Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological Divergence and the Origins of Intrinsic Postmating Isolation with Gene Flow

The evolution of intrinsic postmating isolation has received much attention, both historically and in recent studies of speciation genes. Intrinsic isolation often stems from between-locus genetic incompatibilities, where alleles that function well within species are incompatible with one another when brought together in the genome of a hybrid. It can be difficult for such incompatibilities to originate when populations diverge with gene flow, because deleterious genotypic combinations will be created and then purged by selection. However, it has been argued that if genes underlying incompatibilities are themselves subject to divergent selection, then they might overcome gene flow to diverge between populations, resulting in the origin of incompatibilities. Nonetheless, there has been little explicit mathematical exploration of such scenarios for the origin of intrinsic incompatibilities during ecological speciation with gene flow. Here we explore theoretical models for the origin of intrinsic isolation where genes subject to divergent natural selection also affect intrinsic isolation, either directly or via linkage disequilibrium with other loci. Such genes indeed overcome gene flow, diverge between populations, and thus result in the evolution of intrinsic isolation. We also examine barriers to neutral gene flow. Surprisingly, we find that intrinsic isolation sometimes weakens this barrier, by impeding differentiation via ecologically based divergent selection.
Key Prediction Security of Keyed Sponges

The keyed sponge is a well-accepted method for message authentication. It processes data at a certain rate by sequential evaluation of an underlying permutation. If the key size k is smaller than the rate, currently known bounds are tight, but if it exceeds the rate, state of the art only dictates security up to 2k/2. We take closer inspection at the key prediction security of the sponge and close the remaining gap in the existing security analysis: we confirm key security up to close to 2k, regardless of the rate. The result impacts all applications of the keyed sponge and duplex that process at a rate smaller than the key size, including the STROBE protocol framework, as well as the related constructions such as HMAC-SHA-3 and the sandwich sponge.
Parkinson’s Disease in Sub-Saharan Africa: A Review of Epidemiology, Genetics and Access to Care

A low prevalence of Parkinson’s disease (PD) has been reported in the Sub-Saharan Africa (SSA) region. The genetic causes and clinical features of PD in this region have been poorly described. Very few reports have examined the availability and access to evidence-based quality care for people living with PD in this region. We reviewed all publications focusing on idiopathic PD from SSA published up to May 2016 and observed a prevalence of PD ranging from 7/100,000 in Ethiopia to 67/100,000 in Nigeria. The most recent community-based study reported a mean age at onset of 69.4 years. The infrequent occurrence of mutations in established PD genes was also observed in the region. Treatments were non-existent or at best irregular. Additionally, there is a lack of well-trained medical personnel and multidisciplinary teams in most countries in this region. Drugs for treating PD are either not available or unaffordable. Large-scale genetic and epidemiological studies are therefore needed in SSA to provide further insights into the roles of genetics and other etiological factors in the pathogenesis of PD. The quality of care also requires urgent improvement to meet the basic level of care required by PD patients.
Magnetic properties of strained multiferroic CoCr2O4: A soft x-ray study

Using resonant soft x-ray techniques we follow the magnetic behavior of a strained epitaxial film of CoCr2O4, a type-II multiferroic. The film is [ 110] oriented, such that both the ferroelectric and ferromagnetic moments can coexist in-plane. X-ray magnetic circular dichroism (XMCD) is used in scattering and in transmission modes to probe the magnetization of Co and Cr separately. The transmission measurements utilized x-ray excited optical luminescence from the substrate. Resonant soft x-ray diffraction (RXD) was used to study the magnetic order of the low temperature phase. The XMCD signals of Co and Cr appear at the same ordering temperature TC approximate to 90 K, and are always opposite in sign. The coercive field of the Co and of Cr moments is the same, and is approximately two orders of magnitude higher than in bulk. Through sum rules analysis an enlarged Co2+ orbital moment (m(L)) is found, which can explain this hardening. The RXD signal of the (q q 0) reflection appears below T-S, the same ordering temperature as the conical magnetic structure in bulk, indicating that this phase remains multiferroic under strain. To describe the azimuthal dependence of this reflection, a slight modification is required to the spin model proposed by the conventional Lyons-Kaplan-Dwight-Menyuk theory for magnetic spinels.
In-office tooth bleaching with 38% hydrogen peroxide promotes moderate/severe pulp inflammation and production of ll-1β, TNF-β, GPX, FGF-2 and osteocalcin in rats

Abstract Objectives: To study the intensity of inflammatory infiltrate and production of interleukin-1β (ll-1β), tumor necrosis factor-β (TNF-β), fibroblast growth factor-2 (FGF-2), glutathione peroxidase (GPX), and osteocalcin in response to in-office tooth bleaching in rats. Material and Methods: Twenty male Wistar rats were randomized into four groups (n=5) according to the received treatment (tooth bleaching or no treatment - control) and the period of euthanasia after treatment (24 h or 10 days). We performed tooth bleaching using a 38% hydrogen peroxide gel on maxillary and mandibular incisors. After euthanasia, incisors (20 per group) were processed for histological analysis, immunohistochemistry staining of ll-1β, TNF-β, FGF-2 and GPX and osteocalcin by immunofluorescence. We analyzed data using the Mann-Whitney and Kruskal-Wallis/Dunn tests (p<0.05). Results: The bleached groups presented statistically significant differences regarding the pulp inflammation stage compared with the control groups. Bleached teeth showed moderate/severe inflammatory infiltrate and control groups presented absent inflammatory cells or a negligible number of mononuclear cells (p<0.001) at two times (24 h and 10 days). There was strong staining for ll-1β, TNF-β, and GPX in bleached groups at 24 h and strong staining for ll-1β, TNF-β, GPX and FGF-2 at 10 days. After 10 days of tooth bleaching, the bleached group showed a statistically superior amount of osteocalcin than the other groups (p<0.01). Conclusions: Tooth bleaching with 38% hydrogen peroxide causes severe pulp inflammation, but characteristics of tissue repair after 10 days.
Graph Algebraic Combinatory Categorial Grammar

This paper describes CCG/AMR, a novel grammar for semantic parsing of Abstract Meaning Representations. CCG/AMR equips Combinatory Categorial Grammar derivations with graph semantics by assigning each CCG combinator an interpretation in terms of a graph algebra. We provide an algorithm that induces a CCG/AMR from a corpus and show that it creates a compact lexicon with low ambiguity and achieves a robust coverage of 78% of the examined sentences under ideal conditions. We also identify several phenomena that affect any approach relying either on CCG or graph algebraic approaches for AMR parsing. This includes differences of representation between CCG and AMR, as well as non-compositional constructions that are not expressible through a monotonous construction process. To our knowledge, this paper provides the first analysis of these corpus issues.
Antimicrobial stewardship education in US colleges and schools of pharmacy

Background Pharmacists are key members of antimicrobial stewardship (AS) teams. It is unknown if and how US colleges and schools of pharmacy incorporate AS into their Doctor of Pharmacy (PharmD) curricula. Methods This study was a cross-sectional, multicentre, electronic survey distributed to infectious diseases faculty or department chairs of 137 accredited and candidate-status PharmD programmes. Results One hundred and sixteen programmes participated, representing an 84.7% response rate. AS education was integrated into the required didactic, elective didactic and experiential education components of the curricula in 79 (68.1%), 43 (37.1%) and 97 (83.6%) PharmD programmes, respectively. The most common AS topics in required and elective didactic curricula were AS definitions, principles and purpose (98.7% and 86.0%) and the pharmacist's role in AS (93.7% and 83.7%). In the required and elective didactic curricula, lecture (93.7% and 86.0%) and case-based instruction (57.0% and 83.7%) were the most common instructional methods. For experiential education, the pharmacist's role in AS (96.9%), de-escalation of antimicrobials (96.9%) and antimicrobial dose optimization (95.9%) were the most common AS topics. PharmD programmes employing a faculty member who specializes in AS were more likely to offer AS experiential education than programmes without AS faculty (88.1% versus 71.9%, P = 0.049). Conclusions Integration of AS education in US PharmD curricula is variable and there are considerable differences in the AS activities and topics delivered. PharmD programmes should attempt to expose students to AS education to prepare future pharmacists for AS practice. Efforts should be made to incorporate interprofessional collaboration into AS education.
Energy-efficient workload offloading and power control in vehicular edge computing

In this paper, an energy-efficient vehicular edge computing (VEC) framework is proposed for in-vehicle user equipments (UEs) with limited battery capacity. Firstly, the energy consumption minimization problem is formulated as a joint workload offloading and power control problem, with the explicit consideration of energy consumption and delay models. Queuing theory is applied to derive the stochastic traffic models at UEs and VEC nodes. Then, the original NP-hard problem is transformed to a convex global consensus problem, which can be decomposed into several parallel subproblems and solved subsequently. Next, an alternating direction method of multipliers (ADMM)-based energy-efficient resource allocation algorithm is developed, whose outer loop representing iterations of nonlinear fractional programming, while inner loop representing iterations of primal and dual variable updates. Finally, the relationships between energy consumption and key parameters such as workload offloading portion and transmission power are validated through numerical results.
The Effect of Strong Purifying Selection on Genetic Diversity

Negative selection is a ubiquitous evolutionary force, but its effects on diversity in large samples are poorly understood. Cvijović, Good, and Desai obtain simple analytical expressions for the whole population site frequency spectrum. Purifying selection reduces genetic diversity, both at sites under direct selection and at linked neutral sites. This process, known as background selection, is thought to play an important role in shaping genomic diversity in natural populations. Yet despite its importance, the effects of background selection are not fully understood. Previous theoretical analyses of this process have taken a backward-time approach based on the structured coalescent. While they provide some insight, these methods are either limited to very small samples or are computationally prohibitive. Here, we present a new forward-time analysis of the trajectories of both neutral and deleterious mutations at a nonrecombining locus. We find that strong purifying selection leads to remarkably rich dynamics: neutral mutations can exhibit sweep-like behavior, and deleterious mutations can reach substantial frequencies even when they are guaranteed to eventually go extinct. Our analysis of these dynamics allows us to calculate analytical expressions for the full site frequency spectrum. We find that whenever background selection is strong enough to lead to a reduction in genetic diversity, it also results in substantial distortions to the site frequency spectrum, which can mimic the effects of population expansions or positive selection. Because these distortions are most pronounced in the low and high frequency ends of the spectrum, they become particularly important in larger samples, but may have small effects in smaller samples. We also apply our forward-time framework to calculate other quantities, such as the ultimate fates of polymorphisms or the fitnesses of their ancestral backgrounds.
Nitrogen metabolism and excretion in Allenbatrachus grunniens(L): effects of variable salinity, confinement, high pH and ammonia loading

The nitrogen metabolism and excretion patterns of the grunting toadfish Allenbatrachus grunniens and the effects of salinity on these processes were examined. Individuals of A. grunniens were subjected to several experimental treatments, including variable salinity (2 to 30), high pH (8.5 compared to 7.0 for controls), high environmental ammonia (10mM) and confinement to small water volumes, and measurements were made of activities of selected enzymes of nitrogen metabolism, ammonia and urea excretion rates, and tissue and plasma contents of ammonia, urea and amino acids. Activities of key ornithine-urea cycle enzymes were rather low (e.g. liver carbamoyl phosphate synthetase III activity was 0.001 μmols min -1 g -1 ), and A. grunniens consistently demonstrated a low capacity for urea excretion despite significant elevations of plasma and tissue ammonia contents by the high pH and high ammonia treatments. This species could thus be categorized as ammoniotelic. Total free amino acid contents in plasma and tissues were increased by the high pH and high ammonia treatments, but no patterns were discerned in individual amino acids that would indicate any preferential accumulation (e.g. alanine and glutamine) as has been noted previously in several semi-terrestrial fish species. Thus, it appeared that A. grunniens was not unusual in its patterns of nitrogen metabolism and excretion in comparison to other 'typical' teleosts. Furthermore, manipulation of salinity had no major effects on nitrogen excretion in either this species or in comparative studies with the ureotelic gulf toadfish Opsanus beta. The results are discussed in the context of the broader pattern of nitrogen metabolism and excretion in the Batrachoididae.
Polymorphism of Lactoferrin Gene with PCR - RFLP and its Association with Subclinical Mastitis in Dairy Cows

Incidence of mastitis was checked by the California Mastitis Test (CMT). 120 cows were screened and classified into 2 groups, 60 each group, namely control group (healthy) and experimental group ( subclinical mastitis). Polymorphism of cow lactoferrin gene promoter was determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed that lactorferrin gene promoter was polymorphic among different groups, which indicated that its polymorphism was related to mastitis infection.
Gastrinoma and Zollinger–Ellison syndrome in canids: a literature review and a case in a Mexican gray wolf

Gastrinoma, an infrequent diagnosis in middle-aged dogs, occurs with nonspecific gastrointestinal morbidity. Laboratory tests can yield a presumptive diagnosis, but definitive diagnosis depends on histopathology and immunohistochemistry. We describe a malignant pancreatic gastrinoma with lymph node metastases and corresponding Zollinger–Ellison syndrome in a Mexican gray wolf (Canis lupus baileyi) and review this endocrine neoplasm in domestic dogs. A 12-y-old, captive, male Mexican gray wolf developed inappetence and weight loss. Abdominal ultrasonography revealed a thickened duodenum and peritoneal effusion. Two duodenal perforations were noted on exploratory celiotomy and were repaired. Persisting clinical signs led to a second celiotomy that revealed a mesenteric mass, which was diagnosed histologically as a neuroendocrine carcinoma. During the following 16 mo, the wolf received a combination of H2-receptor antagonists, proton-pump inhibitors, gastroprotectants, and anti-emetics, but had recurrent episodes of anorexia, nausea, acid reflux, and remained underweight. Worsening clinical signs and weakness prompted euthanasia. The antemortem serum gastrin concentration of 414 ng/L (reference interval: 10–40 ng/L) corroborated hypergastrinemia. Autopsy revealed a mass expanding the right pancreatic limb; 3 parapancreatic mesenteric masses; duodenal ulcers; focal duodenal perforation with septic fibrinosuppurative peritonitis; chronic-active ulcerative esophagitis; and poor body condition. The pancreatic mass was diagnosed histologically as a neuroendocrine carcinoma and the parapancreatic masses as lymph node metastases. Immunohistochemistry of the pancreatic mass was positive for gastrin and negative for glucagon, insulin, pancreatic polypeptide, serotonin, somatostatin, and vasoactive intestinal peptide.
A 2.1-GHz Third-Order Cascaded PLL With Sub-Sampling DLL and Clock-Skew-Sampling Phase Detector

A high-order cascaded phase-locked loop (PLL) architecture using a sub-sampling delay-locked loop (DLL) is proposed to break the tradeoff between the loop bandwidth and the number of integrator in the feedback loop without significantly degrading the settling time or reference spur. A clock-skew-sampling phase detector is also proposed to extend the stable detection range of the sub-sampling phase detector. Implemented in a 65-nm CMOS process, a prototype of the proposed two-stage third-order cascaded PLL measures a 4.2-<inline-formula> <tex-math notation="LaTeX">$\mu \text{s}$ </tex-math></inline-formula> settling time, 1.05-ps integrated jitter, and −113-dBc/Hz in-band phase noise at a 2.1-GHz output frequency while consuming 3.84 mW at 1.2-V supply voltage and occupying a core chip area of 0.043 mm<sup>2</sup>.
Image forensic for digital image copy move forgery detection

In recent years, digital image forgery detection has become an active research area due to the advancement of photo editing software. This paper focuses on passive forgery detection on images tampered using copy move technique, better known as Copy Move Forgery Detection (CMFD). A CMFD technique consisting of oriented Features from Accelerated Segment Test and rotated Binary Robust Independent Elementary Features (Oriented FAST and rotated BRIEF) as the feature extraction method and 2 Nearest Neighbour (2NN) with Hierarchical Agglomerative Clustering (HAC) as the feature matching method is proposed. Evaluation of the proposed CMFD technique was performed on images that underwent various geometrical attacks. With the proposed technique, an overall accuracy rate of 84.33% and 82.79% are obtained for evaluation carried out with images from the MICC-F600 and MICC-F2000 databases. Forgery detection achieved True Positive Rate of more than 91% for tampered images with object translation, different degree of rotation and enlargement.
An ADD-Oriented Software Architecture for Structuring Information to Open Government Data

The huge number of heterogeneous and not standardized websites where public records are disclosed is an evidence of how unprepa¬red governments are about Open Government Data movement. This scenario is seen all over the world, especially in organizations which open data prin¬ciples are new e.g. local governments. Thus, not effective law enforcement and the lack of openness result in a waste of resources applied to useless publication of documents, ma¬king it hard to achieve the benefits of open data. Looking for a way to help government at this hardworking task, this paper proposes a software architecture for structuring information into open data from distributed repositories placed at local governments websites. This work follows Attribute-Driven Design (ADD) methodology, where the requirement analysis for proposed ar¬chitecture has been conducted based on availability problems occurred in 561 websites from Brazilian cities. The main contribution of this paper is the proposition of an architecture whose dissemination and instantiation will allow society to focus efforts on more important tasks e.g. review data consistency, making it possible in a near future to automatize the structuring process in a way that data can be used for any purpose.
Analysis of the effect of malicious packet drop attack on packet transmission in wireless mesh networks

Wireless mesh networks (WMNs) are known for possessing good attributes such as low up-front cost, easy network maintenance, and reliable service coverage. This has largely made them to be adopted in various environments such as; school campus networks, community networking, pervasive healthcare, office and home automation, emergency rescue operations and ubiquitous wireless networks. The routing nodes are equipped with self-organized and self-configuring capabilities. However, the routing mechanisms of WMNs depend on the collaboration of all participating nodes for reliable network performance. The authors of this paper have noted that most routing algorithms proposed for WMNs in the last few years are designed with the assumption that all the participating nodes will collaboratively be involved in relaying the data packets originated from a source to a multi-hop destination. Such design approach however exposes WMNs to vulnerability such as malicious packet drop attack. This paper presents an evaluation of the effect of the black hole attack with other influential factors in WMNs. In this study, NS-3 simulator was used with AODV as the routing protocol. The results show that the packet delivery ratio and throughput of WMN under attack decreases sharply as compared to WMN free from attack. On an average, 47.41% of the transmitted data packets were dropped in presence of black hole attack.
Metatrace: Online Step-size Tuning by Meta-gradient Descent for Reinforcement Learning Control

Reinforcement learning (RL) has had many successes in both "deep" and "shallow" settings. In both cases, significant hyperparameter tuning is often required to achieve good performance. Furthermore, when nonlinear function approximation is used, non-stationarity in the state representation can lead to learning instability. A variety of techniques exist to combat this --- most notably large experience replay buffers or the use of multiple parallel actors. These techniques come at the cost of moving away from the online RL problem as it is traditionally formulated (i.e., a single agent learning online without maintaining a large database of training examples). Meta-learning can potentially help with both these issues by tuning hyperparameters online and allowing the algorithm to more robustly adjust to non-stationarity in a problem. This paper applies meta-gradient descent to derive a set of step-size tuning algorithms specifically for online RL control with eligibility traces. Our novel technique, Metatrace, makes use of an eligibility trace analogous to methods like $TD(\lambda)$. We explore tuning both a single scalar step-size and a separate step-size for each learned parameter. We evaluate Metatrace first for control with linear function approximation in the classic mountain car problem and then in a noisy, non-stationary version. Finally, we apply Metatrace for control with nonlinear function approximation in 5 games in the Arcade Learning Environment where we explore how it impacts learning speed and robustness to initial step-size choice. Results show that the meta-step-size parameter of Metatrace is easy to set, Metatrace can speed learning, and Metatrace can allow an RL algorithm to deal with non-stationarity in the learning task.