Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent Historical Migrations Have Shaped the Gene Pool of Arabs and Berbers in North Africa

North Africa is characterized by its diverse cultural and linguistic groups and its genetic heterogeneity. Genomic data has shown an amalgam of components mixed since pre-Holocean times. Though no differences have been found in uniparental and classical markers between Berbers and Arabs, the two main ethnic groups in the region, the scanty genomic data available have highlighted the singularity of Berbers. We characterize the genetic heterogeneity of North African groups, focusing on the putative differences of Berbers and Arabs, and estimate migration dates. We analyze genome-wide autosomal data in five Berber and six Arab groups, and compare them to Middle Easterns, sub-Saharans, and Europeans. Haplotype-based methods show a lack of correlation between geographical and genetic populations, and a high degree of genetic heterogeneity, without strong differences between Berbers and Arabs. Berbers enclose genetically diverse groups, from isolated endogamous groups with high autochthonous component frequencies, large homozygosity runs and low effective population sizes, to admixed groups with high frequencies of sub-Saharan and Middle Eastern components. Admixture time estimates show a complex pattern of recent historical migrations, with a peak around the 7th century C.E. coincident with the Arabization of the region; sub-Saharan migrations since the 1st century B.C. in agreement with Roman slave trade; and a strong migration in the 17th century C.E. , coincident with a huge impact of the trans-Atlantic and trans-Saharan trade of sub-Saharan slaves in the Modern Era. The genetic complexity found should be taken into account when selecting reference groups in population genetics and biomedical studies.
Transfer of Advances in Science into Dental Education The Genome Projects : Implications for Dental Practice and Education

Information from the Human Genome Project (HGP) and the integration of information from related areas of study and technology will dramatically change health care for the craniofacial complex. Approaches to risk assessment and diagnosis, prevention, early intervention, and management of craniofacial conditions are and will continue to evolve through the application of this new knowledge. While this information will advance our health care abilities, it is clear that the dental profession will face challenges regarding the acquisition, application, transfer, and effective and efficient use of this knowledge with regards to dental research, dental education, and clinical practice. Unraveling the human genomic sequence now allows accurate diagnosis of numerous craniofacial conditions. However, the greatest oral disease burden results from dental caries and periodontal disease that are complex disorders having both hereditary and environmental factors determining disease risk, progression, and course. Disease risk assessment, prevention, and therapy, based on knowledge from the HGP, will likely vary markedly for the different complex conditions affecting the head and neck. Integration of Information from the human genome, comparative and microbial genomics, proteomics, bioinformatics, and related technologies will provide the basis for proactive prevention and intervention and novel and more efficient treatment approaches. Oral health care practitioners will increasingly require knowledge of human genetics and the application of new molecular-based diagnostic and therapeutic technologies. Dr. Wright is Professor, Department of Pediatric Dentistry, University of North Carolina School of Dentistry, and Dr. Hart is Associate Professor, Department of Oral Biology, University of Pittsburgh School of Dental Medicine. Direct correspondence and requests for reprints to Dr. Tim Wright, Department of Pediatric Dentistry, School of Dentistry, Brauer Hall #7450, University of North Carolina, Chapel Hill, NC 27599; 919-966-7992 fax; tim_wright@dentistry.unc. edu.
TypeScript: The Next Generation To boldly enforce types where no one has enforced types before

There is increasing interest in integrating dynamically and statically typed programming languages, as witnessed in industry by the development of the languages TypeScript and Dart, and in academia by the development of the theories of gradual types, hybrid types, and the blame calculus. The purpose of our project is to bring the academic and industrial developments together, applying theory to improve practice. Our project focusses on JavaScript, an ECMA standard, and its typed variant TypeScript, an open-source project sponsored by Microsoft. JavaScript plays a central role in web-based applications and the new Windows 8 framework, and TypeScript is seeing rapid takeup, with over 150 JavaScript libraries now provided with TypeScript declarations. Our project has two parts, one aimed at immediate short-term application, and one aimed at fundamental longterm research.
Near Infrared Photoimmunotherapy Targeting EGFR Positive Triple Negative Breast Cancer: Optimizing the Conjugate-Light Regimen

Aim Triple-negative breast cancer (TNBC) is considered one of the most aggressive subtypes of breast cancer. Near infrared photoimmunotherapy (NIR-PIT) is a cancer treatment that employs an antibody-photosensitizer conjugate (APC) followed by exposure of NIR light for activating selective cytotoxicity on targeted cancer cells and may have application to TNBC. In order to minimize the dose of APC while maximizing the therapeutic effects, dosing of the APC and NIR light need to be optimized. In this study, we investigate in vitro and in vivo efficacy of cetuximab (cet)-IR700 NIR-PIT on two breast cancer models MDAMB231 (TNBC, EGFR moderate) and MDAMB468 (TNBC, EGFR high) cell lines, and demonstrate a method to optimize the dosing APC and NIR light. Method After validating in vitro cell-specific cytotoxicity, NIR-PIT therapeutic effects were investigated in mouse models using cell lines derived from TNBC tumors. Tumor-bearing mice were separated into 4 groups for the following treatments: (1) no treatment (control); (2) 300 μg of cet-IR700 i.v. , (APC i.v. only); (3) NIR light exposure only, NIR light was administered at 50 J/cm2 on day 1 and 100 J/cm2 on day 2 (NIR light only); (4) 300 μg of cet-IR700 i.v. , NIR light was administered at 50 J/cm2 on day 1 after injection and 100 J/cm2 of light on day 2 after injection (one shot NIR-PIT). To compare different treatment regimens with a fixed dose of APC, we added the following treatments (5) 100 μg of cet-IR700 i.v. , NIR light administered at 50 J/cm2 on day 1 and 50 μg of cet-IR700 i.v. immediately after NIR-PIT, then NIR light was administered at 100 J/cm2 on day 2, which were performed two times every week (“two split” NIR-PIT) and (6) 100 μg of cet-IR700 i.v. , NIR light was administered at 50 J/cm2 on day 1 and 100 J/cm2 on day 2, which were performed three times per week (“three split” NIR-PIT). Result Both specific binding and NIR-PIT effects were greater with MDAMB468 than MDAMB231 cells in vitro. Tumor accumulation of cet-IR700 in MDAMB468 tumors was significantly higher (p < 0.05) than in MDAMB231 tumors in vivo. Tumor growth and survival of MDAMB231 tumor bearing mice was significantly lower in the NIR-PIT treatment group (p < 0.05). In MDAMB468 bearing mice, tumor growth and survival was significantly improved in the NIR-PIT treatment groups in all treatment regimens (one shot NIR-PIT; p < 0.05, “two split” NIR-PIT; p < 0.01, “three split” NIR-PIT; p < 0.001) compared with control groups. Conclusion NIR-PIT for TNBC was effective regardless of expression of EGFR, however, greater cell killing was shown with higher EGFR expression tumor in vitro. In all treatment regimens, NIR-PIT suppressed tumor growth, resulting in significantly prolonged survival that further improved by splitting the APC dose and using repeated light exposures.
A power allocation technique for fairness and enhanced energy efficiency in future networks

In this paper, we present a power allocation technique that improves the sum rate and energy efficiency without reducing the minimum data rate of an established resource block allocation technique. To achieve this, the technique is implemented in two stages where the first is for ensuring that the minimum data rate remains unchanged. The second stage is for increasing the sum rate by ensuring that more resource blocks are reused by the femtocells that reduce their power. The algorithm is iterative with changes in transmit power resulting in changes in resource block allocation. It will be shown that at the expense of some delay, the proposed technique can result in significant energy savings while maintaining the minimum data rate when compared to equal power allocation. Further, relative to optimal allocation techniques, the proposed technique results in better fairness.
Plasticity localization ahead of a crack tip modeled by 2D discrete dislocation dynamics

The formation of a plastic zone in the presence of a crack, in a bicrystal, is modeled by two-dimensional discrete dislocation dynamics. The influence of a large number of parameters is studied: the misorientation, the emission from the crack tip and the obstacle density which modifies the internal stress (hardening) and degree of localization of mobile dislocations (slip bands). Emphasis is put on obtaining the best ductility, since the focus is on face centered cubic materials. Finally, a strong effect of the plastic model on the dynamics and on the secondary slip (intensity and localization), beyond the influence of the initial distribution of sources and obstacles, is reported.
The SOAR (Stroke Subtype, Oxford Community Stroke Project Classification, Age, Prestroke Modified Rankin) Score Strongly Predicts Early Outcomes in Acute Stroke

Background Previous prognostic scoring systems in predicting stroke mortality are complex, require multiple measures that vary with time and failed to produce a simple scoring system. Aims/Hypothesis The study aims to derive and internally validate a stroke prognostic scoring system to predict early mortality and hospital length of stay. Methods Data from a UK multicenter stroke register were examined (1997–2010). Using a prior hypothesis based on our and others observations, we selected five patient-related factors (age, gender, stroke subtype, clinical classification, and prestroke disability) as candidate prognostic indicators. An 8-point score was derived based on multiple logistic regression model using four out of five variables. Performance of the model was assessed by plotting the estimated probability of in-hospital death against the actual probability by testing for overfitting (calibration) and area under the curve methods (discrimination). Results The total sample consisted of 12 355 acute stroke patients (ischemic stroke 91·0%). The score predicted both in-patient and seven-day mortality. The crude in-patient mortality were 1·57%, 4·02%, 10·65%, 21·41%, 46·60%, 62·72%, and 75·81% for those who scored 0, 1, 2, 3, 4, 5, and 6, respectively. The calibration of the model revealed no evidence of overfitting (estimated overfitting 0·001). The area under the curve values for both in-hospital and seven-day mortality were 0·79. The score predicted length of stay with a higher score was associated with longer median length of stay in those discharged alive and shorter median length of stay in those who died (P for both <0·001). Conclusions A simple 8-point clinical score is highly predictive of acute stroke mortality and length of hospital stay. It could be used as prognostic tool in service planning and also to risk-stratify patients to use these outcomes as markers of stroke care quality across institutions.
Flexible spaces: Dynamic layout generation for infinite walking in virtual environments

Redirected walking techniques enable natural locomotion through immersive virtual environments (VEs) that are larger than the real world workspace. Most existing techniques rely upon manipulating the mapping between physical and virtual motions while the layout of the environment remains constant. However, if the primary focus of the experience is on the virtual world's content, rather than on its spatial layout, then the goal of redirected walking can be achieved through an entirely different strategy. In this paper, we introduce flexible spaces - a novel redirection technique that enables infinite real walking in virtual environments that do not require replication of real world layouts. Flexible spaces overcome the limitations and generalize the use of overlapping (impossible) spaces and change blindness by employing procedural layout generation. Our approach allows VE designers to focus on the content of the virtual world independent of the implementation details imposed by real walking, thereby making spatial manipulation techniques more practical for use in a variety of application domains.
A Bayesian Approach to Constraint Based Causal Inference

We target the problem of accuracy and robustness in causal inference from finite data sets. Some state-of-the-art algorithms produce clear output complete with solid theoretical guarantees but are susceptible to propagating erroneous decisions, while others are very adept at handling and representing uncertainty, but need to rely on undesirable assumptions. Our aim is to combine the inherent robustness of the Bayesian approach with the theoretical strength and clarity of constraint-based methods. We use a Bayesian score to obtain probability estimates on the input statements used in a constraint-based procedure. These are subsequently processed in decreasing order of reliability, letting more reliable decisions take precedence in case of conflicts, until a single output model is obtained. Tests show that a basic implementation of the resulting Bayesian Constraint-based Causal Discovery (BCCD) algorithm already outperforms established procedures such as FCI and Conservative PC. It can also indicate which causal decisions in the output have high reliability and which do not.
Predisposed Visual Memory of Shapes in Quail Chicks

Abstract Newly hatched chicks will spontaneously peck at conspicuous objects in their field of view, and soon learn to distinguish between edible food particles and unpleasant tasting objects. To examine whether the selective pecking is based on the ability to memorize shapes, we analyzed pecking behavior of 1- to 2-days-old quail chicks (Coturnix japonica) by using ball- and triangle-shaped beads both painted in green. Repeated presentation of dry bead (either ball or triangle) resulted in a progressively fewer number of pecks (habituation). When chicks were tested by triangle after repeated presentation of ball, chicks showed a significant increase in the number of pecks at the triangle (dishabituation). On the other hand, when tested by ball after a series of triangle presentations, pecking frequency did not increase (no dishabituation). Chicks thus distinguished the triangle as a novel object after being habituated to ball, but did not respond to the ball after triangle. A similar asymmetry was found in one-trial passive avoidance task. Chicks were pre-trained by water-coated (neutral) triangle and then trained by methylanthranilate-coated (aversive) ball. In this case, most chicks learned to avoid the ball, and half of these successful learners pecked at the triangle; they distinguished triangle from ball. When chicks were pre-trained by neutral ball and trained by aversive triangle, on the other hand, most chicks did not distinguish the ball from triangle, and showed a generalized avoidance for both beads. Chicks may be innately predisposed to memorize a limited category of shapes such as ball, and associate them with selective avoidance.
Background: Physics and Math of Shading

Light is an electromagnetic transverse wave, which means that it oscillates in directions perpendicular to its propagation (see Figure 1). Since it is a wave, light is characterized by its wavelength—the distance from peak to peak. Electromagnetic wavelengths cover a very wide range but only a tiny part of this range (about 400 to 700 nanometers) is visible to humans and thus of interest for shading (see Figure 2). The effect matter has on light is defined by a property called the refractive index. The refractive
Where Do Actions Come From? Autonomous Robot Learning of Objects and Actions

Decades of AI research have yielded techniques for learning, inference, and planning that depend on human-provided ontologies of self, space, time, objects, actions, and properties. Since robots are constructed with low-level sensor and motor interfaces that do not provide these concepts, the human robotics researcher must create the bindings between the required high-level concepts and the available low-level interfaces. This raises the developmental learning problem for robots of how a learning agent can create high-level concepts from its own low-level experience. Prior work has shown how objects can be individuated from low-level sensation, and certain properties can be learned for individual objects. This work shows how high-level actions can be learned autonomously by searching for control laws that reliably change these properties in predictable ways. We present a robust and efficient algorithm that creates reliable control laws for perceived objects. We demonstrate on a physical robot how these high-level actions can be learned from the robot’s own experiences, and can then applied to a learned object to achieve a desired goal.
Acoustic class specific VTLN-warping using regression class trees

In this paper, we study the use of different frequency warpfactors for different acoustic classes in a computationally efficient frame-work of Vocal Tract Length Normalization (VTLN). This is motivated by the fact that all acoustic classes do not exhibit similar spectral variations as a result of physiological differences in vocal tract, and therefore, the use of a single frequency-warp for the entire utterance may not be appropriate. We have recently proposed a VTLN method that implements VTLN-warping through a linear-transformation (LT) of the conventional MFCC features and efficiently estimates the warp-factor using the same sufficient statistics as that are used in CMLLR adaptation. In this paper we have shown that, in this framework of VTLN, and using the idea of regression class tree, we can obtain separate VTLN-warping for different acoustic classes. The use of regression class tree ensures that warp-factor is estimated for each class even when there is very little data available for that class. The acoustic classes, in general, can be any collection of the Gaussian components in the acoustic model. We have built acoustic classes by using data-driven approach and by using phonetic knowledge. Using WSJ database we have shown the recognition performance of the proposed acoustic class specific warp-factor both for the data driven and the phonetic knowledge based regression class tree definitions and compare it with the case of the single warp-factor. Index Terms: VTLN, Acoustic-Class Specific Warping, Regression Class Tree, Linear Transform
A Multicenter Pilot Study of Early (4‐Day) Steroid Cessation in Renal Transplant Recipients Under Simulect, Tacrolimus and Sirolimus

This study presents the first prospective multicenter study assessing sirolimus‐based immunosuppression with early (4‐day) corticosteroid withdrawal (CSWD) in renal transplantation. Immunosuppression included: anti‐IL‐2 receptor antibody and tacrolimus/sirolimus. Inclusion criteria included adult primary recipients. Exclusion criteria included: (i) African Americans, (ii) current PRA >50%, (iii) multiple organ transplants, (iv) WBC < 3000 cells/μL and (v) fasting hypercholesterolemia/hypertriglyceridemia. The primary endpoints were acute rejection and the proportion of patients off corticosteroids. Seventy‐seven patients were enrolled: mean age of 49.7 ± 12 years. Transplants included: cadaveric (26%) and living donor (74%). Patient and graft survival were 100%. Biopsy proven acute rejection occurred in 13%; presumptive rejection in 10.5%. Banff grades included: IA (seven patients), IB (one patient), IIA (one patient) and IIB (one patient). Renal function at 1 year: serum creatinine (1.18 ± 0.06 mg/dL). Mean weight gain was minimal at 1 year: 3 ± 2 kg/patient. Mild increases in total, LDL and HDL cholesterol were observed and new antilipid agent use occurred in 26 patients. In conclusion, early CSWD under tacrolimus/sirolimus‐based immunosuppression in selected, low‐risk renal transplant recipients provides: (i) excellent patient and graft survival, (ii) good renal function, (iii) reduced hyperlipidemia and antilipid agent use and (iv) low acute rejection rates.
Dependence space of concept lattices based on rough set

Rough set theory and Formal concept analysis have much in common, in terms of both goals and methodologies. The combination of rough set theory and formal concept analysis provides new approaches for data analysis. The notions of the object oriented concepts and the attribute oriented concepts are formed by introduced formal concept and formal concept lattice into rough set theory. In this paper, the dependence spaces are constructed according to these two concept lattices. Applying to the congruences on the dependence space, the equivalent classes of the set of attributes can be got and then a closed set is also obtained. And a new approach is discussed by using the closed set to construct formal concepts.
Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols

The structures of F1-ATPase from bovine heart mitochondria inhibited with the dietary phytopolyphenol, resveratrol, and with the related polyphenols quercetin and piceatannol have been determined at 2.3-, 2.4- and 2.7-Å resolution, respectively. The inhibitors bind to a common site in the inside surface of an annulus made from loops in the three α- and three β-subunits beneath the “crown” of β-strands in their N-terminal domains. This region of F1-ATPase forms a bearing to allow the rotation of the tip of the γ-subunit inside the annulus during catalysis. The binding site is a hydrophobic pocket between the C-terminal tip of the γ-subunit and the βTP subunit, and the inhibitors are bound via H-bonds mostly to their hydroxyl moieties mediated by bound water molecules and by hydrophobic interactions. There are no equivalent sites between the γ-subunit and either the βDP or the βE subunit. The inhibitors probably prevent both the synthetic and hydrolytic activities of the enzyme by blocking both senses of rotation of the γ-subunit. The beneficial effects of dietary resveratrol may derive in part by preventing mitochondrial ATP synthesis in tumor cells, thereby inducing apoptosis.
Temperature acclimation and the newvous system in fish.

The studies on temperature acclimation in fish reviewed by Brett (1956) and Fisher (1958) indicate that many types of cell are involved in the process. These reviewers point out that probably modifications occur in the nervous system; however, there appears to be little direct evidence. The work described in this paper is based on the hypothesis that much of temperature acclimation is due to changes in the nervous system which permit normal behaviour at extreme temperatures.