Miracle-dz/UniFAR-FTUs huggingface dataset:
Unusual Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase of Anoxic Archaea

ABSTRACT The predominant pool of organic matter on earth is derived from the biological reduction and assimilation of carbon dioxide gas, catalyzed primarily by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). By virtue of its capacity to use molecular oxygen as an alternative and competing gaseous substrate, the catalytic efficiency of RubisCO and the enzyme’s ability to assimilate CO2 may be severely limited, with consequent environmental and agricultural effects. Recent genomic sequencing projects, however, have identified putative RubisCO genes from anoxic Archaea. In the present study, these potential RubisCO sequences, from Methanococcus jannaschiiand Archaeoglobus fulgidus, were analyzed in order to ascertain whether such sequences might encode functional proteins. We also report the isolation and properties of recombinant RubisCO using sequences obtained from the obligately anaerobic hyperthermophilic methanogen M. jannaschii. This is the first description of an archaeal RubisCO sequence; this study also represents the initial characterization of a RubisCO molecule that has evolved in the absence of molecular oxygen. The enzyme was shown to be a homodimer whose deduced sequence, along with other recently obtained archaeal RubisCO sequences, differs substantially from those of known RubisCO molecules. The recombinantM. jannaschii enzyme has a somewhat low, but reasonable kcat, however, unlike previously isolated RubisCO molecules, this enzyme is very oxygen sensitive yet it is stable to hyperthermal temperatures and catalyzes the formation of the expected carboxylation product. Despite inhibition by oxygen, this unusual RubisCO still catalyzes a weak yet demonstrable oxygenase activity, with perhaps the lowest capacity for CO2/O2 discrimination ever encountered for any RubisCO.
Self-Taught Spectral Clustering via Constraint Augmentation

Although constrained spectral clustering has been used extensively for the past few years, all work assumes the guidance (constraints) are given by humans. Original formulations of the problem assumed the constraints are given passively whilst later work allowed actively polling an Oracle (human experts). In this paper, for the first time to our knowledge, we explore the problem of augmenting the given constraint set for constrained spectral clustering algorithms. This moves spectral clustering towards the direction of selfteaching as has occurred in the supervised learning literature. We present a formulation for self-taught spectral clustering and show that the self-teaching process can drastically improve performance without further human guidance.
Complexity Preserving Functions

It’s widely recognized that compression is useful and even necessary for inductive learning, where a short description will capture the ‘regularities’. We introduce complexitypreserving functions that preserve these regularities of the concept. They are based on the universal information distance [Bennett et al. ‘97] and define for an instance a set of elements sharing the same complexity type. This corresponds to the two-part code [Rissanen ‘89] of the MDL principle, when it is interpreted as the first term describing the set and the second term the element in the set [Rissanen 99]. We investigate its importance in inductive learning.
Trends in the Development of Machinery and Associated Technology ” TMT 2010 , Mediterranean Cruise , 11-18 September 2010 OPTIMIZATION OF THE FEATURES USED IN FACE RECOGNITION

We present an optimization method for the features used in face recognition. The particle swarm algorithm is used to select the optimum parameters for the Gabor filter which is employed in our face recognition algorithm. We generate 40 Gabor filters and determine one optimum filter parameter set from those by using the particle swarm optimization. The face recognition is performed by using only the output of the Gabor filter with optimum parameter set as well as the all 40 filter output feature set. The performance of the proposed method is presented by means of simulations.
Bayesian Wavelet Analysis with a Model Complexity Prior

SUMMARY In this paper Bayesian methods for the selection and shrinkage of wavelet coeecients are considered. The wavelet coeecients are assigned a zero mean normal prior with precision matrix. This allows for a more general model than has been previously studied and uncertainty in can be controlled through a hyperprior. It is argued that model interpretability is improved by foresaking the conjugate Wishart prior for in favour of a non-conjugate hyperprior that penalises the degrees of freedom of the model. The degrees of freedom provides a single intuitive measure of model complexity that accommodates both the number of coeecients and the extent of the shrinkage on them. We compare three diierent sampling strategies and comment on their performance. 1. INTRODUCTION Wavelet analysis has quickly established itself as a standard method for the analysis and smoothing of time series. Of particular importance is the application to the denoising and compression of signals (e.g. Bruce and Gao, 1996). In this paper we consider wavelets within a Bayesian framework. The main motivation is to generalise previous work (Clyde, Parmigiani and Vidakovic, 1998; M uller and Vidakovic, 1999) and to make prior assumptions that can be compared to conventional model selection criteria. In addition we compare the relative performance of three well-used sampling strategies and assess their relative merits. Bayesian analysis begins with the elicitation of prior distributions on the wavelet coeecients that reeect subjective beliefs about the probable values of the coeecients. This prior should be interpretable enough to allow us to use it to reeect our prior beliefs on the true signal. The most commonly used prior, and the one we consider here, is a zero mean normaìshrinkage' prior on the vector of wavelet coeecients with some precision matrix. A suitable value of is rarely known a priori and setting it can prove problematic as ultimately controls the complexity, and hence smoothness, of the wavelet reconstruction. We use a hierarchical Bayesian approach which accommodates uncertainty in by including a hyperprior. We refrain from using the conjugate Wishart prior for because this suuers from a lack of interpretability, eeectively diluting uncertainty on into uncertainty on this hyper-hyper prior. Instead we assign a non-conjugate prior distribution over , motivated by the the degrees of freedom of the wavelet network. We choose this as it ooers a natural vehicle for expressing prior knowledge about the underlying function.
Impact of weight cycling on risk of morbidity and mortality

Unintentional weight gain is commonly observed in adult humans, often provoking intentional weight loss attempts followed by unintentional weight regain. This episodic variation in body weight over a period of time has been referred to as ‘weight cycling’. Over the last two decades, weight cycling has been associated with a number of morbid health conditions and increased mortality. This article provides a comprehensive evaluation of recent weight‐cycling evidence, looks to understand design differences between studies and study outcomes, assesses the need for further research on particular health outcomes, and proposes alternative methodologies that will bridge the needs and capabilities of research. Searches were conducted per PRISMA guidelines. Articles on weight cycling in the literature were initially identified using search strings in PubMed. Eligibility assessment of the remaining articles was performed independently by three reviewers to identify publications that presented direct evidence. Twenty human studies (in addition to seven animal studies) were selected and retained; 12 accounted for the intentionality of weight loss. Although weight regain following successful weight loss remains one of the most challenging aspects of body‐weight regulation, evidence for an adverse effect of weight cycling appears sparse, if it exists at all.
Effects of intensive insulin therapy upon pancreatic β cell function in patients newly diagnosed with type II diabetes.

OBJECTIVE This study was designed to evaluate the clinical efficacy of intensive insulin therapy for patients newly diagnosed with type 2 diabetes. METHODS A total of 219 patients newly diagnosed with type 2 diabetes were randomly assigned into insulin group (n = 55), gliclazide group (n = 52), metformin group (n = 55) and pioglitazone group (n = 57). On the basis of diet and physical interventions, patients in the insulin group received intensive insulin therapy. Those in other three groups were given oral intake of medication. All treatment schemes endured for 12 weeks. A variety of indexes including fasting blood-glucose (FPG), FPG at 2 h after diet (FPG 2 h), hemoglobin A1 c (HbAlc), area under the curve (AUC) for insulin (insulin AUC) after glucose load, C-peptide AUC after glucose load (C-peptide AUC), changes in insulin secretion index (Homa-β) and insulin resistance index( Homa-IR) were accurately measured and statistically among different groups. RESULTS The insulin AUC at 0-30 min, C-peptide AUC at 0-30 min and Homa-β in the insulin group were equally significantly higher compared with those levels in the other three groups. In addition, the level of Homa-IR in the insulin, metformin and pioglitazone groups were all significantly reduced compared with the values prior to respective treatment (all P < 0.05). CONCLUSION Compared with oral administration of hypoglycemic drugs, intensive insulin therapy is able to better improve pancreatic β cell function and insulin resistance for newly-diagnosed type 2 diabetes patients.
Simian Immunodeficiency Virus from the Sooty Mangabey and Rhesus Macaque Is Modified with O-Linked Carbohydrate

ABSTRACT Although stretches of serine and threonine are sometimes sites for O-linked carbohydrate attachment, specific sequence and structural determinants for O-linked attachment remain ill defined. The gp120 envelope protein of SIVmac239 contains a serine-threonine-rich stretch of amino acids at positions 128 to 139. Here we show that lectin protein from jackfruit seed (jacalin), which binds to non- and monosialylated core 1 O-linked carbohydrate, potently inhibited the replication of SIVmac239. Selection of a jacalin-resistant SIVmac239 variant population resulted in virus with specific substitutions within amino acids 128 to 139. Cloned simian immunodeficiency virus (SIV) variants with substitutions in the 128-to-139 region had infectivities equivalent to, or within 1 log unit of, that of SIVmac239 and were resistant to the inhibitory effects of jacalin. Characterization of the SIVmac239 gp120 O-linked glycome showed the presence of core 1 and core 2 O-linked carbohydrate; a 128-to-139-substituted variant gp120 from jacalin-resistant SIV lacked O-linked carbohydrate. Unlike that of SIVmac239, the replication of HIV-1 strain NL4-3 was resistant to inhibition by jacalin. Purified gp120s from four SIVmac and SIVsm strains bound jacalin strongly in an enzyme-linked immunosorbent assay, while nine different HIV-1 gp120s, two SIVcpz gp120s, and 128-to-139-substituted SIVmac239 gp120 did not bind jacalin. The ability or inability to bind jacalin thus correlated with the presence of the serine-threonine-rich stretch in the SIVmac and SIVsm gp120s and the absence of such stretches in the SIVcpz and HIV-1 gp120s. Consistent with sequence predictions, two HIV-2 gp120s bound jacalin, while one did not. These data demonstrate the presence of non- and monosialylated core 1 O-linked carbohydrate on the gp120s of SIVmac and SIVsm and the lack of these modifications on HIV-1 and SIVcpz gp120s.
Learning Science In A Secondary School In Papua New Guinea

This study investigated teaching and learning, and the classroom learning environment in which the electricity topic was taught by the regular class teacher within the prescribed Grade 9 syllabus in a Secondary School in Papua New Guinea. The study was motivated by the perceived problems students had with understanding science concepts and the lack of classroom-based studies that provide a better understanding of teaching and learning science and the influence of the classroom learning environment on students' learning. An interpretive with embedded case study was conducted in a Grade 9 class over a period of 12 weeks in which data was gathered using mixed and multiple methods. Findings of the study revealed the presence and influence of aspects of the indigenous traditional teaching and learning approach impacting on the formal modern Western oriented teaching and learning approach in this particular classroom. The study recommended that in order to maximise students' learning and understanding of science concepts in the classroom observed, cultural sensitivity should be incorporated in the pedagogy.
SFRP1 suppressed hepatoma cells growth through Wnt canonical signaling pathway

Oncogenic activation of the Wnt/β‐catenin signaling pathway is common in hepatocellular carcinoma (HCC). The secreted frizzled‐related proteins (SFRPs) function as negative regulators of Wnt signaling and have important implications for carcinogenesis. Promoter hypermethylation of SFRP genes is common in human cancers. However, the role of SFRPs in HCC is not clear. Recently, we have shown that SFRP1 is frequently downregulated through promoter hypermethylation. To confirm and extend these findings, the methylation status of the other SFRP members, including SFRP2, SFRP4 and SFRP5, was examined by methylation‐specific polymerase chain reaction (MS‐PCR). Hypermethylation of SFRP genes, except for SFRP4, is frequent in HCCs and the levels found here were significantly higher than those seen in cirrhotic livers, chronic hepatitis livers and normal controls (p < 0.0001 for SFRP1 and SFRP2, p < 0.05 for SFRP5). To investigate the role of SFRP1 in HCCs, we used re‐expression of SFRP1 in β‐catenin‐dependent HCC cell lines: Huh6 and HepG2. Restoration of SFRP1 attenuated Wnt signaling in those Huh6 hepatoma cells with a β‐catenin gene point mutation, decreased abnormal accumulation of β‐catenin in the nucleus and suppressed cell growth. Conversely, restoration of SFRP1 in HepG2 hepatoma cells with truncated β‐catenin could not block the Wnt signaling pathway. Furthermore, knocking down SFRP1 by RNA interference in β‐catenin‐deficient cell lines (SK‐Hep1) stimulated Wnt signaling and promoted cell growth. Our data suggested that SFRP1 suppressed liver cancer cells growth through Wnt canonical signaling. Moreover, β‐catenin‐independent noncanonical pathway might be involved in Wnt signaling activation through unknown molecules in HCC. © 2007 Wiley‐Liss, Inc.
Effects of administering testosterone undecanoate in rats subjected to physical exercise: effects on the estrous cycle, motor behavior and morphology of the liver and kidney

The aim of the work was evaluate the effects of testosterone undecanoate (TU) treatment combined with moderate physical training on: the estrous cycle, body weight (BW), motor behavior (MB), and the morphohistology of the reproductive system, the liver and kidney in rats. Female Wistar rats (180 g - 250 g) were divided as follows: sedentary + TU (S + TU), trained + TU (T + TU), sedentary + vehicle (S + V), trained + vehicle (T + V). The rats swam 50 min/Day, strapped with a 5% BW load, for 4 weeks. During this training, (BW) was monitored daily as well as the estrous cycle (EC) by vaginal smear. The TU (15 mg/kg s.c) was administered 3 times/week for 4 weeks. At the end of the study, data on MB, BW and morphohistopathological changes in viscera were compiled. The (T + TU) group had on average, a higher (BW) in the fourth week compared to the first week, and (BW) higher than (S + V) and (S + TU) groups. We noted an interruption in the EC and a decrease in weight of ovaries in animals treated with TU. In addition, there was an increase in the relative weight of the heart in groups (T + V) and (T+ TU), and kidneys in group (T + TU). Histopathological analysis showed periportal congestion and isolated foci of hepatic necrosis in rats with TU. Thus, TU combined with training abolished the EC, promoted ovarian atrophy, liver necrosis, cardiac hypertrophy and a decrease in motor activity.
Alcohol Elicits Functional and Structural Plasticity Selectively in Dopamine D1 Receptor-Expressing Neurons of the Dorsomedial Striatum

Addiction is thought to be a maladaptive form of learning and memory caused by drug-evoked aberrant synaptic plasticity. We previously showed that alcohol facilitates synaptic plasticity in the dorsomedial striatum (DMS), a brain region that drives goal-directed behaviors. The majority of DMS cells are medium spiny neurons (MSNs) that express dopamine D1 receptors (D1Rs) or D2 receptors (D2Rs), which drive “Go” or “No-Go” behaviors, respectively. Here, we report that alcohol induces cell type-specific synaptic and structural plasticity in the DMS. Using mice that express a fluorescence marker to visualize D1R or D2R MSNs, we show that repeated cycles of systemic administration of alcohol or alcohol consumption induces a long-lasting increase in AMPAR activity specifically in DMS D1R but not in D2R MSNs. Importantly, we report that alcohol consumption increases the complexity of dendritic branching and the density of mature mushroom-shaped spines selectively in DMS D1R MSNs. Finally, we found that blockade of D1R but not D2R activity in the DMS attenuates alcohol consumption. Together, these data suggest that alcohol intake produces profound functional and structural plasticity events in a subpopulation of neurons in the DMS that control reinforcement-related learning. SIGNIFICANCE STATEMENT Alcohol addiction is considered maladaptive learning and memory processes. Here we unraveled a long-lasting cellular mechanism that may contribute to the memory of alcohol-seeking behaviors. Specifically, we found that alcohol consumption produces a long-lasting enhancement of channel activity and persistent alterations of neuronal morphology in a part of the brain (DMS) that controls alcohol-drinking behaviors. Furthermore, we show that these alterations occur only in a subpopulation of neurons that positively control reward and reinforcement of drugs of abuse. Finally, we report that blocking the activity of this neuronal population reduces alcohol intake. As such synaptic and structural changes are the cellular hallmarks of learning and memory, and these neuroadaptations may drive the development of pathological heavy alcohol consumption.
Impact of Rotor Losses in a 12-Slot 10-Pole Axial Flux PM Machine

In spite of their several advantages, the fractional-slot PM machines suffer high contents of space harmonics in the air-gap MMF distribution. The MMF space harmonic amplitude and frequency depend on the particular combination of number of slots and poles. The main consequence of such harmonic contents is the induced losses in the rotor. Moreover the slot opening can produce considerable rotor losses due the variation of permeance corresponding to the stator slots. This paper presents the impact of the rotor losses on the performance of a 12-slot 10-pole axial flux PM machine. The influence of both MMF harmonics and slot harmonics is considered. Comparisons between prediction and experimental results are included in the paper.
cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets

In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend.
Adjuvant and salvage radiotherapy after prostatectomy: American Society of Clinical Oncology clinical practice guideline endorsement.

PURPOSE To endorse the American Urological Association (AUA)/American Society for Radiation Oncology (ASTRO) guideline on adjuvant and salvage radiotherapy after prostatectomy. The American Society of Clinical Oncology (ASCO) has a policy and set of procedures for endorsing clinical practice guidelines developed by other professional organizations. METHODS The guideline on adjuvant and salvage radiotherapy after prostatectomy was reviewed for developmental rigor by methodologists. An ASCO endorsement panel then reviewed the content and recommendations. RESULTS The panel determined that the guideline recommendations on adjuvant and salvage radiotherapy after prostatectomy, published in August 2013, are clear, thorough, and based on the most relevant scientific evidence. ASCO endorsed the guideline on adjuvant and salvage radiotherapy after prostatectomy, adding one qualifying statement that not all candidates for adjuvant or salvage radiotherapy have the same risk of recurrence or disease progression, and thus, risk-benefit ratios are not the same for all men. Those at the highest risk for recurrence after radical prostatectomy include men with seminal vesicle invasion, Gleason score 8 to 10, extensive positive margins, and detectable postoperative prostate-specific antigen (PSA). RECOMMENDATIONS Physicians should discuss adjuvant radiotherapy with patients with adverse pathologic findings at prostatectomy (ie, seminal vesicle invasion, positive surgical margins, extraprostatic extension) and salvage radiotherapy with patients with PSA or local recurrence after prostatectomy. The discussion of radiotherapy should include possible short- and long-term adverse effects and potential benefits. The decision to administer radiotherapy should be made by the patient and multidisciplinary treatment team, keeping in mind that not all men are at equal risk of recurrence or clinically meaningful disease progression. Thus, the risk-benefit ratio will differ for each patient.
Cascade Face Detection Based on Histograms of Oriented Gradients and Support Vector Machine

Detecting faces in images is a key step in numerous computer vision applications, such as face recognition or facial expression analysis. Automatic face detection is a difficult task because of the large face intra-class variability which is due to the important influence of the environmental conditions on the face appearance. We propose a cascade face detection method based on histograms of oriented gradients (HOG), using different kinds of features and classifier to exclude non-face step by step. The candidate feature set was constructed by HOG feature of different grain size, at different stages the support vector machine (SVM) was used as the weak classifier with different parameters. Experimental results showed a better performance compared to the state-of-the-art on CMU/MIT datasets.