Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of DNA looped domains organization during Triturus cristatus spermatogenesis

Summary Chromatin from eukaryotes is organized in DNA loops with sequential attachments to a nucleoskeleton named nuclear matrix. This organization plays major roles in replication, transcription, recombination, DNA repair, chromosome condensation and segregation. During spermatogenesis, chromatin undergoes several dynamic transitions, which are often associated with important changes not only in its physical conformation but even in its compositions and structure. To understand the periodical change in the functional organization of chromatin during spermatogenesis, the higher order organization of chromatin in different testicular cell types (pachytene spermatocytes, round spermatids) and the epididymal sperm of Triturus cristatus have been investigated. The expansion and the contraction of nucleoid DNA were measured with a fluorescence microscope following exposure of nucleoids to increasing concentrations of ethidium bromide (EtBr) (2.5–200 μg/ml) as an intercalating dye to induce DNA-positive supercoils. Nucleoids from all studied cell types exhibited a biphasic change (condensed–relaxed–condensed) in size as a consequence of exposure to increasing concentrations of EtBr, indicating that they contained negatively supercoiled DNA. At higher EtBr concentrations, maximum positive supercoiling occurred in pachytene DNA loops. Our data suggest that pachytene DNA is the most open chromatin conformation in terms of EtBr intercalation.
Fifteen-year outcome of surgery for the near angle in patients with accommodative esotropia and a high accommodative convergence to accommodation ratio.

OBJECTIVE To determine the 15-year outcome of patients with partly accommodative esotropia with a high accommodative convergence to accommodation (AC/A) ratio who underwent surgery based on the angle of esotropia at one-third meter while wearing full hyperopic correction. METHODS A retrospective chart review to determine the 15-year outcome of 25 patients whose 6-month outcome had been previously reported as part of a prospective, randomized, masked clinical trial. All patients had partly accommodative esotropia with a high AC/A ratio and underwent surgery based on their esotropia at one-third meter while wearing full-distance optical correction. RESULTS Fifteen years after surgery, 19 of the 22 patients for whom follow-up data are available had between 0 and less than 10 prism diopters of esotropia. Only 6 of the 19 needed to continue to wear optical correction to maintain satisfactory alignment; however, 8 more needed spectacles for visual purposes. Only 1 patient needed to use a bifocal add to have satisfactory alignment at one-third meter. All patients showed some degree of sensory fusion, with 4 obtaining 40 seconds of stereopsis and another 8 obtaining between 60 and 200 seconds of stereopsis. CONCLUSION Surgery for the near angle obtained with patients wearing their full hyperopic distance correction provides excellent motor and sensory results in patients with partly accommodative esotropia with a high AC/A ratio.
Improving Segment-based Speech Recognition by Recovering Missing Segments in Segment Graphs - A Thai Case Study

In segment-based speech recognition systems, the quality of the segmentation step is a major factor highly affecting their accuracies. This paper proposes methods to reduce missing segments caused by boundary insertion errors in segment graphs, which, in the case of Thai, could be generated from a probabilistic segmentation with limited speech resources. Acoustic discontinuities and manners of articulation are used to verify boundaries of the segment graph. Segments are added to the graph in the case of possible falsely detected boundaries. With the proposed insertion error eliminations, the best phonetic recognition accuracy achieved shows a 13.66% error reduction.
Architecture-Adaptable Finite ElementModelling : A Case Study using an OceanCirculation

We describe an architecture-adaptable methodology for the parallel implementation of nite element numerical models of physical systems. We use a model of time-dependent ocean currents as our working example. The heart of the computation is the solution of a banded linear system, and we describe an algorithm based on the domain decomposition method to solve the banded system. The algorithm is represented in a divide-and-conquer framework. The well-deened algebraic structure of this framework makes it relatively easy to predict the performance of the algorithm with high accuracy. Performance prediction makes possible architecture adaptability. In the case of the domain decomposition method described in this paper, performance prediction enables us to make decisions about granularity and the number of processors to use for individual steps of the algorithm. The divide-and-conquer framework facilitates easy implementation of various algorith-mic options. The process is straightforward and amenable to automation. We demonstrate the validity of this approach using two radically diierent target machines: a workstation network and a supercomputer. Our results show very good speedup on both platforms.
Fatty acids induce amylin expression and secretion by pancreatic-cells

Qi D, Cai K, Wang O, Li Z, Chen J, Deng B, Qian L, Le Y. Fatty acids induce amylin expression and secretion by pancreatic -cells. Am J Physiol Endocrinol Metab 298: E99–E107, 2010. First published October 20, 2009; doi:10.1152/ajpendo.00242. 2009. —Amylin is the major component of pancreatic amyloid, which is implicated in the development of type 2 diabetes. It is costored with insulin in the secretory granules of pancreatic -cells and cosecreted with insulin following stimulation with glucose. Here, we investigate the effect of fatty acids (FAs) on amylin expression and secretion by -cells and explore the underlying mechanisms. Palmitate and oleate dose-dependently induced amylin mRNA accumulation in murine pancreatic -cell line MIN6 and primary pancreatic islets. the inductive effect of FAs on amylin expression is independent of glucose concentration. FAs upregulated amylin expression at the transcriptional level, and FAs must be metabolized to induce amylin expression. FAs also significantly induced human amylin promoter activation. Pretreatment of MIN6 cells with Ca chelator (EGTA, BAPTA-AM) PKC inhibitor Gö-6976 or protein synthesis inhibitor cycloheximide significantly inhibited FA-induced amylin mRNA expression. Transcription factors cAMP-responsive element-binding protein, pancreatic and duodenal homeobox factor-1, and peroxisome proliferator-activated receptor were not involved in FA-induced amylin expression. Palmitate and oleate both increased amylin and insulin release from MIN6 cells and stimulated amylin expression but had no effect on insulin expression. Mice refed with Intralipid had significantly higher levels of plasma FFA, amylin, and insulin than those refed with saline. These data demonstrate that FAs differently regulate amylin and insulin expression and induce both amylin and insulin release. Ca and PKC signaling pathways and de novo-synthesized protein(s) were involved in FA-induced amylin expression. Induction of amylin production and release by FA may contribute to its biological functions under physiological conditions.
Long-time decay estimates for the Schr\"odinger equation on manifolds

In this paper we develop a quantitative version of Enss' method to establish global-in-time decay estimates for solutions to Schr\"odinger equations on manifolds. To simplify the exposition we shall only consider Hamiltonians of the form $H := - {1/2} \Delta_M$, where $\Delta_M$ is the Laplace-Beltrami operator on a manifold $M$ which is a smooth compact perturbation of three-dimensional Euclidean space $\R^3$ which obeys the non-trapping condition. We establish a global-in-time local smoothing estimate for the Schr\"odinger equation $u_t = -iHu$. The main novelty here is the global-in-time aspect of the estimates, which forces a more detailed analysis on the low and medium frequencies of the evolution than in the local-in-time theory. In particular, to handle the medium frequencies we require the RAGE theorem (which reflects the fact that $H$ has no embedded eigenvalues), together with a quantitative version of Enss' method decomposing the solution asymptotically into incoming and outgoing components, while to handle the low frequencies we need a Poincare-type inequality (which reflects the fact that $H$ has no eigenfunctions or resonances at zero).
Split-channel pipelined packet scheduling for wireless networks

To reduce medium access control (MAC) overhead and improve channel utilization, there has been extensive research on dynamically adjusting the channel access behavior of a contending station based on channel feedback information. This paper explores an alternative approach, named pipelined packet scheduling, to reduce the MAC overhead. MAC overheads can be divided into bandwidth-dependent and bandwidth-independent components and these overheads can both be reduced by using split-channel pipelining mechanisms, as demonstrated in this paper. In the past, pipelining mechanisms have not been well studied. This paper introduces two total pipelining schemes that attempt to fully pipeline contention resolution with data transmission. Further, the paper identifies shortcomings of total pipelining in the wireless environment and proposes a partial pipelining approach to overcome these shortcomings. Simulation results show that substantial performance improvement in channel utilization, average packet access delay, and access energy cost can be achieved with a properly designed scheme.
Empirical Log-Optimal Portfolio Selections: a Survey

This chapter provides a survey of discrete time, multi-period, sequential investment strategies for financial markets. Under memoryless assumption on the underlying process generating the asset prices the best rebalancing is the log-optimal portfolio, which achieves the maximal asymptotic average growth rate. We show some examples (Kelly game, horse racing, St. Petersburg game) illustrating the surprising possibilities for rebalancing. Semi-log-optimal portfolio selection as a small computational complexity alternative of the log-optimal portfolio selection is studied both theoretically and empirically. For generalized dynamic portfolio selection, when asset prices are generated by a stationary and ergodic process, universally consistent empirical methods are shown. The empirical performance of the methods are illustrated for NYSE data.
Non-Linear Returns to Schooling Among Filipino Men

The issue of possible non-linearities in the relationship between log wages and schooling has received a good deal of attention in the literature on the United States, as well as in Less Developed Countries (LDCs). In this paper, I use data from a recent household survey for the Philippines, the 1998 Annual Poverty Indicator Survey (APIS), to test the fit of the log-linear specification for Filipino men. I present results based on a number of estimation strategies, including discontinuous spline regressions, semi-parametric regressions with a large number of dummies for years of schooling and experience, and kernel regressions. The basic conclusions of the paper are two. First, there appear to be large differences between the rates of return to education across levels in the Philippines. In particular, the wage premia to both primary and secondary education are lower than those for tertiary education. Second, within a given level, the last year of schooling is disproportionately rewarded in terms of higher wages. That is, there are clear sheepskin effects associated with graduation from primary school, secondary school, and university. * Economist, East Asia and the Pacific, Poverty Reduction and Economic Management, The World Bank. 1 I would like to thank Harold Alderman, Ruperto Alonzo, Benu Bidani, Gaurav Datt, Olivier Deschenes, Emanuela Galasso, Hans Hoogeveen, Emmanuel Jimenez, Homi Kharas, Erzo Luttmer, Tamar Manuelyan Atinc, and Lant Pritchett for many useful comments and conversations. Please address correspondence to the author at nschady@worldbank.org. The views and interpretations expressed in this paper are those of the author and do not necessarily represent the views and interpretations of the World Bank, its Executive Directors, or the countries they represent.
LR-GAN: Layered Recursive Generative Adversarial Networks for Image Generation

We present LR-GAN: an adversarial image generation model which takes scene structure and context into account. Unlike previous generative adversarial networks (GANs), the proposed GAN learns to generate image background and foregrounds separately and recursively, and stitch the foregrounds on the background in a contextually relevant manner to produce a complete natural image. For each foreground, the model learns to generate its appearance, shape and pose. The whole model is unsupervised, and is trained in an end-to-end manner with gradient descent methods. The experiments demonstrate that LR-GAN can generate more natural images with objects that are more human recognizable than DCGAN.
End-to-End Weakly-Supervised Semantic Alignment

We tackle the task of semantic alignment where the goal is to compute dense semantic correspondence aligning two images depicting objects of the same category. This is a challenging task due to large intra-class variation, changes in viewpoint and background clutter. We present the following three principal contributions. First, we develop a convolutional neural network architecture for semantic alignment that is trainable in an end-to-end manner from weak image-level supervision in the form of matching image pairs. The outcome is that parameters are learnt from rich appearance variation present in different but semantically related images without the need for tedious manual annotation of correspondences at training time. Second, the main component of this architecture is a differentiable soft inlier scoring module, inspired by the RANSAC inlier scoring procedure, that computes the quality of the alignment based on only geometrically consistent correspondences thereby reducing the effect of background clutter. Third, we demonstrate that the proposed approach achieves state-of-the-art performance on multiple standard benchmarks for semantic alignment.
T-cell suppression mediated by regulatory T cells infiltrating hepatic tumors can be overcome by GITRL treatment

Recently, we reported the accumulation of CD4+FOXP3+ regulatory T cells (Tregs) within the tumor mass of patients bearing liver cancer. Tumor-infiltrating Tregs (TiTregs) are active and potent suppressors of antitumor immunity. Importantly, treatment with GITRL reduced the immunosuppression mediated by TiTregs.
Is Growth-Discordance in Twins a Substantial Risk Factor in Adverse Neonatal Outcomes?

To evaluate whether growth discordance is an independent risk factor in the neonatal outcome of the smaller twin, all medical records of twin pregnancies delivered between 26 and 41 weeks during a 5-year period (January 2004–December 2008) were reviewed. Among the 49 selected twins, weight discordance was 15–20% in 7 infants, 21–30% in 16 infants, 31–40% in 16 infants and > 40% in 10 infants. No significant differences between the four groups were found with regards to obstetric complications and neonatal disease. Occurrence of birthweight below the 10th percentile and rate of admission to the neonatal intensive care unit significantly increased as intra-pair birthweight difference increased (p = .03). The > 40% discordant group had a significantly lower gestational age (p = .03), lower birthweight (p = .007) and a significantly higher mortality rate (4/10 versus 3/39 p = .04) in comparison with the other discordant groups. Multiple logistic regression analysis showed that birthweight was the single independent and consistent factor associated with elevated risks of mortality. For every 250 g increase in birthweight, the risk for mortality decreased by about 84% [RR 0.16(CI 0.00-0.70)]. Gestational age was the most reliable predictor for major neonatal complications. For every 1-week increase in gestational age a significant decreased risk for all outcomes was found. Discordance alone should not be considered as a predictor for adverse neonatal outcome. Neonatal outcome in discordant twins appears to be related to gestational age and birthweight rather than to the degree of discordance.
Characterization of Aldehyde Oxidase Enzyme Activity in Cryopreserved Human Hepatocytes

Substrates of aldehyde oxidase (AO), for which human clinical pharmacokinetics are reported, were selected and evaluated in pooled mixed-gender cryopreserved human hepatocytes in an effort to quantitatively characterize AO activity. Estimated hepatic clearance (Clh) for BIBX1382, carbazeran, O6-benzylguanine, zaleplon, and XK-469 using cryopreserved hepatocytes was 18, 17, 12, <4.3, and <4.3 ml · min−1 · kg−1, respectively. The observed metabolic clearance in cryopreserved hepatocytes was confirmed to be a result of AO-mediated metabolism via two approaches. Metabolite identification after incubations in the presence of H218O confirmed that the predominant oxidative metabolite was generated by AO, as expected isotope patterns in mass spectra were observed after analysis by high-resolution mass spectrometry. Second, clearance values were efficiently attenuated upon coincubation with hydralazine, an inhibitor of AO. The low exposure after oral doses of BIBX1382 and carbazeran (∼5% F) would have been fairly well predicted using simple hepatic extraction (fh) values derived from cryopreserved hepatocytes. In addition, the estimated hepatic clearance value for O6-benzylguanine was within ∼80% of the observed total clearance in humans after intravenous administration (15 ml · min−1 · kg−1), indicating a reasonable level of quantitative activity from this in vitro system. However, a 3.5-fold underprediction of total clearance was observed for zaleplon, despite the 5-oxo metabolite being clearly observed. These data taken together suggest that the use of cryopreserved hepatocytes may be a practical approach for assessing AO-mediated metabolism in discovery and potentially useful for predicting hepatic clearance of AO substrates.
Sensing/Decision-Based Cooperative Relaying Schemes With Multi-Access Transmission: Stability Region And Average Delay Characterization

We consider a cooperative relaying system which consists of a number of source terminals, one shared relay, and a common destination with multi-packet reception (MPR) capability. In this paper, we study the stability and delay analysis for two cooperative relaying schemes; the sensing-based cooperative (SBC) scheme and the decision-based cooperative (DBC) scheme. In the SBC scheme, the relay senses the channel at the beginning of each time slot. In the idle time slots, the relay transmits the packet at the head of its queue, while in the busy one, the relay decides either to transmit simultaneously with the source terminal or to listen to the source transmission. The SBC scheme is a novel paradigm that utilizes the spectrum more efficiently than the other cooperative schemes because the relay not only exploits the idle time slots, but also has the capability to mildly interfere with the source terminal. On the other hand, in the DBC scheme, the relay does not sense the channel and it decides either to transmit or to listen according to certain probabilities. Numerical results reveal that the two proposed schemes outperform existing cooperative schemes that restrict the relay to send only in the idle time slots. Moreover, we show how the MPR capability at the destination can compensate for the sensing need at the relay, i.e., the DBC scheme achieves almost the same stability region as that of the SBC scheme. Furthermore, we derive the condition under which the two proposed schemes achieve the same maximum stable throughput.
Antiretroviral Outcomes in South African Prisoners: A Retrospective Cohort Analysis

Background and Methods Little is known about antiretroviral therapy (ART) outcomes in prisoners in Africa. We conducted a retrospective review of outcomes of a large cohort of prisoners referred to a public sector, urban HIV clinic. The review included baseline characteristics, sequential CD4 cell counts and viral load results, complications and co-morbidities, mortality and loss to follow-up up to 96 weeks on ART. Findings 148 inmates (133 male) initiated on ART were included in the study. By week 96 on ART, 73% of all inmates enrolled in the study and 92% of those still accessing care had an undetectable viral load (<400copies/ml). The median CD4 cell count increased from 122 cells/mm3 at baseline to 356 cells/mm3 by 96 weeks. By study end, 96 (65%) inmates had ever received tuberculosis (TB) therapy with 63 (43%) receiving therapy during the study: 28% had a history of TB prior to ART initiation, 33% were on TB therapy at ART initiation and 22% developed TB whilst on ART. Nine (6%) inmates died, 7 in the second year on ART. Loss to follow-up (LTF) was common: 14 (9%) patients were LTF whilst still incarcerated, 11 (7%) were LTF post-release and 9 (6%) whose movements could not be traced. 16 (11%) inmates had inter-correctional facility transfers and 34 (23%) were released of whom only 23 (68%) returned to the ART clinic for ongoing follow-up. Conclusions Inmates responded well to ART, despite a high frequency of TB/HIV co-infection. Attention should be directed towards ensuring eligible prisoners access ART programs promptly and that inter-facility transfers and release procedures facilitate continuity of care. Institutional TB control measures should remain a priority.
Cross-Country Inequality Trends

The economics profession has made considerable progress in understanding the increase in wage inequality in the U.S. and the UK over the past several decades, but currently lacks a consensus on why inequality did not increase, or increased much less, in (continental) Europe over the same time period. I review the two most popular explanations for these differential trends: that relative supply of skills increased faster in Europe, and that European labor market institutions prevented inequality from increasing. I argue that these two explanations go some way towards accounting for the differential cross-country inequality trends, but do not provide an entirely satisfactory explanation. In addition, it appears that relative demand for skills increased differentially across countries. Motivated by this reasoning, I develop a simple theory where labor market institutions creating wage compression in Europe also encourage more investment in technologies increasing the productivity of less-skilled workers, thus implying less skill-biased technical change in Europe than in the U.S.