Miracle-dz/UniFAR-FTUs huggingface dataset:
Fisher and Shannon Information in Finite Neural Populations

The precision of the neural code is commonly investigated using two families of statistical measures: Shannon mutual information and derived quantities when investigating very small populations of neurons and Fisher information when studying large populations. These statistical tools are no longer the preserve of theorists and are being applied by experimental research groups in the analysis of empirical data. Although the relationship between information-theoretic and Fisher-based measures in the limit of infinite populations is relatively well understood, how these measures compare in finite-size populations has not yet been systematically explored. We aim to close this gap. We are particularly interested in understanding which stimuli are best encoded by a given neuron within a population and how this depends on the chosen measure. We use a novel Monte Carlo approach to compute a stimulus-specific decomposition of the mutual information (the SSI) for populations of up to 256 neurons and show that Fisher information can be used to accurately estimate both mutual information and SSI for populations of the order of 100 neurons, even in the presence of biologically realistic variability, noise correlations, and experimentally relevant integration times. According to both measures, the stimuli that are best encoded are those falling at the flanks of the neuron's tuning curve. In populations of fewer than around 50 neurons, however, Fisher information can be misleading.
Axonal-SMN (a-SMN), a protein isoform of the survival motor neuron gene, is specifically involved in axonogenesis

Spinal muscular atrophy (SMA) is an autosomal recessive disease of childhood due to loss of the telomeric survival motor neuron gene, SMN1. The general functions of the main SMN1 protein product, full-length SMN (FL-SMN), do not explain the selective motoneuronal loss of SMA. We identified axonal-SMN (a-SMN), an alternatively spliced SMN form, preferentially encoded by the SMN1 gene in humans. The a-SMN transcript and protein are down-regulated during early development in different tissues. In the spinal cord, the a-SMN protein is selectively expressed in motor neurons and mainly localized in axons. Forced expression of a-SMN stimulates motor neuron axonogenesis in a time-dependent fashion and induces axonal-like growth in non-neuronal cells. Exons 2b and 3 are essential for the axonogenic effects. This discovery indicates an unexpected complexity of the SMN gene system and may help in understanding the pathogenesis of SMA.
Disclosure of researcher allegiance in meta-analyses and randomised controlled trials of psychotherapy: a systematic appraisal

Objective Psychotherapy research may suffer from factors such as a researcher’s own therapy allegiance. The aim of this study was to evaluate if researcher allegiance (RA) was reported in meta-analyses and randomised controlled trials (RCTs) of psychotherapeutic treatments. Design Systematic approach using meta-analyses of different types of psychotherapies. Data sources Medline, PsycINFO and Cochrane Database of Systematic Reviews. Methods We evaluated meta-analyses of RCTs regarding various types of psychotherapies. Meta-analyses were eligible if they included at least one RCT with RA and they were published in journals in Medline, PsycINFO and Cochrane Database of Systematic Reviews with an impact factor larger than 5. Results We identified 146 eligible meta-analyses that synthesised data from a total of 1198 unique RCTs. Only 25 of the meta-analyses (17.2%) reported allegiance and only 6 (4.1%) used a proper method to control its effect. Of the 1198 eligible primary RCTs, 793 (66.3%) were allegiant. Authors in 25 of these 793 RCTs (3.2%) reported their allegiance while only one study (0.2%) controlled for its effect. Conclusions The vast majority among a group of published meta-analyses and RCTs of psychotherapeutic treatments seldom reported and evaluated the allegiance effect. The results of the present study highlight a major lack of this information in meta-analyses and their included studies, though meta-analyses perform slightly better than RCTs. Stringent guidelines should be adopted by journals in order to improve reporting and attenuate possible effects of RA in future research.
Difusión de la innovación: la red social y el enfoque de aprendizaje organizativo para la gobernanza de un equipo de liderazgo de todo el distrito

District and school leaders play particularly important roles in leading districtwide improvement, as they are increasingly held accountable for bringing about change and improvement for educational innovation and excellence. While conventional districtwide governance places much of its focus on technical and administrative matters such as policy development, supervision, and monitoring progress. This technical focus often overlooks the fundamental aspect that drives the progress of improvement—the social infrastructure shaped by interpersonal relationship. Responding to recent scholarships that calls for a networked approach to governance, this study examined the change effort of a districtwide leadership team over three points in time drawing on social network theory and analysis focused on district governance. Specifically, we focused on the type of interpersonal relationship in which leaders engaged with each other in sharing and exchanging innovative ideas as these efforts may support better governance. Additionally, we explored organizational learning as a way to examine climate in support of districtwide innovative efforts during change process. Our findings from leaders indicated increased innovative behaviors and perceived climate on organizational learning over time. The findings suggested that leaders increased connections around risk taking, regardless of their work level over time. This increased connectedness around innovation was coupled with an increase in leaders’ perception of the district’s learning climate, suggesting a cohesive approach to governance and improvement.
Phenomenological Vessel Scattering Study Based on Simulated Inverse SAR Imagery

This paper presents a study on the origin of the dominating scattering mechanisms observed in polarimetric synthetic aperture radar (SAR) images of ships. The study has been made by using numerical simulations, which have been carried out with a radar cross section (RCS) prediction tool (GRaphical Electromagnetic COmputing) and a SAR simulator. Extensive series of simulations has been run for realistic 3-D geometrical models of ships with various sizes. Different radar parameters, aspect angles, and sea surface states have been considered in the scenario. Data analysis with coherent target decompositions has indicated characteristic polarimetric signatures for particular ships within a specific range of viewing angles. This happens at highly oblique incidences where the responses appear to be less sensitive to changes in the operating frequency and bearing angles. Under such conditions, ship scattering can be schematized by the distribution of a set of guide scatterers with high RCS. Their positions and polarimetric characteristics are quantitatively summarized in a new feature vector, which has been proposed to be the basis for classification algorithms. Key ideas about this vector are presented at the end of this paper, jointly with some examples related to three different ships. Recent publications have shown that they can be successfully cast within a new unsupervised vessel classification scheme.
Survival after extended thymectomy for thymoma.

OBJECTIVES Thymoma is a relatively rare tumour and is uniquely associated with autoimmune diseases such as myasthenia gravis (MG). However, the factors involved in the prognosis of thymoma remain under discussion. METHODS We retrospectively reviewed 162 patients who underwent extended thymectomy via median sternotomy for thymoma at our institute from 1976 to 2009. The histological subtype was classified according to the World Health Organization (WHO) histological classification system. Survival analysis was performed using the Kaplan-Meier method and the Cox proportional hazards model. RESULTS Tumours comprised 7 Type A tumours, 38 Type AB, 49 Type B1, 45 Type B2 and 23 Type B3. Various types of autoimmune diseases were comorbid in 66 patients. The median follow-up period was 94 months, and 14 patients experienced recurrence. Seven patients died of recurrent tumour, and 18 patients died of causes other than thymoma. The 10-year overall survival was 85.7%, and the 10-year disease-free survival (DFS) was 76.8%. The 10-year DFS was 62.5% for Type A, 86.3% for Type AB, 91.5% for Type B1, 77.1% for Type B2 and 26.3% for Type B3. In multivariate analysis, age, Type B3 and MG were determined as prognostic factors for survival. On the other hand, Masaoka's stage did not influence survival. CONCLUSIONS Type B3 classified by the WHO histological classification system is a poor prognostic factor for survival of thymoma after extended thymectomy. Association with MG is possibly an indicator of poor survival. Age is an independent prognostic factor, suggesting favourable prognosis of thymoma after surgical treatment. Considering thymoma is a rare tumour, it would be necessary to build a multi-institutional database as soon as possible.
Pathogen Associated Molecular Pattern (PAMP)-Triggered Immunity Is Compromised under C-Limited Growth

In the interaction between plants and pathogens, carbon (C) resources provide energy and C skeletons to maintain, among many functions, the plant immune system. However, variations in C availability on pathogen associated molecular pattern (PAMP) triggered immunity (PTI) have not been systematically examined. Here, three types of starch mutants with enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000 hrcC were examined for PTI. In a dark period-dependent manner, the mutants showed compromised induction of a PTI marker, and callose accumulation in response to the bacterial PAMP flagellin, flg22. In combination with weakened PTI responses in wild type by inhibition of the TCA cycle, the experiments determined the necessity of C-derived energy in establishing PTI. Global gene expression analyses identified flg22 responsive genes displaying C supply-dependent patterns. Nutrient recycling-related genes were regulated similarly by C-limitation and flg22, indicating re-arrangements of expression programs to redirect resources that establish or strengthen PTI. Ethylene and NAC transcription factors appear to play roles in these processes. Under C-limitation, PTI appears compromised based on suppression of genes required for continued biosynthetic capacity and defenses through flg22. Our results provide a foundation for the intuitive perception of the interplay between plant nutrition status and pathogen defense.
Antioxidant Pre-Treatment Reduces the Toxic Effects of Oxalate on Renal Epithelial Cells in a Cell Culture Model of Urolithiasis

Urolithiasis is characterized by the formation and retention of solid crystals within the urinary tract. Kidney stones are mostly composed of calcium oxalate, which predominantly generates free radicals that are toxic to renal tubular cells. The aim of the study is to explore possible effects of antioxidant pre-treatment on inhibition of oxidative stress. Three cell lines were used as in vitro model of urolithiasis: MDCK I, MDCK II and LLC-PK1. Oxidative stress was induced by exposure of cells to sodium oxalate in concentration of 8 mM. In order to prevent oxidative stress, cells were pre-treated with three different concentrations of l-arginine and vitamin E. Oxidative stress was evaluated by determining the expression of superoxide dismutase (SOD), osteopontin (OPN), and by the concentration of glutathione (GSH). In all three cell lines, pre-treatment of antioxidants increased cell survival. Positive correlation of SOD and OPN expression as well as GSH concentration was observed in all groups of cells. Our results indicate that an antioxidant pre-treatment with l-arginine and vitamin E is able to hamper oxalate-induced oxidative stress in kidney epithelial cells and as such could play a role in prevention of urolithiasis.
D2 dissection in laparoscopic and open gastrectomy for gastric cancer.

AIM To evaluate the radicalness and safety of laparoscopic D2 dissection for gastric cancer. METHODS Clinicopathological data from 209 patients with gastric cancer, who underwent radical gastrectomy with D2 dissection between January 2007 and February 2011, were analyzed retrospectively. Among these patients, 131 patients underwent laparoscopy-assisted gastrectomy (LAG) and 78 underwent open gastrectomy (OG). The parameters analyzed included operative time, blood loss, blood transfusion, morbidity, mortality, the number of harvested lymph nodes (HLNs), and pathological stage. RESULTS There were no significant differences in sex, age, types of radical resection [radical proximal gastrectomy (PG + D2), radical distal gastrectomy (DG + D2) and radical total gastrectomy (TG + D2)], and stages between the LAG and OG groups (P > 0.05). Among the two groups, 127 cases (96.9%) and 76 cases (97.4%) had 15 or more HLNs, respectively. The average number of HLNs was 26.1 ± 11.4 in the LAG group and 24.2 ± 9.3 in the OG group (P = 0.233). In the same type of radical resection, there were no significant differences in the number of HLNs between the two groups (PG + D2: 21.7 ± 7.5 vs. 22.4 ± 9.3; DG + D2: 25.7 ± 11.0 vs. 22.3 ± 7.9; TG + D2: 30.9 ± 13.4 vs. 29.3 ± 10.4; P > 0.05 for all comparisons). Tumor free margins were obtained in all cases. Compared with OG group, the LAG group had significantly less blood loss, but a longer operation time (P < 0.001). The morbidity of the LAG group was 9.9%, which was not significantly different from the OG group (7.7%) (P = 0.587). The mortality was zero in both groups. CONCLUSION Laparoscopic D2 dissection is equivalent to OG in the number of HLNs, regardless of tumor location. Thus, this procedure can achieve the same radicalness as OG.
ISEM: a multiagent Simulator for testing agent market strategies

With the increasing importance of e-commerce across the Internet, the need for software agents to support customers and suppliers in buying and selling goods/services is growing rapidly. It is becoming increasingly evident that in a few years the Internet will host a large number of interacting software agents. Most of them will be economically motivated, and will negotiate a variety of goods and services. It is therefore important to consider the economic incentives and behaviors of economic software agents, and to use all available means to anticipate their collective interactions. This paper addresses this concern by presenting a multiagent market simulator designed for analyzing agent market strategies based on a complete understanding of buyer and seller behaviors, preference models and pricing algorithms, and considering risk preferences. The system includes agents that are capable of improving their performance with their own experience, by adapting to the market conditions. The results of the negotiations between agents are analyzed by data mining algorithms to extract rules that give agents feedback to improve their strategies
Improving of bowel cleansing effect for polyethylene glycol with ascorbic acid using simethicone

Background and Aim: Low-volume polyethylene glycol with ascorbic acid (PEG-Asc) use is reported to be as safe and effective as traditional 4-L polyethylene glycol use. However, PEG-Asc produces bubbles, which cause problems during colonoscopy. Data on the effects of using antifoaming agents such as simethicone with PEG-Asc are lacking. The aim of this CONSORT-prospective, randomized, observer-blinded, controlled trial is to compare the quality of bowel preparation and compliance between PEG-Asc users and PEG-Asc plus simethicone users. Methods: Adult outpatients aged 18 to 80 years undergoing colonoscopy were recruited to the study. Two hundred sixty patients were randomly assigned to 1 of 2 treatment arms, PEG-Asc or PEG-Asc plus simethicone. The primary outcome measure was the bowel cleansing quality using Boston bowel preparation scale and bubble scores. The secondary outcome measures were patient tolerability and doctor tolerability. Results: The simethicone group showed superior cleansing results (6–9 Boston scale scores: 99% vs. 84%, <5% bubble scores: 96% vs. 49%, P < 0.001) and fewer gastrointestinal symptoms (abdominal fullness: 24% vs. 55%, colicky pain: 5% vs. 24%, P < 0.001) than the non-simethicone group. Moreover, endoscopist fatigue during colonoscopy was lower in the simethicone group than in the non-simethicone group (1.31 ± 0.75 vs. 2.97 ± 2.14, P < 0.001). Conclusion: PEG-Asc plus simethicone use was more effective and associated with better patient and endoscopist tolerance than PEG-Asc use. Therefore, this combination is recommended as one of the promising methods for bowel preparation before colonoscopy.
Energy Efficient User Association and Power Allocation in Millimeter-Wave-Based Ultra Dense Networks With Energy Harvesting Base Stations

Millimeter wave (mmWave) communication technologies have recently emerged as an attractive solution to meet the exponentially increasing demand on mobile data traffic. Moreover, ultra dense networks (UDNs) combined with mmWave technology are expected to increase both energy efficiency and spectral efficiency. In this paper, user association and power allocation in mmWave-based UDNs is considered with attention to load balance constraints, energy harvesting by base stations, user quality of service requirements, energy efficiency, and cross-tier interference limits. The joint user association and power optimization problem are modeled as a mixed-integer programming problem, which is then transformed into a convex optimization problem by relaxing the user association indicator and solved by Lagrangian dual decomposition. An iterative gradient user association and power allocation algorithm is proposed and shown to converge rapidly to an optimal point. The complexity of the proposed algorithm is analyzed and its effectiveness compared with existing methods is verified by simulations.
Stochastic Models and Analysis for Resource Management in Server Farms

Server farms are popular architectures for computing infrastructures such as supercomputing centers, data centers and web server farms. As server farms become larger and their workloads more complex, designing efficient policies for managing the resources in server farms via trial-anderror becomes intractable. In this thesis, we employ stochastic modeling and analysis techniques to understand the performance of such complex systems and to guide design of policies to optimize the performance. There is a rich literature on applying stochastic modeling to diverse application areas such as telecommunication networks, inventory management, production systems, and call centers, but there are numerous disconnects between the workloads and architectures of these traditional applications of stochastic modeling and how compute server farms operate, necessitating new analytical tools. To cite a few: (i) Unlike call durations, supercomputing jobs and file sizes have high variance in service requirements and this critically- affects the optimality and performance of scheduling policies. (ii) Most existing analysis of server farms focuses on the First-Come-First-Served (FCFS) scheduling discipline, while time sharing servers (e.g., web and database servers) are better modeled by the Processor-Sharing (PS) scheduling discipline. (iii)Time sharing systems typically exhibit thrashing (resource contention) which limits the achievable concurrency level, but traditional models of time sharing systems ignore this fundamental phenomenon. (iv) Recently, minimizing energy consumption has become an important metric in managing server farms. State-of-the-art servers come with multiple knobs to control energy consumption, but traditional queueing models don't take the metric of energy consumption into account. In this thesis we attempt to bridge some of these disconnects by bringing the stochastic modeling and analysis literature closer to the realities of today's compute server farms. We introduce new queueing models for computing server farms, develop new stochastic analysis techniques to evaluate anti understand these queueing models, and use the analysis to propose resource management algorithms to optimize their performance.
Study on the association between gene polymorphism of COMT and attempted suicide

Objective To understand the association between gene polymorphism of catechol-o-methyltransferase (COMT) and attempted suicide, and to find out the correlation factors related to attempted suicide with COMT Val/Val. Methods 220 cases were collected from seven polyclinics at city or county level in Shandong province. The general information was investigated and 1ml blood from elbow vein was also took out from each suicide attempters. PCR-RFLP was used to analyze gene polymorphism of COMT. The case-case study was adopted to analyze the relativity between COMT Val/Val genotype and the other factors. Results The ratio of female to male was 1.23∶1, the age was mainly in 20～49 years old (70.1%), the education level was mainly on high school level (60.9%), the quality of sleep was mainly not well (60%), most of them had depression ( 69.5%) and affective conflicts ( 81.0%). The most of the COMT genotype of attempted suicide was Val/Met ( 54.5%), the least was Met/Met, about 0.3%. The association between mental disorders and COMT Val/Val in suicide attempters was found (χ2=6.110, P=0.013). Conclusions There were more female, youth, low education level, poor quality of sleep, depression and affective conflicts among suicide attempters. And there was interaction between mental disorders and COMT Val/Val in the suicide attempters.
Human Liver Sinusoid on a Chip for Hepatitis B Virus Replication Study

We have developed a miniature human liver (liver-sinusoid-on-a-chip) model using a dual microchannel separated by a porous membrane. Primary human hepatocytes and immortalized bovine aortic endothelial cells were co-cultured on opposite sides of a microporous membrane in a dual microchannel with continuous perfusion. Primary human hepatocytes in this system retained their polygonal morphology for up to 26 days, while hepatocytes cultured in the absence of bovine aortic endothelial cells lost their morphology within a week. In order to demonstrate the utility of our human-liver-sinusoid-on-a-chip, human hepatocytes in this system were directly infected by Hepatitis B Virus (HBV). Expression of the HBV core antigen was detected in human hepatocytes in the microchannel system. HBV replication, measured by the presence of cell-secreted HBV DNA, was also detected. Importantly, HBV is hepatotropic, and expression of HBV RNA transcripts is dependent upon expression of hepatocyte-specific factors. Moreover, HBV infection requires expression of the human-hepatocyte-specific HBV cell surface receptor. Therefore, the ability to detect HBV replication and Hepatitis B core Antigen (HBcAg) expression in our microfluidic platform confirmed that hepatocyte differentiation and functions were retained throughout the time course of our studies. We believe that our human-liver-sinusoid-on-a-chip could have many applications in liver-related research and drug development.