Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell type-specific long-range connections of basal forebrain circuit

The basal forebrain (BF) plays key roles in multiple brain functions, including sleep-wake regulation, attention, and learning/memory, but the long-range connections mediating these functions remain poorly characterized. Here we performed whole-brain mapping of both inputs and outputs of four BF cell types – cholinergic, glutamatergic, and parvalbumin-positive (PV+) and somatostatin-positive (SOM+) GABAergic neurons – in the mouse brain. Using rabies virus -mediated monosynaptic retrograde tracing to label the inputs and adeno-associated virus to trace axonal projections, we identified numerous brain areas connected to the BF. The inputs to different cell types were qualitatively similar, but the output projections showed marked differences. The connections to glutamatergic and SOM+ neurons were strongly reciprocal, while those to cholinergic and PV+ neurons were more unidirectional. These results reveal the long-range wiring diagram of the BF circuit with highly convergent inputs and divergent outputs and point to both functional commonality and specialization of different BF cell types. DOI: http://dx.doi. org/10.7554/eLife.13214. 001
Dissecting Colony Development of Neurospora crassa Using mRNA Profiling and Comparative Genomics Approaches

ABSTRACT Colony development, which includes hyphal extension, branching, anastomosis, and asexual sporulation, is a fundamental aspect of the life cycle of filamentous fungi; genetic mechanisms underlying these phenomena are poorly understood. We conducted transcriptional profiling during colony development of the model filamentous fungus Neurospora crassa, using 70-mer oligonucleotide microarrays. Relative mRNA expression levels were determined for six sections of defined age excised from a 27-h-old N. crassa colony. Functional category analysis showed that the expression of genes involved in cell membrane biosynthesis, polar growth, and cellular signaling was enriched at the periphery of the colony. The relative expression of genes involved in protein synthesis and energy production was enriched in the middle section of the colony, while sections of the colony undergoing asexual development (conidiogenesis) were enriched in expression of genes involved in protein/peptide degradation and unclassified proteins. A cross-examination of the N. crassa data set with a published data set of Aspergillus niger revealed shared patterns in the spatiotemporal regulation of gene orthologs during colony development. At present, less than 50% of genes in N. crassa have functional annotation, which imposes the chief limitation on data analysis. Using an evolutionary approach, we observed that the expression of phylogenetically conserved groups of genes was enriched in the middle section of an N. crassa colony whereas expression of genes unique to euascomycete species and of N. crassa orphan genes was enriched at the colony periphery and in the older, conidiating sections of a fungal colony.
Resection of Motor Eloquent Metastases Aided by Preoperative nTMS-Based Motor Maps—Comparison of Two Observational Cohorts

Introduction Preoperative mapping of motor areas with navigated transcranial magnetic stimulation (nTMS) has been shown to improve surgical outcomes for peri-Rolandic lesions and, in particular, for gliomas. However, the impact of this technique on surgical outcomes for peri-Rolandic metastatic lesions is yet unknown. Objective To investigate the impact of nTMS on surgical outcomes for peri-Rolandic metastatic lesions, various clinical parameters were analyzed in our international study group. Methods Two prospectively enrolled cohorts were compared by investigating patients receiving preoperative nTMS (2010–2015; 120 patients) and patients who did not receive preoperative nTMS (2006–2015; 130 patients). Tumor location, pathology, size, and preoperative deficits were comparable. Results The nTMS group showed a lower rate of residual tumor on postoperative magnetic resonance imaging (odds ratio 0.3025; 95% confidence interval 0.1356–0.6749). On long-term follow-up, surgery-related paresis was decreased in the nTMS group (nTMS vs. non-nTMS; improved: 30.8 vs. 13.1%, unchanged: 65.8 vs. 73.8%, worse: 3.4 vs. 13.1% of patients; p = 0.0002). Moreover, the nTMS group received smaller craniotomies (nTMS: 16.7 ± 8.6 cm2 vs. non-nTMS: 25.0 ± 17.1 cm2; p < 0.0001). Surgical time differed significantly between the two groups (nTMS: 128.8 ± 49.4 min vs. non-nTMS: 158.0 ± 65.8 min; p = 0.0002). Conclusion This non-randomized study suggests that preoperative motor mapping by nTMS may improve the treatment of patients undergoing surgical resection of metastases in peri-Rolandic regions. These findings suggest that further evaluation with a prospective, randomized trial may be warranted.
Thoracoscopic versus open lobectomy debate: the pro argument

Introduction: Controversy persists about the role of VATS lobectomy for patients with lung cancer. This is particularly true in Europe, where VATS (video assisted thoracic surgery) lobectomy is performed for lung cancer less often than in the USA or Japan. This article reviews existing data comparing the results of VATS vs. open lobectomy for the treatment of lung cancer in order to provide a scientific basis for a rational assessment of this issue. Methods: The review of the data presented here draws heavily from a 2007 metaanalysis by Cheng et al. [1] published in 2007, as it employed rigorous methodology in performing a systematic review and metaanalysis, and involved a detailed analysis of many major and minor endpoints on an intent to treat basis. This included 36 trials, three of them randomized, and 3589 patients, reported between 1995 and 2007. Summary results for individual endpoints are shown as a mean value with 95% confidence intervals (CI). These values are taken from the summary results of the Forrest plots in the source article. Dichotomized variables are expressed as an Odds Ratio, with values <1 being in favor of VATS lobectomy. Continuous variables are reported as weighted mean differences. Results: The operative time for a VATS lobectomy was statistically longer, but only by 16 minutes. The conversion rate from VATS to open was 6%. There was no significant difference in the rates of major bleeding, blood transfusion or re-operation. VATS lobectomy was associated with a significantly lower rate of complications in general and pulmonary complications in particular. Postoperative pain was reduced, functional outcome was better, whereas overall quality of life was not. Mediastinal staging was equal with regard to the number of nodes or the number of nodal stations sampled. The ability of patients to receive adjuvant chemotherapy was improved following VATS. There was no difference in survival at 1 and 3 years for lung cancer (all stages combined). There was no difference in survival at 5 years for each tumor stage, and no difference in the rate of deaths at maximal follow-up. Conclusion: The data suggests that VATS lobectomy for NSCLC is safe, results in fewer complications, less pain, and more rapid return of normal functioning. There appears to be either no difference or a slight benefit in long term survival after VATS lobectomy. These conclusions are demonstrated by a comprehensive, rigorous metaanalysis of the controlled clinical trials, but are weakened by the fact that most of the studies were not randomized. However, because a large randomized trial is not likely to ever be conducted, this represents the best assessment of the value of VATS lobectomy that is available.
Modeling serious games using AOSE methodologies

Lately, serious games are a useful tool to learn how humans interact with each other and their environment. The best serious games are simulations that have the appearance of a game, but whose events and / or processes are non-game. Usually they include business domains and military operations (many games are popular entertainment on the basis of business and military operations, but with simpler rules). On the other hand, one of the purposes of Agent-Oriented Software Engineering is the creation of methodologies and tools that enable inexpensive development and maintenance of agent-based software. The relationship between serious games and Agent-Oriented Software Engineering is also clear given that software agents (perhaps intelligent) are used as virtual players or actors in many computer games and simulations, that the agent paradigm is of great interest in social behavior and interaction among agents (that can be thought of as players in a game), and also that the development process for agents is very close to the process of game development.
Can Multi-Level Cell PCM Be Reliable and Usable ? Analyzing the Impact of Resistance Drift Sungkap

There are several emerging memory technologies looming on t he horizon to compensate the physical scaling challenges of DR AM. Phase change memory (PCM) is one of such candidates proposed for being part of the main memory in computing systems. One salient feature of PCM is its multi-level cell (MLC) propert y which can be used to multiply the memory capacity at the cell level. However, due to the nature of PCM that the value written to the cel l can drift over time, PCM is prone to a unique type of soft errors, p osing a great challenge for their practical deployment. To add ress this reliability issue, many researchers proposed materia l-based or architectural solutions. In this paper, we analyze the resi stance drift problem using both analytical models and Monte Carlo simula tion and show the fundamental limit in prior architectural solut ions. According to our findings, four-level PCM is unusable given its soft error rate and scrubbing time needed.
Characterization of PTZ-Induced Seizure Susceptibility in a Down Syndrome Mouse Model That Overexpresses CSTB

Down syndrome (DS) is a complex genetic syndrome characterized by intellectual disability, dysmorphism and variable additional physiological traits. Current research progress has begun to decipher the neural mechanisms underlying cognitive impairment, leading to new therapeutic perspectives. Pentylenetetrazol (PTZ) has recently been found to have positive effects on learning and memory capacities of a DS mouse model and is foreseen to treat DS patients. But PTZ is also known to be a convulsant drug at higher dose and DS persons are more prone to epileptic seizures than the general population. This raises concerns over what long-term effects of treatment might be in the DS population. The cause of increased propensity for epilepsy in the DS population and which Hsa21 gene(s) are implicated remain unknown. Among Hsa21 candidate genes in epilepsy, CSTB, coding for the cystein protease inhibitor cystatin B, is involved in progressive myoclonus epilepsy and ataxia in both mice and human. Thus we aim to evaluate the effect of an increase in Cstb gene dosage on spontaneous epileptic activity and susceptibility to PTZ-induced seizure. To this end we generated a new mouse model trisomic for Cstb by homologous recombination. We verified that increasing copy number of Cstb from Trisomy (Ts) to Tetrasomy (Tt) was driving overexpression of the gene in the brain, we checked transgenic animals for presence of locomotor activity and electroencephalogram (EEG) abnormalities characteristic of myoclonic epilepsy and we tested if those animals were prone to PTZ-induced seizure. Overall, the results of the analysis shows that an increase in Cstb does not induce any spontaneous epileptic activity and neither increase or decrease the propensity of Ts and Tt mice to myoclonic seizures suggesting that Ctsb dosage should not interfere with PTZ-treatment.
Sperm DNA Integrity in Men Treated for Childhood Cancer

Purpose: It is not known whether childhood cancer and its treatment are associated with sperm DNA damage, which subsequently affects fertility and might be transmitted to the offspring. The aim of this study is to assess DNA fragmentation index (DFI) as an indicator of sperm DNA integrity in childhood cancer survivors (CCS), with treatment regimen taken into account. Experimental Design: In 99 CCS and 193 age-matched healthy controls, DFI was assessed by using sperm chromatin structure assay. Results: In the whole group of CCS, DFI was increased compared with the controls, with borderline statistical significance [mean difference, 1.8%; 95% confidence interval (95% CI), −0.0088%-3.7%]. Those treated with radiotherapy only (mean difference, 6.0%; 95% CI, 1.6–10%) or surgery only (mean difference, 2.9%; 95% CI, 0.083–5.8%) had statistically significantly higher DFI than the controls. The odds ratio (OR) for having DFI >20%, which is associated with reduced fertility, was significantly increased in CCS compared with the control group (OR, 2.2; 95% CI, 1.1–4.4). For the radiotherapy-only group, the OR was even higher (OR, 4.9; 95% CI, 1.3–18). DFI was not associated with dose of scattered testicular irradiation or type of chemotherapy given. Conclusions: DFI was increased in CCS, with those treated with chemotherapy being the only exception. This sperm DNA impairment may be associated with the disease per se rather than due to the treatment, and may have negative consequences in terms of fertility and risk of transmission to the offspring. Clin Cancer Res; 16(15); 3843–50. ©2010 AACR.
Virginity Testing Beyond a Medical Examination

Apart from religious values, virginity is important in different communities because of its prominent role in reducing sexually transmitted diseases and teen pregnancies. Even though virginity testing has been proclaimed an example of violence against women by the World Health Organization, it is still conducted in many countries, including Iran. 16 in-depth, semi-structured interviews were conducted with participants aged 32 to 60 years to elucidate the perceptions and experiences of Iranian examiners of virginity testing. The perception and experience of examiners were reflected in five main themes. The result of this study indicated that virginity testing is more than a medical examination, considering the cultural factors involved and its overt and covert consequences. In Iran, testing is performed for both formal and informal reasons, and examiners view such testing with ambiguity about the accuracy and certainty of the diagnosis and uncertainty about ethics and reproductive rights. Examiners are affected by the overt and covert consequences of virginity testing, beliefs and cultural values underlying virginity testing, and informal and formal reasons for virginity testing.
An extract from date seeds having a hypoglycemic effect. Is it safe to use?

OBJECTIVE To investigate the safety of date seed extract administration, and to compare between toxic effects of diabetes on rats treated with insulin versus rats treated with insulin-seed extract. METHODS This study was performed in the Anatomy Department, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia from August to December 2010. One hundred rats were divided into 5 groups. Group 1 served as control. Group 2 was given daily ingestions of 10 ml of date seed extract. Animals of groups 3 and 4 were made diabetic by streptozotocin injection, and were given daily subcutaneous injections of 3 IU/day of insulin for 8 weeks. Group 4 received, in addition, daily ingestions of 10 ml of seed extract. Group 5 were made diabetic with streptozotocin and then given the seed extract only. At the end of experiment, rats were decapitated, and the sera were separated for estimation of alanine aminotransferase (ALT), aspartate aminotransferase, gamma glutamyl transferase, blood urea nitrogen, and serum creatinine levels. Livers and kidneys were processed for light microscopic study. RESULTS The mean values of all tested serum levels were significantly higher in Group 3 compared to Groups 1, 2 and 4 (with the exception of ALT in the case of Group 4). There was no significant change when comparing the mean values of Groups 1, 2, and 4. Livers and kidneys of rats in Groups 1, 2, and 4 showed normal histology, while those of Group 3 showed histopathological changes. CONCLUSION Date seed extract administration is safe on the liver and kidney. In addition, insulin-date seed extract combination minimizes the toxic effects of diabetes on these organs.
Effect of Feed Restriction during Pregnancy on Performance and Productivity of New Zealand White Rabbit Does

This study aimed to evaluate effect of stage of feed restriction on performance and productivity of pregnant does. New Zealand white female rabbits were randomly divided into three groups. Control group was provided daily with 185 g of food increased to 200 g from the 15th day of gestation. R 1 was offered daily a restricted amount of food (60% restriction, 111 g) for the first half of pregnancy and then offered 200 g of food daily till parturition. R 2 was provided with 185 g of food daily through the first half of pregnancy and then offered daily a restricted amount of food (60% restriction, 120 g) for the second half. After parturition, food was provided adlibitum. Maternal body weights, litter size, litter weight, and average body weight of kits at kindling of R 1 showed no change, whereas R 2 showed significant reduction in the weights of does at the 4th week of pregnancy and at kindling. The birth weight and weaning weight of R 2 were significantly reduced. The highest mortality was recorded in kits of R 2. No significant differences in blood parameters or serum prolactin were observed. The serum protein was significantly reduced R 2.
A functional limit theorem for a 2d-random walk with dependent marginals

We prove a non-standard functional limit theorem for a two dimensional simple random walk on some randomly oriented lattices. This random walk, already known to be transient, has different horizontal and vertical fluctuations leading to different normalizations in the functional limit theorem, with a non-Gaussian horizontal behavior. We also prove that the horizontal and vertical components are not asymptotically independent.
Function-Follows-Form Transformations in Scientific Problem Solving

This paper presents a pattern of reasoning called “function-follows-form” (FFF) uncovered through a study of scientific problem solving. In the study we modeled eleven “think-out-loud” problem-solving protocols taken by John Clement (1989). Our work involved computationally modeling the reasoning processes of eleven scientists each attempting to solve the same problem about springs. We describe experiments with two computational systems, ToRQUE and ToRQUE2, which were used to model salient reasoning found in the protocols, and we show how the use of function-follows-form reasoning patterns enables exploration and conceptual change.
Developing an ‘ethics for neuroscientists’ course: between emancipation, practicality, and postmodernity in educational action research

Abstract With the advances in neuroscience in the twenty-first century, there is an increased risk that this research could be used for non-peaceful purposes by state or non-state actors. The latter issue is generally referred to as the dual-use problem, which has created a heated debate among scientists and security experts about the duties and responsibilities of researchers where each side is reluctant to engage with the other in a cooperative manner. In order to break this stalemate, a project on how to improve ethics education for neuroscientists was carried out which led to the development of an open access, online 12-lecture module. This article discusses how the project followed an action research methodology. While theory proposes that action research can either deliver on a practical level or enable emancipation, the article will discuss how this research project managed to accomplish both. Furthermore, it draws on a critique of emancipation in the form of postmodern theory to discuss the emergence of power and its application.
The Uniqueness of Changes: Characteristics and Applications

Changes in software development come in many forms. Some changes are frequent, idiomatic, or repetitive (e.g. Adding checks for nulls or logging important values) while others are unique. We hypothesize that unique changes are different from the more common similar (or non-unique) changes in important ways, they may require more expertise or represent code that is more complex or prone to mistakes. As such, these unique changes are worthy of study. In this paper, we present a definition of unique changes and provide a method for identifying them in software project history. Based on the results of applying our technique on the Linux kernel and two large projects at Microsoft, we present an empirical study of unique changes. We explore how prevalent unique changes are and investigate where they occur along the architecture of the project. We further investigate developers' contribution towards uniqueness of changes. We also describe potential applications of leveraging the uniqueness of change and implement two of those applications, evaluating the risk of changes based on uniqueness and providing change recommendations for non-unique changes.
What About Toom-Cook Matrices Optimality ?

Karatsuba and Toom-Cook are well-known methods used to multiply efficiently two long integers. There have been different proposal about the interpolating values used to determine the matrix to be inverted and the sequence of operations to invert it. A definitive word about which is the optimal matrix (values) and the (number of) basic operations to invert it seems still not to have been said. In this paper we present some particular examples of useful matrices and a method to generate automatically, by means of optimised exhaustive searches on a graph, the best sequence of basic operations to invert them. AMS Subject Classification: 11A05, 11A25, 11K65, 11Y70
Foreign Currency Loans and Systemic Risk in Europe

Foreign currency loans to the unhedged non-banking sector are remarkably prevalent in Europe and create a significant exchange-rate-induced credit risk to European banking sectors. In particular, Swiss franc (CHF)-denominated loans, popular in Eastern European countries, could trigger simultaneous bank failures if depreciation of the domestic currencies prevents unhedged borrowers from servicing the loans. Foreign currency loans thus pose a systemic risk from a “common market shock” perspective. The author uses a novel dataset of foreign-currency loans from 17 countries for 2007-11 (collected by the Swiss National Bank) and builds on the method suggested by Ranciere, Tornell, and Vamvakidis (2010) to quantify this systemic risk. The author finds that systemic risk is substantial in the non-euro area, while it is relatively low in the euro area. However, CHF-denominated loans are not the underlying source of the high systemic risk: Loans denominated in other foreign currencies (probably to a large extent in euros) contribute significantly more to the systemic risk in the non-euro area than CHF-denominated loans. Furthermore, systemic risk shows high persistence and low volatility during the sample period. The author also finds that banks in Europe have continuously held more foreign-currency denominated assets than liabilities, indicating their awareness of the exchange-rate-induced credit risk they face.