Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying the similarity of topological domains across normal and cancer human cell types

Motivation Three‐dimensional chromosome structure has been increasingly shown to influence various levels of cellular and genomic functions. Through Hi‐C data, which maps contact frequency on chromosomes, it has been found that structural elements termed topologically associating domains (TADs) are involved in many regulatory mechanisms. However, we have little understanding of the level of similarity or variability of chromosome structure across cell types and disease states. In this study, we present a method to quantify resemblance and identify structurally similar regions between any two sets of TADs. Results We present an analysis of 23 human Hi‐C samples representing various tissue types in normal and cancer cell lines. We quantify global and chromosome‐level structural similarity, and compare the relative similarity between cancer and non‐cancer cells. We find that cancer cells show higher structural variability around commonly mutated pan‐cancer genes than normal cells at these same locations. Availability and implementation Software for the methods and analysis can be found at https://github.com/Kingsford‐Group/localtadsim
Inference of species phylogenies from bi-allelic markers using pseudo-likelihood

Motivation Phylogenetic networks represent reticulate evolutionary histories. Statistical methods for their inference under the multispecies coalescent have recently been developed. A particularly powerful approach uses data that consist of bi-allelic markers (e.g., single nucleotide polymorphism data) and allows for exact likelihood computations of phylogenetic networks while numerically integrating over all possible gene trees per marker. While the approach has good accuracy in terms of estimating the network and its parameters, likelihood computations remain a major computational bottleneck and limit the method’s applicability. Results In this paper, we first demonstrate why likelihood computations of networks take orders of magnitude more time when compared to trees. We then propose an approach for inference of phylo-genetic networks based on pseudo-likelihood using bi-allelic markers. We demonstrate the scalability and accuracy of phylogenetic network inference via pseudo-likelihood computations on simulated data. Furthermore, we demonstrate aspects of robustness of the method to violations in the underlying assumptions of the employed statistical model. Finally, we demonstrate the application of the method to biological data. The proposed method allows for analyzing larger data sets in terms of the numbers of taxa and reticulation events. While pseudo-likelihood had been proposed before for data consisting of gene trees, the work here uses sequence data directly, offering several advantages as we discuss. Availability The methods have been implemented in PhyloNet (http://bioinfocs.rice.edu/phylonet). Contact jiafan.zhu@rice.edu, nakhleh@rice.edu
Reinforcement Learning-Based ACB in LTE-A Networks for Handling Massive M2M and H2H Communications

Using cellular networks for providing machine-to- machine (M2M) connectivity offers numerous advantages regarding coverage, deployment costs, security and management, among others. Nevertheless, having a large number of M2M devices activated simultaneously is difficult to tackle at the evolved Node B, and it causes complications in the connection establishment. The random access channel (RACH) in LTE-A is adequate for handling human-to-human (H2H) communications. However, for the efficient provision of simultaneous H2H/M2M communications, it is necessary to optimize the available access control mechanisms so that network overload is avoided and a better QoS can be offered. Access Class Barring (ACB) has shown to be effective in reducing the number of simultaneous users contending for access. However, it is still not clear how to dynamically adapt its parameters, especially in highly changing scenarios with bursty traffic as it can occur when M2M communications are involved. We propose a dynamic algorithm based on reinforcement learning to adapt the barring rate parameter of ACB. This algorithm can adapt it to different traffic conditions, reducing congestion and hence the number of collisions in the RACH. The results show that our proposed mechanism increases the access success probability for all the users while barely impacting H2H users and other key performance indicators.
Nociceptive blink reflex habituation biofeedback in migraine

Reduced habituation of the nociceptive blink reflex (NBR) is considered a trait marker for genetic predisposition to migraine. In this open-label randomized controlled study, we aimed to test the efficacy of a biofeedback training based on learning of habituation of the NBR (NBR biofeedback) compared with pharmacological (topiramate) treatment and NBR biofeedback plus topiramate treatment in a cohort of migraine without aura patients eligible for prophylaxis. Thirty-three migraine patients were randomly assigned to three months of treatment with: 1) NBR biofeedback, 2) NBR biofeedback plus topiramate 50 mg (b.i.d.), or 3) topiramate 50 mg (b.i.d.). Frequency of headache and disability changes were the main study outcomes. Anxiety, depression, sleep, fatigue, quality of life, allodynia and pericranial tenderness were also evaluated. NBR biofeedback reduced the R2 area, without improving R2 habituation. However, it reduced the frequency of headache and disability, similarly to the combined treatment and topiramate alone. Reduced habituation of the NBR is a stable neurophysiological pattern, scarcely modifiable by learning procedures. Training methods able to act on stress-related responses may modulate cortical mechanisms inducing migraine onset and trigeminal activation under stressful trigger factors.
Can Working Memory and Inhibitory Control Predict Second Language Learning in the Classroom?

The role of executive functioning in second language (L2) aptitude remains unclear. Whereas some studies report a relationship between working memory (WM) and L2 learning, others have argued against this association. Similarly, being bilingual appears to benefit inhibitory control, and individual differences in inhibitory control are related to online L2 processing. The current longitudinal study examines whether these two components of executive functioning predict learning gains in an L2 classroom context using a pretest/posttest design. We assessed 25 university students in language courses, who completed measures of WM and inhibitory control. They also completed a proficiency measure at the beginning and end of a semester and reported their grade point average (GPA). WM was positively related to L2 proficiency and learning, but inhibitory control was not. These results support the notion that WM is an important component of L2 aptitude, particularly for predicting the early stages of L2 classroom learning.
Whole genome sequence of the heterozygous clinical isolate Candida 1 krusei 81-B-5 2 3

Genome Report: Whole genome sequence of the heterozygous clinical isolate Candida 1 krusei 81-B-5 2 3 Christina A. Cuomo, Terrance Shea, Bo Yang, Reeta Rao, Anja Forche 4 1 Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA 5 2 Worcester Polytechnic Institute, Biology & Biotechnology, Worcester, MA 01609 USA 6 3 Bowdoin College, Department of Biology, Brunswick, ME 04011 USA 7 *corresponding authors: cuomo@broadinstitute.org, aforche@bowdoin.edu 8 9 Data access: All genome sequence data (reads, assembly, and annotation) is available in 10 GenBank under BioProject PRJNA381554. 11 12 G3: Genes|Genomes|Genetics Early Online, published on July 10, 2017 as doi:10.1534/g3.117. 043547
Vulnerability of human settlements to flood risk in the core area of Ibadan metropolis, Nigeria

Flood disasters continue to wreak havoc on the lives of millions of people worldwide, causing death and massive economic losses. In most African cities, residents and their assets are among the most vulnerable to flood risks in the world. The nature and scale of this urban risk are changing because of the dynamic patterns of land use, unplanned growth and impacts of climate change. Flood risk is the product of the flood hazards, the vulnerability and exposure of the people and their physical environment. In order to minimise flood disaster, there is an urgent need to understand, invest in flood disaster risk reduction for resilience and to enhance disaster preparedness for an effective response as articulated in the recent Sendai Framework for Disaster Risk Reduction. This research utilises a new proposed flood vulnerability assessment framework for flood risk in a traditional community in the heart of Ibadan metropolis, in the context of their households’ exposure, susceptibility and coping capacity through a well-designed questionnaire survey. The study uses descriptive and inferential statistics techniques to provide a detailed understanding of the vulnerability profiles of the community and the levels of residents’ preparedness to mitigate the flood risk. The results of the statistical analysis show that there is a significant relationship between residents’ flood awareness and having previous flood experience, but there is no significant association between their awareness of risk and the level of preparedness for flooding. To minimise exposure and vulnerability to flood risk, we advocate effective adaptation policies to achieve disaster risk reduction and resilience on flood risk rather than focusing merely on reactive measures after disaster strikes.
Cryopreservation of Ovarian Tissue: Opportunities Beyond Fertility Preservation and a Positive View Into the Future

In current years, ovarian tissue cryopreservation (OTC) and transplantation is gaining ground as a successful method of preserving fertility in young women with primarily cancer diseases, hereby giving them a chance of becoming biological mothers later on. However, OTC preserves more than just the reproductive potential; it restores the ovarian endocrine function and thus the entire female reproductive cycle with natural levels of essential hormones. In a female population with an increased prevalence in the loss of ovarian function due to induced primary ovarian insufficiency (POI) and aging, there is now, a need to develop new treatments and provide new opportunities to utilize the enormous surplus of follicles that most females are born with and overcome major health issues associated with the lack of ovarian hormones. Cell/tissue-based hormone replacement therapy (cHRT) by the use of stored ovarian tissue could be one such option comprising both induction of puberty in prepubertal POI girls, treatment of POI and premature menopause, and as primary prevention at the onset of menopause. In the current review, we explore known and entirely new applications for the potential utilization of OTC including cHRT, social freezing, culture of immature oocytes, and a modern ovarian resection for women with polycystic ovaries, and discuss the indications hereof.
Roles of PLODs in Collagen Synthesis and Cancer Progression

Collagen is the major component of extracellular matrix. Collagen cross-link and deposition depend on lysyl hydroxylation, which is catalyzed by procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD). Aberrant lysyl hydroxylation and collagen cross-link contributes to the progression of many collagen-related diseases, such as fibrosis and cancer. Three lysyl hydroxylases (LH1, LH2, and LH3) are identified, encoded by PLOD1, PLOD2, and PLOD3 genes. Expression of PLODs is regulated by multiple cytokines, transcription factors and microRNAs. Dysregulation of PLODs promotes cancer progression and metastasis, suggesting that targeting PLODs is potential strategy for cancer treatment. Here, we summarize the recent progress in the investigation of function and regulation of PLODs in normal tissue development and disease progression, especially in cancer.
Correlation between EML4-ALK, EGFR and clinicopathological features based on IASLC/ATS/ERS classification of lung adenocarcinoma

Abstract To investigate the correlation between echinodermmicro tubule associated protein-like 4 (EML4)-anaplasticlymphomakinase (ALK), epidermal growth factor receptor (EGFR) and clinicopathological features in patients diagnosed with lung adenocarcinoma according to International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society (IASLC/ATS/ERS) international multidisciplinary classification of lung adenocarcinoma. Ninety patients diagnosed with lung adenocarcinoma underwent surgical pathological classification. Ventana immunohistochemical staining of the EML4-ALK was performed. The mutation of EGFR and EML4-ALK was detected by real-time polymerase chain reaction (RT-PCR) using the amplification refractory mutation system. The positive rate of EML4-ALK mutation was calculated as 6.7% (6/90), dominantly occurring in patients aged < 60 years. However, it was not correlated with the gender, smoking history, maximal tumor diameter, pleural invasion, lymphatic metastasis, or clinical staging. EML4-ALK fusion gene mutation was mainly associated with the predominant subtypes of acinar and solid tumors with mucin secretion. The mutation rate of EGFR was 60% (27/45). EGFR gene mutation mainly occurred in the female, those with no smoking history and tumor size < 3 cm, whereas it had no association with age, pleural invasion, lymphatic metastasis, or clinical staging. It was histologically characterized with micropapillary, lepidic, and papillary subtypes. The mutation rate of EML4-ALK is relatively high in lung adenocarcinoma patients aged<60 years, pathologically characterized with acinar and solid subtypes with mucin secretion. Female patients with no smoking habit, tumor size<3 cm, pathologically characterized with micropapillary, lepidic, and papillary subtypes had a high mutation rate of EGFR.
Pricing Initial Public Offerings in Premature Capital Markets: The Case of Hungary

This paper investigates the determinants of underpricing at initial public offerings in the Hungarian Initial Public Offerings (IPO) market in 1990-1998, a period of transition from socialist to market economy and immaturity of the domestic capital market. The evidence suggests that political issues played a significant role in the process: we have found greater discount at privatization IPOs than at private issues, and a positive relation between underpricing and the proportion of shares offered for compensation coupons. These findings reinforce the hypothesis that governments in transition may pursue political objectives by selling shares at discount. Besides, the results show larger initial returns at early IPOs compared to later issues, which implies a negative relation between the discount and the maturing of the capital market. Most of the asymmetric information theories, empirically justified for well-developed stock markets, receive no support. Some results suggest that the transition related determinants of underpricing disappear as the securities market becomes more mature.
Cross-Cultural Dimensions of Business Communication: Evidence from Sri Lanka

Cross-cultural dimensions have become as an essential factor for understanding miscellaneous type of social, economic and business environments. It can be define as a learned system of knowledge, attitudes, behaviors, belief and norms which are shared among a group of people in different nations or cultures. This study examines the effect of the ethical corporate cultural dimensions on the business participation and activities in Sri Lanka. The survey directed over the 181 employees who belong to four ethnic groups provided the data for empirical investigation. In order to test the hypothesis, correlation and regression techniques were basically applied. The study result clearly shows that, workplace collectivism has a strong and significant effect on the business activities and participation rather other underlined variables.
A simple unit root testing methodology that does not require knowledge regarding the presence of a break

ABSTRACT We develop a simple methodology that allows practitioners to test for the presence of a unit root without a priori knowledge regarding the occurrence of a break under the null hypothesis. We use a pre-test that is readily available in the estimated regression used to calculate the unit root statistics, and so our methodology is very easy to implement. The t-statistic corresponding to the impulse dummy variables evaluated at break date estimator is used as a pre-test to ascertain whether a break exists under the null hypothesis. Finite sample simulations show that our methodology yields tests that maintain their size.
Use of the Minimally Invasive Reduction Instrumentation System for Facilitating Alignment and Reduction When Performing Minimally Invasive Plate Osteosynthesis in Three Dogs

The Minimally Invasive Reduction Instrumentation System (MIRIS) was utilized to facilitate minimally invasive plate osteosynthesis (MIPO) of distal limb diaphyseal comminuted fractures (2 crural, 1 antebrachial) in three dogs. The MIRIS facilitated efficient MIPO in all three fractures. Radial and tibial lengths were restored within 2% of the length of the intact bone and postoperative frontal and sagittal plane angulation were within 3° of the normal contralateral limb for each of the fractures. Fixation failed in one of the tibial fractures when the plates bent a week following surgery. The implants were removed and the fracture was restabilized via MIPO facilitated by the MIRIS. Inappropriate implant selection was considered the primary reason for implant failure. All three fractures achieved union by 10 weeks following surgery. The dog that underwent revision surgery developed a surgical site infection 5 months following revision surgery, which necessitated implant removal. All three dogs had excellent limb function at the time of the final evaluation. This system resulted in reductions that were near anatomic, with acceptable restoration of length and alignment and excellent limb function.
Energy harvesting through flow-induced oscillations of a foil

By using a Navier–Stokes model, we examine a novel flow energy harvesting device consisting of a flapping foil mounted on a damper (representing the power generator) and a rotational spring. Self-induced and self-sustained flapping motions, including a heaving motion h(t) and a pitching motion α(t), are excited by an incoming flow and power extraction is achieved from the heaving response. Depending upon the configuration of the system and the mechanical parameters (e.g., the location of the pitching axis and the stiffness of the rotational spring), four different responses are recorded: (i) the foil remains stable in its initial position (α=0 and h=0); (ii) periodic pitching (around α=0) and heaving motions are excited; (iii) the foil undergoes irregular motions characterized by switching between oscillations around two pitching angles; and (iv) the foil rotates to a position with an angle to the incoming flow and oscillates around it. The existence of response (ii) suggests the feasibility of controllab.
Dietary Patterns in Secondary Prevention of Heart Failure: A Systematic Review

Background: Diet is an important factor in secondary prevention of heart failure (HF) but there is still no consensus as to which dietary model should be adopted by this population. This systematic review aims to clarify the relationship between dietary patterns and secondary prevention in HF. Methods: We searched the Medline, Embase and Cochrane databases for studies with different dietary patterns and outcomes of secondary prevention in HF. No limitation was used in the search. Results: 1119 articles were identified, 12 met the inclusion criteria. Studies with Dietary Approaches to Stop Hypertension (DASH), Mediterranean, Hyperproteic and Low-carb diets were found. The DASH pattern showed improvement in cardiac function, functional capacity, blood pressure, oxidative stress and mortality. The Mediterranean diet had a correlation with inflammation, quality of life and cardiac function but just on cross-sectional studies. Regarding the Hyperproteic and Low-carb diets only one study was found with each pattern and both were able to improve functional capacity in patients with HF. Conclusions: DASH pattern may have benefits in the secondary prevention of HF. The Mediterranean diet demonstrated positive correlation with factors of secondary prevention of HF but need more RCTs and cohort studies to confirm these effects. In addition, the Hyperproteic and Low-carb diets, despite the lack of studies, also demonstrated positive effects on the functional capacity in patients with HF.
Belief Propagation List Decoding of Polar Codes

We propose a belief propagation list (BPL) decoder with comparable performance to the successive cancellation list (SCL) decoder of polar codes, which already achieves the maximum likelihood (ML) bound of polar codes for sufficiently large list size $L$ . The proposed decoder is composed of multiple parallel independent belief propagation (BP) decoders based on differently permuted polar code factor graphs. A list of possible transmitted codewords is generated and the one closest to the received vector, in terms of Euclidean distance, is picked. To the best of our knowledge, the proposed BPL decoder provides the best performance of plain polar codes under iterative decoding known so far. The proposed algorithm does not require any changes in the polar code structure itself, rendering the BPL into an alternative to the SCL decoder, equipped with a soft output capability enabling, e.g., iterative detection and decoding to further improve performance. Further benefits are the lower decoding latency than the SCL decoder and the possibility of high throughput implementations. Additionally, we show that a different selection strategy of frozen bit positions can further enhance the error-rate performance of the proposed decoder.
Information As Regulation: The Effect of Community Right to Know Laws on Toxic Emissions

Abstract There is growing academic and policy-level interest in the use of information as quasi-regulatory mechanisms, such as toxic release inventory (TRI) and “green labels. ” Mandatory disclosure requirements have been touted as “market-based incentives” that may affect firm behavior. We provide new evidence on the effectiveness of disclosure requirements by examining firm behavior in response to disclosures of TRI emissions. We find that firms with the largest stock price decline on the day this information became public subsequently reduced emissions more than their industry peers. This is consistent with the view that financial markets may provide strong incentives for firms to change their environmental behavior.
The performance of univariate goodness-of-fit tests for normality based on the empirical characteristic function in large samples

An empirical power comparison is made between two tests based on the empirical characteristic function and some of the best performing tests for normality. A simple normality test based on the empirical characteristic function calculated in a single point is shown to outperform the more complicated Epps-Pulley test and the frequentist tests included in the study in large samples.
COMPORTAMIENTO COLECTIVO DE ANIMALES "SWARMING" Y PATRONES COMPLEJOS COLLECTIVE BEHAVIOR OF ANIMALS: SWARMING AND COMPLEx PATTERNS

In this short note we review some of the individual based models of the collective motion of agents, called swarming. These models based on ODEs (ordinary differential equations) ex- hibit a complex rich asymptotic behavior in terms of patterns, that we show numerically. Moreover, we comment on how these particle models are connected to partial differential equations to describe the evolution of densities of individuals in a continuum manner. The mathematical questions behind the stability issues of these PDE (partial differential equations) models are questions of actual interest in mathematical biology research.