Miracle-dz/UniFAR-FTUs huggingface dataset:
Further results on controlling the false discovery proportion

The probability of false discovery proportion (FDP) exceeding $\gamma\in[0,1)$, defined as $\gamma$-FDP, has received much attention as a measure of false discoveries in multiple testing. Although this measure has received acceptance due to its relevance under dependency, not much progress has been made yet advancing its theory under such dependency in a nonasymptotic setting, which motivates our research in this article. We provide a larger class of procedures containing the stepup analog of, and hence more powerful than, the stepdown procedure in Lehmann and Romano [Ann. Statist. 33 (2005) 1138-1154] controlling the $\gamma$-FDP under similar positive dependence condition assumed in that paper. We offer better alternatives of the stepdown and stepup procedures in Romano and Shaikh [IMS Lecture Notes Monogr. Ser. 49 (2006a) 33-50, Ann. Statist. 34 (2006b) 1850-1873] using pairwise joint distributions of the null $p$-values. We generalize the notion of $\gamma$-FDP making it appropriate in situations where one is willing to tolerate a few false rejections or, due to high dependency, some false rejections are inevitable, and provide methods that control this generalized $\gamma$-FDP in two different scenarios: (i) only the marginal $p$-values are available and (ii) the marginal $p$-values as well as the common pairwise joint distributions of the null $p$-values are available, and assuming both positive dependence and arbitrary dependence conditions on the $p$-values in each scenario. Our theoretical findings are being supported through numerical studies.
Effects of Maternal Health During Pregnancy and Child Immunization on Mother-to-Child Transmission of Hepatitis B Virus: A Multicentre, Large-Sample Study in Southeast China

Purpose High hepatitis B infection rates in China are a major public health issue, and mother-to-child transmission (MTCT) is a significant risk factor. Patients and Methods This study was conducted with a prospective multicentre design from January 2021 to December 2022 in 245 hospitals providing midwifery services in southeastern China. The participants were pregnant women who were positive for hepatitis B surface antigen (HBs Ag) and their children. The HBs Ag concentration was tested in children aged 8–12 months. The odds ratio for each risk factor was calculated by logistic regression analysis, and the decision tree model was used. Results A total of 5369 children born to hepatitis B-infected mothers between 8 and 12 months of age were enrolled, among whom 81 (1.51%) were positive for HBsAg. The risk factors for hepatitis B infection in 5369 children under one-year-old were a high intrauterine hepatitis B exposure level, a history of hepatitis B immunoglobulin (HBIG) delay beyond 12 hours after birth, and lack of full hepatitis B vaccine (HepB), with risks of 3.356 (1.223~9.209), 5.691 (1.931~16.773), and 5.137 (2.265~11.650), respectively. The discrimination accuracy of the decision tree was 98.5%. The risk factors for hepatitis B infection in 4542 children under one year old with high exposure risk were nonstandard treatment by the mother during pregnancy, HBIG delay beyond 12 hours after birth, and no complete HepB administration, with risks of 2.925 (1.063–8.047), 5.354 (1.806–15.871) and 5.147 (2.258–11.733), respectively. The discrimination accuracy of the decision tree was 98.3%. Conclusion To prevent mother-to-child transmission of hepatitis B, it is necessary to standardize the treatment of pregnant women with a high exposure risk of hepatitis B, implement combined vaccination within 12 hours of birth, and standardise the full course of HepB.
Messenger RNA expression and protein localization of growth hormone in bovine ovarian tissue and in cumulus oocyte complexes (COCs) during in vitro maturation

The aim of this study was to investigate whether bovine cumulus oocyte complexes (COCs) obtained from 2 to 8 mm follicles synthesize growth hormone (GH) during in vitro maturation. In addition the expression of growth hormone releasing hormone receptor (GHRH‐r) in the COCs before and after in vitro maturation was investigated. Therefore, COCs obtained from small and medium sized follicles were cultured in M199 supplemented with 10% FCS and gonadotropins for 24 hr. At 0, 6, 12, and 24 hr after the onset of culture, COCs were removed and were prepared for immunohistochemical staining to detect the presence of GH. In addition, sections of ovary were stained to study the differential localization of GH in the ovary. At 0 and 24 hr COCs were removed and together with samples from granulosa cells and theca cells were prepared for reverse transcriptase polymerase chain reaction (RT‐PCR) to assess the expression of mRNA of GH and GHRH‐r. Within COCs, cumulus cells and oocytes showed GH immunoreactivity, while expression of GH mRNA was only found in the oocyte. At the onset of culture, oocytes and cumulus cells in the majority of COCs generally showed moderate and strong staining intensity for GH, respectively. While GH staining in the cumulus cells did hardly change during 24 hr of culture, GH staining in the oocyte was absent after 24 hr of culture in 70% of COCs. Within the ovary, GH was localized in antral follicles larger than 2 mm and no staining was found in primordial, primary and secondary follicles or in the stroma. The intensity of the staining increased with the size of the follicles. Within the follicular wall the GH was persistently observed in granulosa cells, while theca cells were occasionally negative. GH mRNA in follicular compartments was only found in the oocyte and mural granulosa cells. No GHRH‐r mRNA was found in the COCs nor in the granulosa or the stroma. In conclusion, the gradual increase of GH staining during follicular development and the consistent synthesis of GH in oocytes and granulosa cells, suggest a paracrine and/or autocrine action for GH in bovine follicular growth and oocyte maturation. The absence of mRNA for GHRH receptor in the COCs indicates that ovarian production of GH is not regulated by GHRH. Mol. Reprod. Dev. 53:398–406, 1999. © 1999 Wiley‐Liss, Inc.
Suicide and friendships among American adolescents.

OBJECTIVES We investigated the relationship between friendships and suicidality among male and female adolescents. METHODS We analyzed friendship data on 13,465 adolescents from the National Longitudinal Survey of Adolescent Health to explore the relationship between friendship and suicidal ideation and suicide attempts. We controlled for known factors associated with suicidality. RESULTS Having had a friend who committed suicide increased the likelihood of suicidal ideation and attempts for both boys and girls. Socially isolated females were more likely to have suicidal thoughts, as were females whose friends were not friends with each other. Among adolescents thinking about suicide, suicide attempts appear largely stochastic, with few consistent risk factors between boys and girls. CONCLUSIONS The friendship environment affects suicidality for both boys and girls. Female adolescents' suicidal thoughts are significantly increased by social isolation and friendship patterns in which friends were not friends with each other.
Opioids, dopamine, stress, and the addictions

The articulated goals of Dialogues in Clinical Neuroscience are to serve as “an interface between clinical neuropsychiatry and the neurosciences by providing state-of-the-art information and original insights into relevant clinical, biological, and therapeutic aspects. ” My laboratory, the Laboratory of the Biology of Addictive Diseases at The Rockefeller University, has for years been focused on “bi-directional translational research,” that is, learning by careful observations and study in patient populations with the disorders under study, in this case primarily specific addictive diseases, and then using that knowledge to create improved animal models or other laboratory-based research paradigms, while, at the same time, taking research findings made at the bench into the clinic as promptly as that is appropriate and feasible. In this invited review, therefore, the focus will be on perspectives of our Laboratory of the Biology of Addictive Diseases and related National institutes of Health/National institute on Drug Abuse research Center, including laboratory-based molecular neurobiological research, research using several animal models designed to mimic human patterns of drug abuse and addiction, as well as basic clinical research, intertwined with treatment-related research.
Testing the Ability of Non-Methylamine Osmolytes Present in Kidney Cells to Counteract the Deleterious Effects of Urea on Structure, Stability and Function of Proteins

Human kidney cells are under constant urea stress due to its urine concentrating mechanism. It is believed that the deleterious effect of urea is counteracted by methylamine osmolytes (glycine betaine and glycerophosphocholine) present in kidney cells. A question arises: Do the stabilizing osmolytes, non-methylamines (myo-inositol, sorbitol and taurine) present in the kidney cells also counteract the deleterious effects of urea? To answer this question, we have measured structure, thermodynamic stability (ΔG D o) and functional activity parameters (K m and k cat) of different model proteins in the presence of various concentrations of urea and each non-methylamine osmolyte alone and in combination. We observed that (i) for each protein myo-inositol provides perfect counteraction at 1∶2 ([myo-inositol]:[urea]) ratio, (ii) any concentration of sorbitol fails to refold urea denatured proteins if it is six times less than that of urea, and (iii) taurine regulates perfect counteraction in a protein specific manner; 1.5∶2.0, 1.2∶2.0 and 1.0∶2.0 ([taurine]:[urea]) ratios for RNase-A, lysozyme and α-lactalbumin, respectively.
Automatic Remote-sensing Image Registration Using SURF

—Image registration is a key, essential element in analysis of Remote sensing images. Registration is critical both for initial processing and for end-user processing of those image products for data fusion, and change detection. This paper focused on the feature-based category of image registration algorithms. Many techniques for the detection and description of images' local characteristics have been proposed to register a set of images without user intervention. However, it is unclear which descriptors are more appropriate. The descriptors should be distinctive and at the same time robust to changes in viewing conditions as well as to errors of the sensor. In our evaluation, we have separated the detector from the descriptor as their performance depends on the interest point detector used. The descriptors are compared according to their recall and runtime efficiency and this deals with several geometric and photometric changes. We also propose an extension to the SURF descriptor and the results show the effectiveness of proposed improvements compared to base SURF method. Furthermore, we observe that the SURF descriptor outperforms the others' descriptors. Finally, based on the test results, we propose an approach to register automatically remotely sensed images.
A Document Image Model and Estimation Algorithm for Optimized JPEG Decompression

The JPEG standard is one of the most prevalent image compression schemes in use today. While JPEG was designed for use with natural images, it is also widely used for the encoding of raster documents. Unfortunately, JPEG's characteristic blocking and ringing artifacts can severely degrade the quality of text and graphics in complex documents. We propose a JPEG decompression algorithm which is designed to produce substantially higher quality images from the same standard JPEG encodings. The method works by incorporating a document image model into the decoding process which accounts for the wide variety of content in modern complex color documents. The method works by first segmenting the JPEG encoded document into regions corresponding to background, text, and picture content. The regions corresponding to text and background are then decoded using maximum a posteriori (MAP) estimation. Most importantly, the MAP reconstruction of the text regions uses a model which accounts for the spatial characteristics of text and graphics. Our experimental comparisons to the baseline JPEG decoding as well as to three other decoding schemes, demonstrate that our method substantially improves the quality of decoded images, both visually and as measured by PSNR.
QuOnto: Querying Ontologies

One of the most important lines of research in Description Logics (DLs) is concerned with the trade-off between expressive power and computational complexity of sound and complete reasoning. Research carried out in the past on this topic has shown that many DLs with efficient, i.e., worstcase polynomial time, reasoning algorithms lack the modeling power required for capturing conceptual models and basic ontology languages, while most DLs with sufficient modeling power suffer from inherently worst-case exponential time behavior of reasoning [1, 2]. Although the requirement of polynomially tractable reasoning might be less stringent when dealing with relatively small ontologies, we believe that the need of efficient reasoning algorithms is of paramount importance when the ontology system is to manage large amount of objects (e.g., from thousands to millions of instances). This is the case of several important applications where the use of ontologies is advocated nowadays. For example, in the Semantic Web, ontologies are often used to describe the relevant concepts of Web repositories, and such repositories may incorporate very large data sets, which constitute the instances of the concepts in the ontology. In such cases, two requirements emerge that are typically overlooked in DLs. First, the number of objects in the knowledge bases requires managing instances of concepts (i.e., ABoxes) in secondary storage. Second, significant queries to be posed to the knowledge base are more complex than the simple queries (i.e., concepts and roles) usually considered in DL research. Unfortunately, in these contexts, whenever the complexity of reasoning is exponential in the size of the instances (as for example in Fact1, Racer2 and in [3]), there is little hope for effective instance management and query answering algorithms. In [4] a new DL, called DL-Lite, was proposed specifically tailored to capture basic ontology languages, while keeping low complexity of reasoning. A DL-Lite knowledge base (KB) is constituted by two components: an intensional level (called TBox in DL jargon), used to model the concepts and the relations (roles) of the ontologies, and an exten-
Spectral compatibility of in-home and access technologies

While in-home and access technologies are located at different places in the end-to-end communication chain, they have been shown to mutually interfere. In this contribution, we quantify the mutual impact of an in-home network and a Digital Subscriber Line access link. Both regular and vectored VDSL2 links are considered. For newer in-home technologies, which are able to use a large bandwidth, the access network becomes the bottleneck in the end-to-end communication. In this case, we recommend removing the interference from the in-home distribution network to the access network by shaping the transmit spectrum of the in-home distribution network. We show that this does not impact the performance of the end-to-end communication link. For older in-home technologies, which use a lower bandwidth, the attainable data rate of the in-home and access networks should be balanced by adapting the transmit power spectral density on the overlapping frequency band.
The Representation of Parts and Wholes in Face-selective Cortex

Although face perception is often characterized as depending on holistic, rather than part-based, processing, there is behavioral evidence for independent representations of face parts. Recent work has linked face-selective regions defined with functional magnetic resonance imaging (fMRI) to holistic processing, but the response of these areas to face parts remains unclear. Here we examine part-based versus holistic processing in face-selective visual areas using face stimuli manipulated in binocular disparity to appear either behind or in front of a set of stripes [Nakayama, K. , Shimojo, S. , & Silverman, G. H. Stereoscopic depth: Its relation to image segmentation, grouping, and the recognition of occluded objects. Perception, 18, 5568, 1989]. While the first case will be filled in by the visual system and perceived holistically, we demonstrate behaviorally that the latter cannot be completed amodally, and thus is perceived as parts. Using these stimuli in fMRI, we found significant responses to both depth manipulations in inferior occipital gyrus and middle fusiform gyrus (MFG) face-selective regions, suggesting that neural populations in these areas encode both parts and wholes. In comparison, applying these depth manipulations to control stimuli (alphanumeric characters) elicited much smaller signal changes within face-selective regions, indicating that the part-based representation for faces is separate from that for objects. The combined adaptation data also showed an interaction of depth and familiarity within the right MFG, with greater adaptation in the back (holistic) condition relative to parts for familiar but not unfamiliar faces. Together, these data indicate that face-selective regions of occipito-temporal cortex engage in both part-based and holistic processing. The relative recruitment of such representations may be additionally influenced by external factors such as familiarity.
The use (and misuse) of PISA in guiding policy reform: the case of Spain

In 2013 Spain introduced a series of educational reforms explicitly inspired by the Programme for International Student Assessment (PISA) 2012 results. These reforms were mainly implemented in secondary education – based upon the assumption that this is where Spain’s educational problems lie. This paper questions this assumption by attempting to identify the point where Spanish children fall behind young people in other developed counties in terms of their reading skills. Specifically, by drawing data from multiple international assessments, we are able to explore how cross-national differences in reading skills change as children age. Consideration is given to both the average level of achievement and the evolution of educational inequalities. Our conclusion is that policymakers have focused their efforts on the wrong part of the education system; educational achievement is low in Spain (and educational inequalities large) long before children enter secondary school. This study therefore serves as a note of caution against simplistic interpretation of the PISA rankings; policymakers must take a more nuanced approach when enacting important educational reforms.
Evaluation of acute bronchodilator reversibility in patients with symptoms of GOLD stage I COPD

Background: Patients with symptoms of GOLD stage I chronic obstructive pulmonary disease (COPD) can have significant abnormalities of ventilatory mechanics with greater exertional symptoms and exercise limitation than age-matched healthy subjects. In such patients the impact of bronchodilator therapy remains unknown and is difficult to evaluate. Methods: The acute effects of nebulised ipratropium bromide 500 μg (IB) on resting pulmonary function and on dyspnoea and ventilatory parameters during symptom-limited constant work rate cycle exercise were measured. In a randomised double-blind crossover study, 16 patients with COPD (mean (SD) post-bronchodilator forced expiratory volume in 1 s (FEV1) 90 (7)% predicted, FEV1/forced vital capacity (FVC) 59 (7)%) with a significant smoking history (mean (SD) 44 (16) pack-years) inhaled either IB or placebo on each of two separate visits. Pulmonary function tests and cycle exercise at 80–85% of each subject’s maximal work capacity were performed 2 h after dosing. Results: Compared with placebo, FEV1 increased 5 (9)% predicted, residual volume decreased 12 (20)% predicted and specific airway resistance decreased 81 (93)% predicted (all p<0.05) after IB. At a standardised time during exercise, dynamic inspiratory capacity and tidal volume significantly increased in tandem by 0.12 and 0.16 litres, respectively (each p<0.05), dyspnoea fell by 0.9 (1.8) Borg units (p = 0.07) and dyspnoea/ventilation ratios fell significantly (p<0.05). The fall in dyspnoea intensity at higher submaximal ventilations correlated with the concurrent decrease in end-expiratory lung volume (p<0.05). Conclusion: In patients with symptoms of GOLD stage I COPD, IB treatment is associated with modest but consistent improvements in airway function, operating lung volumes and dyspnoea intensity during exercise. These results provide a physiological rationale for a trial of bronchodilator therapy in selected patients with milder but symptomatic COPD.
Changes in the level and pattern of mortality rates in Peninsular Malaysia, 1971-1983

The study is concerned with the changes in the level and pattern of mortality rates in Peninsular Malaysia during 1971-1983. Changes in mortality rates are considered by ethnic group, sex, state and urban and rural residence. Along with the mortality rates, mortality indexes were also calculated and used for examining mortality change over time. Correlation analysis is used to examine the relationship between mortality change and the change in socio-economic and health indicators. The analysis indicates that mortality rates in Peninsular Malaysia have declined and a declining trend is evident for all groups by ethnicity, sex, state, and urban and rural residence. By the year 1983, the mortality rate (measured by the comparative mortality index) was 26 per cent lower than in 1971. For females it was 27 per cent lower and for males 24 per cent lower. The decline in overall mortality was largely attributed to the drop in infant and child mortality. These two age groups combined contributed about 49 per cent to the total decline in overall mortality between 1971 and 1983, 52 per cent for males and 45 per cent for females. The decline in mortality rates in Peninsular Malaysia during the study period are attributable to the combined effect of socio-economic development and the public health programmes. A reduction in families living in poverty, infrastructural improvements, including the increase in access to piped water, electricity, and sanitation, and the increase in the number of medical personnel are among the important factors in effecting mortality decline in Peninsular Malaysia.