Miracle-dz/UniFAR-FTUs huggingface dataset:
An approach to confirmatory testing of subpopulations in clinical trials

In oncology studies with immunotherapies, populations of “super‐responders” (patients in whom the treatment works particularly well) are often suspected to be related to biomarkers. In this paper, we explore various ways of confirmatory statistical hypothesis testing for joint inference on the subpopulation of putative “super‐responders” and the full study population. A model‐based testing framework is proposed, which allows to define, up‐front, the strength of evidence required from both full and subpopulations in terms of clinical efficacy. This framework is based on a two‐way analysis of variance (ANOVA) model with an interaction in combination with multiple comparison procedures. The ease of implementation of this model‐based approach is emphasized and details are provided for the practitioner who would like to adopt this approach. The discussion is exemplified by a hypothetical trial that uses an immune‐marker in oncology to define the subpopulation and tumor growth as the primary endpoint.
Effects of heat stress on growth, some blood variables and lipid oxidation in broilers exposed to high temperature at an early age

1. This study was conducted to determine metabolic and physiological responses of 2 commercial broiler strains, Hubbard (H) and Cobb (C), exposed to an ambient temperature of 38°±1°C for 2 h at 14 and 15 d of age. 2. Exposure to high temperature at an early age resulted in weight loss in strain C, which was not compensated for by 35 d of age but there was no weight loss in strain H. 3. Exposure of broilers to heat stress (38°±1°C) at 35 d of age resulted in an increase in rectal temperature, regardless of previously high temperature experience but acid-base balance and haematocrit values were not affected by heat stress. 4. Malondialdehyde concentration was higher in unexposed birds than in previously exposed ones and did not significantly differ between strains.
Tworzenie i rodzaje wiedzy społecznej

he article focuses on types of social knowledge. Apart from analytic and systemic thinking, understanding of social beings requires modular thinking, which involves primarily a new interpretation of social reality. To recognize the existence of several types of social knowledge is tantamount to rejecting the concept of determinism in the operation of the social world. If we renounce determinism in favour of probabilism or contingency, i.e. an indispensable necessity, we admit, in principle, that there may exist a series of situations (states), which are not random and which open up a range of entirely new possibilities.
Evaluation of decision rules for identifying low bone density in postmenopausal African-American women.

OBJECTIVE While African-American women tend to have greater bone mineral density (BMD) than caucasian women, they are still at risk of developing osteoporosis later in life. Clinical decision rules (i.e., algorithms) have been developed to assist clinicians identify women at greatest risk of low BMD. However, such tools have only been validated in caucasian and Asian populations. Accordingly, the objective of this study was to compare the performance of five clinical decision rules in identifying postmenopausal African-American women at greatest risk for low femoral BMD. METHODOLOGY One hundred-seventy-four (n=174) postmenopausal African-American women completed a valid and reliable oral questionnaire to assess lifestyle characteristics, and completed height and weight measures. BMD at the femoral neck was measured via dual energy x-ray absorptiometry (DXA). We calculated sensitivity, specificity, positive predictive value, and negative predictive value for identifying African-American women with low BMD (T-Score < or = -2.0 SD) using five clinical decision rules: Age, Body Size, No Estrogen (ABONE), Osteoporosis Risk Assessment Instrument (ORAI), Osteoporosis Self-Assessment Tool (OST), Simple Calculated Osteoporosis Risk Estimation (SCORE), and body weight less than 70 kg. RESULTS Approximately 30% of African-American women had low BMD, half of whom had osteoporosis (BMD T-Score < or = -2.5 SD). Sensitivity for identifying women with a low BMD (T-Score < or = -2.0 SD) ranged from 65.57-83.61%, while specificity ranged from 53.85-78.85%. Positive predictive values ranged from 80.95-87.91%, while negative predictive values ranged from 48.44-58.33%. CONCLUSION Our data suggest that the clinical decision rules analyzed in this study have some usefulness for identifying postmenopausal African-American women with low BMD. However, there is a need to establish cut-points for these clinical decision rules in a larger, more diverse sample of African-American women.
The exon junction complex is detected on CBP80‐bound but not eIF4E‐bound mRNA in mammalian cells: dynamics of mRNP remodeling

Newly spliced mRNAs in mammalian cells are characterized by a complex of proteins at exon–exon junctions. This complex recruits Upf3 and Upf2, which function in nonsense‐mediated mRNA decay (NMD). Both Upf proteins are detected on mRNA bound by the major nuclear cap‐binding proteins CBP80/CBP20 but not mRNA bound by the major cytoplasmic cap‐binding protein eIF4E. These and other data indicate that NMD targets CBP80‐bound mRNA during a ‘pioneer’ round of translation, but whether nuclear eIF4E also binds nascent but dead‐end transcripts is unclear. Here we provide evidence that nuclear CBP80 but not nuclear eIF4E is readily detected in association with intron‐containing RNA and the C‐terminal domain of RNA polymerase II. Consistent with this evidence, we demonstrate that RNPS1, Y14, SRm160, REF/Aly, TAP, Upf3X and Upf2 are detected in the nuclear fraction on CBP80‐bound but not eIF4E‐bound mRNA. Each of these proteins is also detected on CBP80‐bound mRNA in the cytoplasmic fraction, indicating a presence on mRNA after export. The dynamics of mRNP composition before and after mRNA export are discussed.
The Emotional Brain Weighs Its Options

NEUROSCIENCEA team of cognitive neuroscientists reports findings on page [684][1] of this issue of Science that link the so-called framing effect, in which the language used to describe options often influences people's choices, to neural activity in a key emotion center in the human brain, the amygdala. ([Read more][2].) [1]: http://www.sciencemag. org/cgi/content/short/313/5787/684 [2]: http://www.sciencemag. org/cgi/content/full/313/5787/600b
A Gibbs Sampler for Spatial Clustering with the Distance-dependent Chinese Restaurant Process

The distance-dependent Chinese Restaurant Process (dd-CRP) is a flexible class of distributions over partitions which was recently introduced by [1, 2]. In their description and experiments Blei and Frazier focus on the sequential setting such as clustering over time. Their Gibbs sampler, while general in nature, does not explicitly handle the case of non-sequential (also called spatial) clustering. In this case further details are needed for a correct implementation. We introduce the Gibbs sampler for spatial clustering with the dd-CRP. For simplicity, we focus on infinite Gaussian mixture models (IGMM) [9].
Dynamic IPC/clock rate optimization

Current microprocessor designs set the functionality and clock rate of the chip at design time based on the configuration that achieves the best overall performance over a range of target applications. The result may be poor performance when running applications whose requirements are not well-matched to the particular hardware organization chosen. We present a new approach called Complexity-Adaptive Processors (CAPs) in which the IPC/clock rate tradeoff can be altered at runtime to dynamically match the changing requirements of the instruction stream. By exploiting repeater methodologies used increasingly in deep sub-micron designs, CAPs achieve this flexibility with potentially no cycle time impact compared to a fixed architecture. Our preliminary results in applying this approach to on-chip caches and instruction queues indicate that CAPs have the potential to significantly outperform conventional approaches on workloads containing both general purpose and scientific applications.
A review of etiologies of depression in COPD

There is significant evidence supporting an increased prevalence of depression in patients with COPD, but that depression is not a homogenous entity because there are multiple contributing etiologies for the depressive symptoms. Additionally the relationship between COPD and depression is neither exclusively linear, nor unidirectional. “Early onset” depression is defined as depression that develops prior to the diagnosis of COPD, often during an individual’s youth. This is often reflective of a genetic vulnerability to depression which increases adolescents’ risk for developing addiction to nicotine, setting up a life-long exposure to tobacco – the single greatest risk factor for the development of COPD. When COPD does develop it brings with it attendant losses, particularly in level of independent function and self image that contribute to a “reactive” depression that is not distinct from the losses experienced by those suffering with other chronic illnesses. Lastly there is increasing evidence through magnetic resonance imaging (MRI) and biochemical markers that systemic, physiologic changes associated with COPD have direct effects on the brain’s vasculature that have also been associated with depression in the elderly, termed “late onset” depression. The conclusion is that the presence of depression in a COPD patient does not reflect a single pathologic pathway. Rather the two disorders each contribute to the morbidity of the other. This review discusses the evidence supporting each of these contributors and suggests that an understanding of these varying elements can direct healthcare interventions.
An analysis of free-text queries for a multi-field web form

We report how users interact with an experimental system that transforms single-field textual input into a multi-field query for an existing travel planner system. The experimental system was made publicly available and we collected over 30,000 queries from almost 12,000 users. From the free-text query log, we examined how users formulated structured information needs into free-text queries. The query log analysis shows that there is great variety in query formulation, over 400 query templates were found that occurred at least 4 times. Furthermore, with over 100 respondents to our questionnaire, we provide both quantitative and qualitative evidence indicating that end-users significantly prefer a single field interface over a multi-field interface when performing structured search.
tinyFLP and tinyCAT: software for automatic peak selection and scoring of AFLP data tables

Amplified fragment length polymorphism (AFLP) is a well‐established method for DNA fingerprinting. In the last years, fragment separation gradually changed from using gel to capillary electrophoresis, resulting in large, digital data sets. Automatic scoring softwares available to date are proprietary and expensive. tinyFLP/tinyCAT is a compact, open‐source software for automatic scoring of AFLP data. It reads from PeakScanner© generated tables, optimizes the conversion of peak data into a binary allelic matrix and removes operator‐mediated ambiguities from the scoring process. The output is formatted for direct use in MrBayes and other phylogenetic applications.
Preoperative Imaging for DIEA Perforator Flaps: A Comparative Study of Computed Tomographic Angiography and Doppler Ultrasound

Background: Abdominal donor-site flaps, including the transverse rectus abdominis musculocutaneous (TRAM) and deep inferior epigastric artery (DIEA) perforator flaps, are standard in autologous breast reconstruction. With significant variation in the vascular anatomy of the abdominal wall, preoperative imaging is essential for preoperative planning and reducing intraoperative error. Doppler and color duplex sonography have been used with varying results, and the quest continues for optimal preoperative assessment. Computed tomographic angiography has recently been proposed as a noninvasive modality for this purpose. This is the first study to formally compare preoperative Doppler ultrasound with computed tomographic angiography for imaging the DIEA. Methods: Eight consecutive patients undergoing DIEA perforator flap surgery for breast reconstruction underwent both computed tomographic angiography and Doppler ultrasound preoperatively. All investigations and procedures were performed at the same institution with the same primary and assisting surgeons and the same radiology team. Results: Computed tomographic angiography was superior to Doppler ultrasound at identifying the course of the DIEA and its branching pattern, and in visualizing its perforators. Preoperative computed tomographic angiography was highly specific (100 percent) and more sensitive in mapping and visualizing perforators (p = 0.0078). It was also proficient at identifying the superficial epigastric arterial system and for effectively displaying the results intraoperatively. It was substantially quicker and removed the interobserver error associated with Doppler ultrasonography. The study was ceased after eight patients because of the overwhelming benefit of computed tomographic angiography over Doppler ultrasonography. Conclusion: Computed tomographic angiography is a valuable imaging modality for the preoperative assessment of the donor-site vascular supply for TRAM and DIEA perforator flaps.
Thermal-Comfort Design of Personalized Casts

This paper introduces a novel method for designing personalized orthopedic casts which are aware of thermal-comfort while satisfying mechanical requirements. Our pipeline starts from thermal images taken by an infrared camera, by which the distribution of thermal-comfort sensitivity is generated on the surface of a 3D scanned model. We formulate a hollowed Voronoi tessellation pattern to represent the covered region for a web-like cast design. The pattern is further optimized according to the thermal-comfort sensitivity calculated from thermal images. Working together with a thickness variation method, we generate a solid model for a personalized cast maximizing both thermal comfort and mechanical stiffness. To demonstrate the effectiveness of our approach, 3D printed models of personalized casts are tested on body parts of different individuals.
Study on Hot Topic Discovery from Chinese Texts

With the development of information technology, there has been an increased popularity in the use of electronic texts. Topic detection and tracking can identify hot information from isolated texts. Obtaining hot topics has become an important issue in recent years. The combination of statistics and natural language processing was utilized in the current study to discover hot topics from texts. First, the statistics technique was adopted to obtain frequent and high weighted words. Then, the linguistic grammar rules were used to generate the candidate phrases. Finally, the hot phrase topics were obtained based on the weight computation method of phrases. Experiment results showed that the proposed approach was effective in that the extracted topics can express more comprehensive information. This study's results are meaningful in the areas of text classification, text clustering, information retrieval, and construction of high-quality Tibetan corpus.
Literacy Teaching and Bilingualism in Visual Learning Processes: Contributions from Deaf Epistemologies

Reading/writing teaching and learning processes for deaf students enrolled in bilingual contexts are examined in this study. The objective is to contribute to theoretical and practical reflection on the educational answers to the demands of literacy teaching for this particular population. The type of education now being offered in Chile and in other Latin American countries does not respond to the linguistic, cultural and learning characteristics of the deaf. In other words, current educational proposals do not consider the features of visual learning, the incorporation of sign language in learning processes, nor the cultural beliefs and modes of the deaf. A model of bilingual intercultural education (IBE) that is based on deaf epistemologies, values the language and culture of deaf communities, and inspires models for literacy instruction and teaching practices centered on the features of visual learning by the deaf is needed.
Characterization and Therapeutic Potential of Induced Pluripotent Stem Cell-Derived Cardiovascular Progenitor Cells

Background Cardiovascular progenitor cells (CPCs) have been identified within the developing mouse heart and differentiating pluripotent stem cells by intracellular transcription factors Nkx2.5 and Islet 1 (Isl1). Study of endogenous and induced pluripotent stem cell (iPSC)-derived CPCs has been limited due to the lack of specific cell surface markers to isolate them and conditions for their in vitro expansion that maintain their multipotency. Methodology/Principal Findings We sought to identify specific cell surface markers that label endogenous embryonic CPCs and validated these markers in iPSC-derived Isl1+/Nkx2.5+ CPCs. We developed conditions that allow propagation and characterization of endogenous and iPSC-derived Isl1+/Nkx2.5+ CPCs and protocols for their clonal expansion in vitro and transplantation in vivo. Transcriptome analysis of CPCs from differentiating mouse embryonic stem cells identified a panel of surface markers. Comparison of these markers as well as previously described surface markers revealed the combination of Flt1+/Flt4+ best identified and facilitated enrichment for Isl1+/Nkx2.5+ CPCs from embryonic hearts and differentiating iPSCs. Endogenous mouse and iPSC-derived Flt1+/Flt4+ CPCs differentiated into all three cardiovascular lineages in vitro. Flt1+/Flt4+ CPCs transplanted into left ventricles demonstrated robust engraftment and differentiation into mature cardiomyocytes (CMs). Conclusion/Significance The cell surface marker combination of Flt1 and Flt4 specifically identify and enrich for an endogenous and iPSC-derived Isl1+/Nkx2.5+ CPC with trilineage cardiovascular potential in vitro and robust ability for engraftment and differentiation into morphologically and electrophysiologically mature adult CMs in vivo post transplantation into adult hearts.
The effects of overconfidence on the index of discrimination ability and the judgment criterion in investment decision An experiment based on signal detection theory

The paper examines the effects of overconfidence on the index of discrimination ability and the judgment criterion in investment decision-making by a scenario-simulated experiment based on signal detection theory. We perform the experiment with 55 undergraduates of business majors recruited freely, and adopt corporation investment decisions as experiment task to do our research. The result indicates: Overconfident is a conditional compound concept, the overconfidence measured by the overestimate of the investment outcomes has significant impact on the individual' discrimination ability and judgment criterion in investment decision-making. The overconfident participants have lower hit rate, lower correct rejection rate and weaker index of discrimination ability, as well as higher miss rate, higher false alarm rate and higher index of judgment criterion than the rational ones. Moreover, the indeterminate decision situation, the opportunity acceptance pattern, the low risk-low income pattern of decision condition as well as the medium/low risk - medium/low income patterns of decision objects may intensify the overconfident individual's irrationality.
Using PCA and LVQ neural network for automatic recognition of five types of white blood cells

Designing an effective classifier has been a challenging task in the previous methods proposed in the literature. In this paper, we apply a combination of feature selection algorithm and neural network classifier in order to recognize five types of white blood cells in the peripheral blood. For this purpose, first nucleus and cytoplasm are segmented using Gram-Schmidt method and snake algorithm, respectively; second, three kinds of features are extracted from the segmented areas. Then the best features are selected using Principal Component Analysis (PCA). Finally, five types of white blood cells are classified using Learning Vector Quantization (LVQ) neural network. The performance analysis of the proposed algorithm is validated by an expert's classification results. The efficiency of the proposed algorithm is highlighted by comparing our results with those reported in a recent article which proposed a method based on the combination of Sequential Forward Selection (SFS) as the feature selection algorithm and Support Vector Machines (SVM) as the classifier.
Effect of oestrogen and an LH-RH agonist on the release of gonadotrophins in ovariectomized ewes deprived of LH-RH.

Endogenous LH-RH in ewes was inhibited by active immunization or by injection of LH-RH antiserum. Plasma levels of LH and FSH were elevated in 3 ovariectomized control ewes but low in 3 LH-RH immunized ovariectomized ewes. Oestradiol benzoate (50 microgram i.m.) caused a marked rise in LH concentrations in control ewes but not in the immunized ewes. In the immunized ewes the low plasma levels of FSH decreased even further 8-36 h after injection of oestrogen, indicating a direct inhibitory action of the steroid on the pituitary. Both groups responded to the oestrogen injection by a rise in plasma levels of prolactin and by exhibiting normal oestrous behaviour. When the control ewes were again challenged with oestradiol benzoate and, after 10 h, given an i.v. injection of 75 ml antiserum to LH-RH, the LH surge was abolished in one animal and reduced in another. These experiments indicate that the continued presence of LH-RH is necessary for the occurrence of the oestrogen-induced LH surge in the ewe. Administration of a stimulatory analogue of LH-RH released LH and FSH in control and immunized ewes but the responsiveness to further injections at intervals of 3 h decreased, particularly for FSH.
The medial reticular formation: a brainstem substrate for simple action selection?

The search for the neural substrate of vertebrate action selection has focused on structures in the foreand midbrain, particularly on the basal ganglia. Yet, the behavioural repertoire of decerebrate and neonatal animals suggests the existence of a relatively self-contained neural substrate for action selection in the brainstem. We propose that the medial reticular formation (mRF) is this substrate’s main component, reviewing evidence that the mRF’s inputs, outputs, and intrinsic organisation are consistent with the requirements of an action selection system. We argue that the internal architecture of the mRF is composed of interconnected neuron clusters; our quantitative model of this anatomy suggests the mRF’s intrinsic circuitry constitutes a small-world network, and may have evolved to reduce axonal wiring. We use computational models to enumerate and illustrate potential configurations of action representation within the internal circuitry of the mRF. We show that each cluster’s output could represent activation of an action component; thus, co-activation of a set of these clusters would lead to the co-ordinated behavioural response observed in the animal. New results are presented that provide evidence for an alternative scheme: inputs to the mRF are organised to contact clusters, but recruit a pattern of reticulo-spinal neurons from across clusters to generate an action. We propose that this reconciles the anatomical structure with behavioural data showing action sequencing is degraded, rather than individual actions lost, as the mRF is progressively lesioned. Finally, we consider the potential integration of the basal ganglia and mRF substrates for selection and suggest they may collectively form a layered/hierarchical control system.