Miracle-dz/UniFAR-FTUs huggingface dataset:
Low-redshift quasar Lyα absorption-line systems associated with galaxies

In this paper we present semi-analytic models and Monte-Carlo simulations of QSO Lyabsorption line systems which originate in gaseous galactic haloes, galaxy discs and dark matter (DM) satellites around big central haloes. The aim is to estimate the number density per unit redshift of Lyabsorption lines related with galaxies and to investigate the properties of the predicted galaxy/absorber systems, such as equivalent widths Wr, projected distances �, galaxy luminosities LB, as well as absorber redshifts z. It is found that for strong Lyabsorption lines (Wr � 0.3u galactic haloes and satellites can explain � 20 per cent and 40 per cent of the line number density of the HST QSO Absorption Line Key Project respectively. The population of DM satellites is adopted from numerical simulations by Klypin et al. (1999). If big galaxies indeed possess such large numbers of DM satellites and they possess gas, these satellites may play an important role for strong Lylines. However the predicted number density of Lyman-limit systems by satellites is � 0.1 (per unit redshift), which is four times smaller than that by halo clouds. Including galactic haloes, satellites and HI discs of spirals, the predicted number density of strong lines can be as much as 60 per cent of the HST result. The models can also predict all of the observed Lyman-limit systems. For strong lines the average covering factor within 250h 1 kpc is estimated to be � 0.36, which is in good agreement with observations. And the effective absorption radius of a galaxy (with unit covering factor) is estimated to be � 150h 1 kpc. There exist correlations of Wr versus �, LB and z. The models predict Wr / � � L � (1+z) with � � 0.5,� � 0.15, � 0.5. To compare with results of imaging and spectroscopic surveys, we study the se- lection effects of selection criteria similar to the surveys. We simulate mock observa- tions through known QSO lines-of-sight and find that selection effects can statistically tighten the dependence of line width on projected distance. This result confirms pre- vious suggestions in the literature. After applying selection criteria, the models can predict similar distributions of Wr, �, LB, absolute magnitudes and absorber red- shifts to those of imaging and spectroscopic surveys. Finally we find that the total redshift interval of present observations (� 5) is not large enough for the models to reveal the real relationships if adopting the selection criteria. An adequate total red- shift interval might be � 10. This may conciliate contraditious conclusions about the anti-correlation of equivalent widths versus projected distances by different authors.
Association study of paroxetine therapeutic response with SERT gene polymorphisms in patients with major depressive disorder

We investigated the relationships between LS promoter (SERTPR) and ls intron2 (SERTin2) genetic variants of serotonin transporter (SERT) polymorphisms with treatment response in 130 patients with major depressive disorder (MDD) treated with paroxetine (20 mg/day) for 6 weeks. To assess and evaluate therapeutic response to paroxetine all patients were rated weekly using the HAMD-17 scale. Responders were defined as those subjects with a decrease in HAMD scale by≥50% at week 6 of treatment. Comparison of genotypes and alleles frequency of the SERTPR between responders and non-responders revealed significant differences among genotypes and overrepresentation of the S allele in the group of non-responders (P=0.0004). SERTin2-ss genotype bearing subjects showed better treatment response compared to ls and ll genotype from the fourth week of treatment (P=0.035). Statistical differences were also found in distributions of the estimated haplotypes between responders and non-responders, while subsequent analysis revealed overrepresentation of S/l haplotype (P=0.006) in the group of non-responders. SERTPR and SERTin2 were found to be in linkage disequilibrium in studied population. These findings identify genetic factors associated with paroxetine treatment response in MDD patients.
Diagnostic Value of Immunohistochemical IMP3 Expression in Core Needle Biopsies of Pancreatic Ductal Adenocarcinoma

The oncofetal protein, insulin-like growth factor II messenger ribonucleic acid-binding protein 3 (IMP3), has been analyzed in many different tumors. Various studies have found that IMP3 is a marker for malignancy and is correlated with increased tumor aggressiveness and reduced overall survival. The diagnosis of pancreatic ductal adenocarcinoma (PDAC) in core needle biopsies can be challenging, and immunohistochemical markers are needed. We studied IMP3 expression in 177 core needle biopsies of the pancreas, including 112 PDACs, 55 cases with chronic sclerosing pancreatitis, and 10 biopsies with tumor-free pancreatic tissue without inflammation. An additional 18 biopsies of PDAC metastases (16 liver biopsies and 2 lymph node biopsies) were analyzed. To study IMP3 expression in large tissue sections, 45 pancreatic resection specimens (26 with PDAC and 19 with chronic sclerosing pancreatitis) were investigated. In contrast to normal or inflamed pancreatic tissue, which was negative in 47 of 65 (72.3%) cases and weakly positive in 15 of 65 (23.1%) cases, strong IMP3 expression was found in 99 of 112 (88.4%) PDACs. Therefore, sensitivity and specificity of IMP3 expression in the differential diagnosis of PDAC and chronic sclerosing pancreatitis using core needle biopsies were found to be 88.4% and 94.6%, respectively. These results were confirmed in the pancreas resection specimens. Furthermore, strong IMP3 expression was found in 17 of 18 (94.4%) of the PDAC metastases that were analyzed. Our study shows that IMP3 is an easy to use and potentially new immunohistochemical marker for the diagnosis of PDAC in core needle biopsies.
Dendritic Excitability and Gain Control in Recurrent Cortical Microcircuits

Layer 5 thick tufted pyramidal cells (TTCs) in the neocortex are particularly electrically complex, owing to their highly excitable dendrites. The interplay between dendritic nonlinearities and recurrent cortical microcircuit activity in shaping network response is largely unknown. We simulated detailed conductance-based models of TTCs forming recurrent microcircuits that were interconnected as found experimentally; the network was embedded in a realistic background synaptic activity. TTCs microcircuits significantly amplified brief thalamocortical inputs; this cortical gain was mediated by back-propagation activated N-methyl-d-aspartate depolarizations and dendritic back-propagation-activated Ca2+ spike firing, ignited by the coincidence of thalamic-activated somatic spike and local dendritic synaptic inputs, originating from the cortical microcircuit. Surprisingly, dendritic nonlinearities in TTCs microcircuits linearly multiplied thalamic inputs—amplifying them while maintaining input selectivity. Our findings indicate that dendritic nonlinearities are pivotal in controlling the gain and the computational functions of TTCs microcircuits, which serve as a dominant output source for the neocortex.
A multiple population XCS: Evolving condition-action rules based on feature space partitions

XCS is an accuracy-based machine learning technique, which combines reinforcement learning and evolutionary algorithms to evolve a set of classifiers (or rules) for pattern classification tasks. In this paper, we investigate the effects of alternative feature space partitioning techniques in a multiple population island-based parallel XCS. Here, each of the isolated populations evolve rules based on a subset of the features. The behavior of the multiple population model is carefully analyzed and compared with the original XCS using the Boolean logic multiplexer problem as a test case. Simulation results show that our multiple population XCS produced better performance and better generalization than the single population XCS model, especially when the problem increased in size. A caveat, however, is that the effectiveness of the model was dependent upon the feature space partitioning strategy used.
A threshold requirement for Gbx2 levels in hindbrain development

Gbx2 is a homeobox gene that plays a crucial role in positioning the mid/hindbrain organizer (isthmus), which regulates midbrain and cerebellar development primarily through the secreted factor FGF8. In Gbx2 null homozygotes, rhombomeres (r) 1-3 fail to develop and the isthmic expression of Fgf8 is reduced and disorganized. These mutants fail to form a cerebellum, as it is derived from r1. Here, we analyze mice homozygous for a Gbx2 hypomorphic allele (Gbx2neo). Quantitative RT-PCR and RNA in situ analyses indicate that the presence of a neo-resistance cassette impairs normal Gbx2 splicing thus reducing wild-type Gbx2 mRNA levels to 6-10% of normal levels in all domains and stages examined. In Gbx2 hypomorphic mutants, gene marker and neuronal patterning analyses indicate that reduced Gbx2 expression is sufficient to support the development of r3 but not r2. The posterior region of r1, from which the lateral cerebellum develops, is unaffected in these mutants. However, the anterior region of r1 is converted to an isthmus-like tissue. Hence, instead of expressing r1 markers, this region displays robust expression of Fgf8 and Fgf17, as well as the downstream FGF targets Spry1 and Spry4. Additionally, we demonstrate that the cell division regulator cyclin D2 is downregulated, and that cellular proliferation is reduced in both the normal isthmus and in the mutant anterior r1. As a result of this transformation, the cerebellar midline fails to form. Thus, our studies demonstrate different threshold requirements for the level of Gbx2 gene product in different regions of the hindbrain.
Simulations of Supersonic Turbulence in Molecular Clouds: Evidence for a New Universality

We use three-dimensional simulations to study the statistics of supersonic turbulence in molecular clouds. Our numerical experiments describe driven turbulent flows with an isothermal equation of state, Mach numbers around 10, and various degrees of magnetization. We first support the so-called 1/3-rule of Kritsuk et al. 2007 with our new data from a larger 2048^3 simulation. We then attempt to extend the 1/3-rule to supersonic MHD turbulence and get encouraging preliminary results based on a set of 512^3 simulations. Our results suggest an interesting new approach to tackle universal scaling relations and intermittency in supersonic MHD turbulence.
Reducing Cache Traffic and Energy with Macro Data Load

This paper presents a study on macro data load, an efficient mechanism to enhance loaded value reuse. A macro data load brings into the processor a maximum-width data value the cache port allows, saves it in an internal structure, and facilitates reuse by later loads. A comprehensive limit study using a generalized memory value reuse table (MVRT) shows the significantly increased reuse opportunities provided by macro data load. We also describe a modified load store queue design as an implementation of the proposed concept. Our quantitative study shows that over 35% of L1 cache accesses in the SPEC2k integer and MiBench programs can be eliminated, resulting in a related energy reduction of 24% and 35% on average, respectively
Using humans as sensors: An estimation-theoretic perspective

The explosive growth in social network content suggests that the largest “sensor network” yet might be human. Extending the participatory sensing model, this paper explores the prospect of utilizing social networks as sensor networks, which gives rise to an interesting reliable sensing problem. In this problem, individuals are represented by sensors (data sources) who occasionally make observations about the physical world. These observations may be true or false, and hence are viewed as binary claims. The reliable sensing problem is to determine the correctness of reported observations. From a networked sensing standpoint, what makes this sensing problem formulation different is that, in the case of human participants, not only is the reliability of sources usually unknown but also the original data provenance may be uncertain. Individuals may report observations made by others as their own. The contribution of this paper lies in developing a model that considers the impact of such information sharing on the analytical foundations of reliable sensing, and embed it into a tool called Apollo that uses Twitter as a “sensor network” for observing events in the physical world. Evaluation, using Twitter-based case-studies, shows good correspondence between observations deemed correct by Apollo and ground truth.
Islet Oxygen Consumption Rate (OCR) Dose Predicts Insulin Independence in Clinical Islet Autotransplantation

Background Reliable in vitro islet quality assessment assays that can be performed routinely, prospectively, and are able to predict clinical transplant outcomes are needed. In this paper we present data on the utility of an assay based on cellular oxygen consumption rate (OCR) in predicting clinical islet autotransplant (IAT) insulin independence (II). IAT is an attractive model for evaluating characterization assays regarding their utility in predicting II due to an absence of confounding factors such as immune rejection and immunosuppressant toxicity. Methods Membrane integrity staining (FDA/PI), OCR normalized to DNA (OCR/DNA), islet equivalent (IE) and OCR (viable IE) normalized to recipient body weight (IE dose and OCR dose), and OCR/DNA normalized to islet size index (ISI) were used to characterize autoislet preparations (n = 35). Correlation between pre-IAT islet product characteristics and II was determined using receiver operating characteristic analysis. Results Preparations that resulted in II had significantly higher OCR dose and IE dose (p<0.001). These islet characterization methods were highly correlated with II at 6–12 months post-IAT (area-under-the-curve (AUC) = 0.94 for IE dose and 0.96 for OCR dose). FDA/PI (AUC = 0.49) and OCR/DNA (AUC = 0.58) did not correlate with II. OCR/DNA/ISI may have some utility in predicting outcome (AUC = 0.72). Conclusions Commonly used assays to determine whether a clinical islet preparation is of high quality prior to transplantation are greatly lacking in sensitivity and specificity. While IE dose is highly predictive, it does not take into account islet cell quality. OCR dose, which takes into consideration both islet cell quality and quantity, may enable a more accurate and prospective evaluation of clinical islet preparations.
The Prognostic Value and Reproducibility of the Radiological Features of the Fractured Scaphoid

We investigated whether the radiological features of the fractured scaphoid could be reproducibly measured and used to predict the likelihood of union with conservative plaster cast immobilization. We found that the inter- and intra-observer reproducibility of the Compson, Herbert and Russe classification systems were only fair and that none predicted fracture union. Assessments of fracture level, comminution and displacement showed moderate inter- and intra-observer reproducibility but did not predict the likelihood of fracture union. We conclude that the radiological features of acute scaphoid fractures cannot be used to predict the likelihood of fracture union.
Force pattern characterisation of Caenorhabditis elegans in motion

Caenorhabditis elegans is a worm that could be mutated to have different muscle arms, which may generate distinct force patterns when the worm moves. In this paper, an integrated system employing both a novel PDMS device and a visual feedback from the device is reported. The silicone elastomer-based PDMS device consists of arrays of pillars, which form open channels for the worm to move in and bend the pillars in contact. Enabled by a single vision sensor (CCD/CMOS) camera, the computer vision system is able to transform the forces generated by C. elegans, through detecting the deflection of the pillars with sub-pixel accuracy. The experimental results demonstrate that the current vision-based force sensing system is capable of performing robust force measurements at a full 30 Hz with a 1.52 μN resolution. The framework has the potential to significantly facilitate the study on the relationship between muscle arms and force patterns of C. elegans in motion, and thus gives a better understanding of muscle arms development and modelling.
Influence of the Environment on Body Temperature of Racing Greyhounds

Heat strain is a potential risk factor for racing greyhounds in hot climates. However, there have been limited studies into the incidence of heat strain (when excess heat causes physiological or pathological effects) in racing greyhounds. The aim of this study was to determine if heat strain occurs in racing greyhounds, and, if so, whether environmental factors (e.g., ambient temperature and relative humidity) or dog-related factors (e.g., sex, bodyweight, color) are associated with the risk of heat strain. A total of 229 greyhounds were included in over 46 race meetings and seven different race venues in South Australia, Australia. Rectal temperatures of dogs were measured pre- and postrace and urine samples collected for analysis of myoglobinuria. Ambient temperature at race times ranged between 11.0 and 40.8°C and relative humidity ranged from 17 to 92%. There was a mean increase in greyhound rectal temperature of 2.1°C (range 1.1–3.1°C). A small but significant association was present between ambient temperature and increase in rectal temperature (r2 = 0.033, P = 0.007). The mean ambient temperature at race time, of dogs with postrace rectal temperature of or exceeding 41.5°C, was significantly greater than at race time of dogs with a postrace rectal temperature ≤41.5°C (31.2 vs. 27.3°C, respectively, P = 0.004). When the ambient temperature reached 38oC, over one-third (39%) of dogs had a rectal temperature >41.5°C. Over half of postrace urine samples were positive by Dipstick reading for hemoglobin/myoglobin, and of 77 urine samples positive for Dipstick readings, 95% were positive for myoglobin. However, urinary myoglobin levels were not associated with ambient temperature or postrace rectal temperatures. The mean increase in rectal temperature was greater in dark (black, blue, brindle) than light (fawn and white) colored greyhounds. The results suggest heat strain occurs in racing greyhounds, evidenced by postrace rectal temperatures over 41.5°C and postrace myoglobinuria. Risk of heat strain may be increased in higher ambient temperatures and in darker colored greyhounds. Further research into the incidence of heat strain in racing greyhounds, and longer term physiological responses to heat strain, are warranted.
Association Analysis in Rice: From Application to Utilization

Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding.
Non-Detection of Human Herpesvirus 8 (HHV-8) DNA in HHV-8-Seropositive Blood Donors from Three Brazilian Regions

Human herpesvirus 8 (HHV-8), also known as Kaposi's sarcoma-associated herpesvirus (KSHV), is the etiologic agent of all forms of Kaposi's sarcoma, primary effusion lymphoma and the plasmablastic cell variant of multicentric Castleman disease. In endemic areas of sub-Saharan Africa, blood transfusions have been associated with a substantial risk of HHV-8 transmission. By contrast, several studies among healthy blood donors from North America have failed to detect HHV-8 DNA in samples of seropositive individuals. In this study, using a real-time PCR assay, we investigated the presence of HHV-8 DNA in whole-blood samples of 803 HHV-8 blood donors from three Brazilian states (São Paulo, Amazon, Bahia) who tested positive for HHV-8 antibodies, in a previous multicenter study. HHV-8 DNA was not detected in any sample. Our findings do not support the introduction of routine HHV-8 screening among healthy blood donors in Brazil. (WC = 140).
The chicken type III GnRH receptor homologue is predominantly expressed in the pituitary, and exhibits similar ligand selectivity to the type I receptor

Two GnRH isoforms (cGnRH-I and GnRH-II) and two GnRH receptor subtypes (cGnRH-R-I and cGnRH-R-III) occur in chickens. Differential roles for these molecules in regulating gonadotrophin secretion or other functions are unclear. To investigate this we cloned cGnRH-R-III from a broiler chicken and compared its structure, expression and pharmacological properties with cGnRH-R-I. The broiler cGnRH-R-III cDNA was 100% identical to the sequence reported in the red jungle fowl and white leghorn breed. Pituitary cGnRH-R-III mRNA was ∼1400-fold more abundant than cGnRH-R-I mRNA. Northern analysis indicated a single cGnRH-R-III transcript. A pronounced sex and age difference existed, with higher pituitary transcript levels in sexually mature females versus juvenile females. In contrast, higher expression levels occurred in juvenile males versus sexually mature males. Functional studies in COS-7 cells indicated that cGnRH-R-III has a higher binding affinity for GnRH-II than cGnRH-I (Kd: 0·57 vs 19·8 nM) with more potent stimulation of inositol phosphate production (ED50: 0·8 vs 4·38 nM). Similar results were found for cGnRH-R-I, (Kd: 0·51 vs 10·8 nM) and (ED50: 0·7 vs 2·8 nM). The initial rate of internalisation was faster for cGnRH-R-III than cGnRH-R-I (26 vs 15·8%/min). Effects of GnRH antagonists were compared at the two receptors. Antagonist #27 distinguished between cGnRH-R-I and cGnRH-R-III (IC50: 2·3 vs 351 nM). These results suggest that cGnRH-R-III is probably the major mediator of pituitary gonadotroph function, that antagonist #27 may allow delineation of receptor subtype function in vitro and in vivo and that tissue-specific recruitment of cGnRH-R isoforms has occurred during evolution.
Information Processing by a Noisy Binary ChannelElka Korutcheva

We study the information processing properties of a binary channel receiving data from a gaussian source. A systematic comparison with linear processing is done. A remarkable property of the binary sytem is that, as the ratio between the number of output and input units increases, binary processing becomes equivalent to linear processing with a quantization output noise that depends on. In this regime , that holds up to O(? 4) , information processing occurs as if populations of binary units cooperate to represent one-bit output unit. Unsupervised learning of a noisy environment by optimization of the parameters of the binary channel is also considered.