (P = 0.03) groups. In the OA group, there was no significant difference in peak KAM when walking in the modified shoe as compared to walking barefoot. In the overweight and the healthy weight groups, the peak KAM when walking in the modified shoe was significantly higher than that when walking barefoot (P < 0.001). Irrespective of group, the KAM impulse was significantly reduced when walking in the modified shoe as compared to the control shoe (P < 0.001) and was significantly higher during both shoe conditions as compared to walking barefoot (P < 0.001). There was no change in the KFM between walking conditions for any group. CONCLUSION The findings illustrate that a shoe incorporating both a lateral wedge and a variable-stiffness sole can significantly reduce medial knee joint load. Further research examining the effects of these shoes on pain, function, and structural changes in the joint is warranted.
Conflicting needs for a Salmonella hypervirulence gene in host and non‐host environments

The Gram‐negative pathogen Salmonella enterica harbours a periplasmic D‐Ala‐D‐Ala dipeptidase (termed PcgL), which confers the ability to grow on D‐Ala‐D‐Ala as sole carbon source. We now demonstrate that inactivation of the pcgL gene renders Salmonella hypervirulent. This phenotype results from the accumulation of peptidoglycan‐derived D‐Ala‐D‐Ala in the pcgL mutant and not from an intrinsically faster growth rate. Synthetic D‐Ala‐D‐Ala (but not L‐Ala‐L‐Ala or D‐Ala) increased the number of wild‐type Salmonella in the liver and spleen of mice within 24 h of injection, suggesting that D‐Ala‐D‐Ala interferes with some aspect of innate immunity. However, the pcgL mutant was unable to grow on D‐Ala‐D‐Ala as sole carbon source and was defective for survival in nutrient‐poor conditions. We identified clinical isolates lacking D‐Ala‐D‐Ala dipeptidase activity and unable to grow on D‐Ala‐D‐Ala because of inactivation of the pcgL gene. Our data suggest that genes (such as pcgL) that, when mutated make pathogens more virulent, may be retained because their contribution to pathogen fitness in non‐host environments outweighs potential advantages of the hypervirulent vari‐ant in the infected host.
The Effect of Continuous Release of Recombinant Human Epidermal Growth Factor (rh-EGF) in Chitosan Film on Full Thickness Excisional Porcine Wounds

The purpose of this article is to evaluate the effect of continuously released recombinant human epidermal growth factor (rh-EGF) in chitosan film in full thickness porcine wounds. A total of 10 domestic pigs (Yorkshire species) weighing 18 to 22 kg between the ages of 50 to 60 days were used. The wounds were divided into 3 groups and treated selectively with rh-EGF in chitosan film (EGF 20 ug/wound/d), chitosan film without rh-EGF, or remained as the control group. One hundred percent healing time was observed, and hematoxylin and eosin and Anti Ki-67 antibody immunohistochemical staining were performed. The 100% healing time and Anti Ki-67 antibody immunohistochemical staining showed statistical significance of the rh-EGF chitosan film-treated group against the control group (P < 0.05). But it did not reveal any statistical significance over the chitosan film-treated group. In this preliminary study, although continuous release of rh-EGF in chitosan film accelerates epithelialization, the benefit of the combination of rh-EGF in chitosan cannot be determined over the use of chitosan alone. Further analysis using complex wound models such as diabetes or infection, which may have different pathology in healing, will be needed to evaluate the potential benefit/synergistic effectiveness.
Non‐obese diabetic–recombination activating gene‐1 (NOD–Rag 1 null) interleukin (IL)‐2 receptor common gamma chain (IL 2 rγnull) null mice: a radioresistant model for human lymphohaematopoietic engraftment

Immunodeficient hosts engrafted with human lymphohaematopoietic cells hold great promise as a preclinical bridge for understanding human haematopoiesis and immunity. We now describe a new immunodeficient radioresistant non‐obese diabetic mice (NOD) stock based on targeted mutations in the recombination activating gene‐1 (Rag1null) and interleukin (IL)‐2 receptor common gamma chain (IL2rγnull), and compare its ability to support lymphohaematopoietic cell engraftment with that achieved in radiosensitive NOD.CB17–Prkdcscid (NOD–Prkdcscid) IL2rγnull mice. We observed that immunodeficient NOD–Rag1null IL2rγnull mice tolerated much higher levels of irradiation conditioning than did NOD–Prkdcscid IL2rγnull mice. High levels of human cord blood stem cell engraftment were observed in both stocks of irradiation‐conditioned adult mice, leading to multi‐lineage haematopoietic cell populations and a complete repertoire of human immune cells, including human T cells. Human peripheral blood mononuclear cells also engrafted at high levels in unconditioned adult mice of each stock. These data document that Rag1null and scid stocks of immunodeficient NOD mice harbouring the IL2rγnull mutation support similar levels of human lymphohaematopoietic cell engraftment. NOD–Rag1null IL2rγnull mice will be an important new model for human lymphohaematopoietic cell engraftment studies that require radioresistant hosts.
Audio Super Resolution using Neural Networks

We introduce a new audio processing technique that increases the sampling rate of signals such as speech or music using deep convolutional neural networks. Our model is trained on pairs of low and high-quality audio examples; at test-time, it predicts missing samples within a low-resolution signal in an interpolation process similar to image super-resolution. Our method is simple and does not involve specialized audio processing techniques; in our experiments, it outperforms baselines on standard speech and music benchmarks at upscaling ratios of 2x, 4x, and 6x. The method has practical applications in telephony, compression, and text-to-speech generation; it demonstrates the effectiveness of feed-forward convolutional architectures on an audio generation task.
Immunoregulation of genetically controlled acquired responses to Leishmania donovani infection in mice: demonstration and characterization of suppressor T cells in noncure mice

On a B10 genetic background, genes in the I region of H-2 influence the development of acquired T-cell mediated immunity to Leishmania donovani infection in mice. In previous studies, noncure in H-2d mice could be abrogated by pretreatments with cyclophosphamide or sublethal irradiation. The prophylactic effect of these pretreatments was consistent with deletion of the precursors of suppressor T cells suppressing T-cell-mediated immune responses. In this study, cell transfer experiments provide direct evidence for the role of suppressor T cells in the noncure response. T-cell-enriched populations isolated from the spleens of B10.D2/n mice infected 30, 61, or 85 days previously reversed the prophylactic effect of sublethal irradiation when injected before infection into B10.D2/n mice that had received 550 rads. B-cell-enriched populations failed to transfer suppression in this manner, and T-cell-enriched populations from the spleens of normal B10.D2/n mice had only a transient effect on liver parasite loads. Transfer of suppression with the T-cell-enriched populations from infected donors was abrogated by pretreatment with anti-Thy-1.2 and anti-Lyt-1.2 antisera plus complement but not by pretreatment with anti-Lyt-2.2 plus complement, indicating that the suppressor T cell involved has an Lyt-1+2- surface phenotype. Results are discussed in relation to the possible mechanism of H-2-linked control.
Dark Triad, Perceptions of Organizational Politics and Counterproductive Work Behaviors: The Moderating Effect of Political Skills

The aim of this work focuses on the relationship among the Dark Triad (psychopathy, narcissism, and Machiavellianism), perceptions of organizational politics, political skills, and counterproductive work behavior. This study empirically tests the mediating role of perceptions of organizational politics in the relationship between the Dark Triad and counterproductive work behavior. Furthermore, the study investigates the moderating role of political skills in strengthening the link between the Dark Triad and the perceptions of organizational politics. A sample of 149 participants was randomly selected. To analyze the data of the present work, we employed a structural equation model using partial least square and PROCESS. From empirical findings, we imply an inference that perception of organizational politics partially mediates the Dark Triad's influence on the counterproductive work behavior. Moreover, the results identify the moderating role of political skills in strengthening the link between the Dark Triad and the perceptions of organizational politics. Empirical findings suggest important policy implications for the hospitality industry.
Risk factors associated with the incidence of foal mortality in an extensively managed mare herd.

The purpose of this study was to determine the incidence of neonatal mortality in a large, extensively managed mare herd and what risk factors were involved in foal mortality. For a 6 wk period between April 18, 1994, and May 31, 1994, 334 foals were born, of which 74 died before reaching 10 d of age, giving an overall mortality of 22% for this period. Seventy four percent of the foal deaths occurred within 48 h of parturition. The major causes of foal mortality included starvation/exposure 27%, septicemia 26%, and dystocia 20%. Weekly incidences varied significantly, ranging from 67% for week 1 to 14% for week 5 (P < 0.01). Other risk factors that were associated with foal death included failure of passive transfer (P < 0.0001), poor mothering ability (P < 0.0001), the presence of dystocia (P < 0.0001), low birth weight (p < 0.05), lack of rainfall (P < 0.01), and low temperatures (P < 0.1). The effect of sire, mare age, mare body condition, and foal sex were not significant risk factors for foal survival (P > 0.1). Further studies are required to determine if changing management procedures will be effective in reducing the incidence of neonatal foal mortality in this extensively managed herd.
Effect of 1-year treatment with roflumilast in severe chronic obstructive pulmonary disease.

RATIONALE The oral phosphodiesterase-4 (PDE4) inhibitor, roflumilast, can improve lung function in moderate chronic obstructive pulmonary disease (COPD). Whether treatment is effective in more severe COPD (GOLD [Global Initiative for Chronic Obstructive Lung Disease] stages III and IV) over a longer period is unknown. OBJECTIVES To determine whether roflumilast improves lung function and decreases exacerbation frequency over 1 year in patients with stable COPD. METHODS We conducted a randomized, placebo-controlled, double-blind, parallel-group trial for 1 year. We recruited 1,513 patients (mean post-bronchodilator FEV1 41% predicted), 760 receiving oral 500 microg roflumilast and 753 receiving placebo once daily. MEASUREMENTS AND MAIN RESULTS We recorded post-bronchodilator FEV1, exacerbation rate, St. George's Respiratory Questionnaire total score at the study end point, and number and type of reported adverse events during treatment. Post-bronchodilator FEV1 increased by 39 ml with roflumilast compared with placebo by 52 weeks (p=0.001). The mean exacerbation rate was low and comparable in both treatment groups (0.86 vs. 0.92 exacerbations/patient/yr for roflumilast and placebo, respectively). In a retrospective analysis, the exacerbation rate in patients in GOLD stage IV disease was 36% lower in patients treated with roflumilast than in those treated with placebo (1.01 vs. 1.59 exacerbations/patient/year, respectively; p=0.024). The St. George's Respiratory Questionnaire total score did not differ between treatments. The commonest adverse events related to roflumilast treatment were diarrhea, nausea, and headache, which usually subsided during continued treatment. However, roflumilast resulted in more withdrawals within the first 3 to 4 weeks of administration. CONCLUSIONS In severe, stable COPD, PDE4 inhibition with roflumilast produced a modest but significant improvement in lung function without changing the exacerbation rate or health status. However, patients with very severe disease experienced fewer exacerbations with roflumilast.