Miracle-dz/UniFAR-FTUs huggingface dataset:
Stop and Go – Waves of Tarsier Dispersal Mirror the Genesis of Sulawesi Island

The Indonesian island of Sulawesi harbors a highly endemic and diverse fauna sparking fascination since long before Wallace’s contemplation of biogeographical patterns in the region. Allopatric diversification driven by geological or climatic processes has been identified as the main mechanism shaping present faunal distribution on the island. There is both consensus and conflict among range patterns of terrestrial species pointing to the different effects of vicariant events on once co-distributed taxa. Tarsiers, small nocturnal primates with possible evidence of an Eocene fossil record on the Asian mainland, are at present exclusively found in insular Southeast Asia. Sulawesi is hotspot of tarsier diversity, whereby island colonization and subsequent radiation of this old endemic primate lineage remained largely enigmatic. To resolve the phylogeographic history of Sulawesi tarsiers we analyzed an island-wide sample for a set of five approved autosomal phylogenetic markers (ABCA1, ADORA3, AXIN1, RAG1, and TTR) and the paternally inherited SRY gene. We constructed ML and Bayesian phylogenetic trees and estimated divergence times between tarsier populations. We found that their arrival at the Proto-Sulawesi archipelago coincided with initial Miocene tectonic uplift and hypothesize that tarsiers dispersed over the region in distinct waves. Intra-island diversification was spurred by land emergence and a rapid succession of glacial cycles during the Plio-Pleistocene. Some tarsier range boundaries concur with spatial limits in other taxa backing the notion of centers of faunal endemism on Sulawesi. This congruence, however, has partially been superimposed by taxon-specific dispersal patterns.
Second order total generalized variation (TGV) for MRI

Total variation was recently introduced in many different magnetic resonance imaging applications. The assumption of total variation is that images consist of areas, which are piecewise constant. However, in many practical magnetic resonance imaging situations, this assumption is not valid due to the inhomogeneities of the exciting B1 field and the receive coils. This work introduces the new concept of total generalized variation for magnetic resonance imaging, a new mathematical framework, which is a generalization of the total variation theory and which eliminates these restrictions. Two important applications are considered in this article, image denoising and image reconstruction from undersampled radial data sets with multiple coils. Apart from simulations, experimental results from in vivo measurements are presented where total generalized variation yielded improved image quality over conventional total variation in all cases. Magn Reson Med, 2011. © 2010 Wiley‐Liss, Inc.
Stromal Vascular Cells and Adipogenesis: Cells within Adipose Depots Regulate Adipogenesis

A collection of investigations indicate the importance of adipose tissue stromal/stem cells to vasculogenesis and angiogenesis during adipogenesis. Early in development the stromal-vascular (S-V) elements control and dictate the extent of adipogenesis. For instance, the vasculature and connective tissue collagen matrix develops before overt adipocyte differentiation. Definitive studies of human adipose tissue stem cells (ADSC) provided an understanding of stem cell identity and function. In this regard, a novel vascular stem cell theory proposes that ADSC are a mixed population of vascular stem cells (VSC) with differential potential proportional to the angiogenic potential of the vasculature. The differential potential of VSC can range considerably in a continuous fashion and can include vascular smooth cells, endothelial cells (EC) and adipocytes. These observations are consistent with fetal adipose tissue studies that show location-dependent angiogenic potential ranging from more to less in regards to a predominant presence of EC and developing arterioles before overt adipogenesis.
AN ONTOLOGY OF CLIMATE CHANGE Integral Pluralism and the Enactment of Multiple Objects

[I]f ontology is multiple, then it is also political. Ecological debates are becoming both more complex and epistemologically distant. The days of environmental crises that can be easily seen and quickly contained are rapidly becoming distant memory. The global environmental problems of the twenty-fi rst century are thus likely to become increasingly multiple as they move further and further beyond our epistemological reach. What, then, are we to do? With people ultimately talking about different objects, how can we ever hope for consensus and cooperation? there is still hope. Remember, multiplicity does not necessarily mean fragmentation. All that is solid does not melt into thin air. – Michael Carolan1
Epidemiology of community-acquired pneumonia and implications for vaccination of children living in developing and newly industrialized countries: A systematic literature review

ABSTRACT This systematic review evaluated the epidemiology of community-acquired pneumonia in children <6 y of age within 90 developing and newly industrialized countries. Literature searches (1990–2011), based on MEDLINE, EMBASE, Cochrane, CAB Global Health, WHO, UNICEF, country-specific websites, conferences, health-technology-assessment agencies, and the reference lists of included studies, yielded 8,734 records; 62 of 340 studies were included in this review. The highest incidence rate among included studies was 0.51 episodes/child-year, for children <5 y of age in Bangladesh. The highest prevalence was in Chinese children <6 months of age (37.88%). The main bacterial pathogens were Streptococcus pneumoniae, Haemophilus influenzae and Mycoplasma pneumoniae and the main viral pathogens were respiratory syncytial virus, adenovirus and rhinovirus. Community-acquired pneumonia remains associated with high rates of morbidity and mortality. Improved and efficient surveillance and documentation of the epidemiology and burden of community-acquired pneumonia across various geographical regions is warranted.
A Random Walk Framework to Compute Textual Semantic Similarity: A Unified Model for Three Benchmark Tasks

A network of concepts is built from Wikipedia documents using a random walk approach to compute distances between documents. Three algorithms for distance computation are considered: hitting/commute time, personalized page rank, and truncated visiting probability. In parallel, four types of weighted links in the document network are considered: actual hyperlinks, lexical similarity, common category membership, and common template use. The resulting network is used to solve three benchmark semantic tasks – word similarity, paraphrase detection between sentences, and document similarity – by mapping pairs of data to the network, and then computing a distance between these representations. The model reaches state-of-the-art performance on each task, showing that the constructed network is a general, valuable resource for semantic similarity judgments.
Mining Brand Perceptions from Twitter Social Networks

Consumer perceptions are important components of brand equity and therefore marketing strategy. Segmenting these perceptions into attributes such as eco-friendliness, nutrition, and luxury enable a fine-grained understanding of the brand’s strengths and weaknesses. Traditional approaches towards monitoring such perceptions (e.g., surveys) are costly and time consuming, and their results may quickly become outdated. Extant data mining methods are unsuitable for this goal, and generally require extensive hand-annotated data or context customization, which leads to many of the same limitations as direct elicitation. Here, we investigate a novel, general, and fully automated method for inferring attribute-specific brand perception ratings by mining the brand’s social connections on Twitter. Using a set of over 200 brands and three perceptual attributes, we compare the method’s automatic ratings estimates with directly-elicited survey data, finding a consistently strong correlation. The approach provides a reliable, flexible, and scalable method for monitoring brand perceptions, and offers a foundation for future advances in understanding brand-consumer social media relationships.Data, as supplemental material, are available at http://dx.doi. org/10.1287/mksc.2015. 0968 .
Infection after pacemaker implantation: infection rates and risk factors associated with infection in a population-based cohort study of 46299 consecutive patients

Aims Infection is a serious complication of pacemaker (PM) systems. Although the rate of infection has been debated, the figures are largely unknown. We therefore studied the incidence of PM infection and its associated risk factors in the Danish population. Methods and results Since 1982, all PM implantation and removal procedures performed in Denmark have been prospectively recorded in the Danish Pacemaker Register. All patients (n = 46299) who underwent implantation between 1982 and 2007 were included. The total length of surveillance was 236 888 PM-years. The incidence of infection was calculated according to the total number of PM-years. The incidence of surgical site infection (≤365 days after PM implantation) was compared with later infection in first implant and replacement procedures. Multiple-record and multiple-event-per-subject proportional hazards analyses were used to identify the independent risk factors of PM infection. Surgical site infection occurred in 192 cases after first implantation (incidence rate 4.82/1000 PM-years), and in 133 cases after replacement (12.12/1000 PM-years). Infections occurring more than 365 days after the first implantation occurred in 153 cases (1.02/1000 PM-years), and in 118 cases after replacement (3.26/1000 PM-years). Independent factors associated with an increased risk of PM infection were a greater number of PM operations (including replacements), male sex, younger age, implantation during the earliest part of the study period, and absence of antibiotics (P< 0.001). Conclusion The overall risk of infection after PM implantation was low. A greater number of operations augmented the risk of infection. This should be taken into account when considering revisions of PM systems.
A local mechanism mediates NAD-dependent protection of axon degeneration

Axon degeneration occurs frequently in neurodegenerative diseases and peripheral neuropathies. Important insight into the mechanisms of axon degeneration arose from findings that the degeneration of transected axons is delayed in Wallerian degeneration slow (Wlds) mice with the overexpression of a fusion protein with the nicotinamide adenine dinucleotide (NAD) synthetic enzyme, nicotinamide mononucleotide adenylyltransferase (Nmnat1). Although both Wlds and Nmnat1 themselves are functional in preventing axon degeneration in neuronal cultures, the underlying mechanism for Nmnat1- and NAD-mediated axon protection remains largely unclear. We demonstrate that NAD levels decrease in degenerating axons and that preventing this axonal NAD decline efficiently protects axons from degeneration. In support of a local protective mechanism, we show that the degeneration of axonal segments that have been separated from their soma could be prevented by the exogenous application of NAD or its precursor nicotinamide. Furthermore, we provide evidence that such Nmnat1/NAD-mediated protection is primarily mediated by their effects on local bioenergetics. Together, our results suggest a novel molecular pathway for axon degeneration.
Investigating Classroom Interaction: Teacher and Learner Participation

This study on teacher and learner interaction was carried out with the sole purpose of understanding the collaborative behavior and the impact of different individuals on classroom environment. The study further analyzed the suitable methods of improving and maintaining a good learning environment. The administration of the questionnaire is the best method apart from observation and interviews among other approaches to effectively analyze learning in the classroom.The research further observed the impact of communication, behavior, and attitude in the learning environment (Fraser, 2012). This study also observed how the teacher can influence the student’s career directly or indirectly based on the mode of conducting their teaching practices in a classroom environment. Also, the model of classroom interaction formulated is comprehensive of interrelated factors such as effects of a foreign language on learning, outer contexts surrounding classroom, learning materials, and learning objectives.
A qualitative exploration of basic emotions and the affective phenomena of post-traumatic stress disorder

13 Introduction . 15 Method . 18 Research design . 18 Phase 1: Finding the studies and searching the literature . 19 Phase 2: Reading the studies and quality assessment . 22 Analysis . 23 Phase 3: Determining how studies are related . 23 Phase 4: Translating the studies into one another . 24 Phase 5 & 6: Synthesising the translations and reporting conclusions . 24 Trustworthiness . 25 Results . 25 Quality and characteristics of the included studies . 25 Meta-synthesis . 27 Second-order interpretation . 30 Trauma shatters safety schemas: . 30 Relational ‘non-specifics’ encourage treatment engagement: . 30
Frequencies of two functionally significant SNPs and their haplotypes of organic anion transporting polypeptide 1B1 SLCO1B1 gene in six ethnic groups of Pakistani population

Objective(s): Organic anion transporter polypeptide 1B1 (OATP1B1) encoded by solute carrier organic transporter 1B1 (SLCO1B1) gene; a transporter involved in the uptake of drugs and endogenous compounds is present in hepatocyte sinusoidal membrane. Aim of this study was to investigate the frequencies of functionally significant SNPs (388A>G and 521T>C) and their haplotypes in 6 ethnic groups of Pakistani population through the development of rapid and efficient Tetra amplification refractory mutation system (T. ARMS) genotyping assay. Materials and Methods: Frequencies of alleles, genotype, and haplotypes of two functionally significant Single nucleotide polymorphism in 180 healthy Pakistani subjects and distributions in six ethnic groups by using a single step T. ARMS genotyping assay. Results: The allelic frequency for 388A>G SNP was 50% in total Pakistani population with Single nucleotide polymorphism distributions of 9.7%, 15.1%, 19.4%, 16.1%, 18.3%, and 21.5% in Punjabi, Sindhi, Balouchi, Pathan, Kashmiri and Hazara/Baltistan groups respectively; and for 521T>C SNP it was 23.9% in total Pakistani population with distributions of 11.1%, 8.9%, 15.6%, 11.1%, 31.1% and 22.2% in Punjabi, Sindhi, Balouchi, Pathan, Kashmiri, and Hazara/Baltistan groups. Both functionally significant SNPs occurred in four major haplotypes with a frequency of 35.5% for 388A/521T (*1A), 40.5% for 388G/521T (*1B), 14.4% for 388A/521C (*5), and 9.4% for 388G/521C (*15) with varying distributions among six ethnic groups. Conclusion: The 388A>G and 521T>C genotypes and corresponding haplotypes are present at varying frequencies in various ethnic groups of Pakistani population. Pharmacokinetic and pharmacodynamic profiling is needed to assess and characterize the effects of these haplotypes in our population.
Differential Modulation of Corticospinal Excitability by Different Current Densities of Anodal Transcranial Direct Current Stimulation

Background Novel non-invasive brain stimulation techniques such as transcranial direct current stimulation (tDCS) have been developed in recent years. TDCS-induced corticospinal excitability changes depend on two important factors current intensity and stimulation duration. Despite clinical success with existing tDCS parameters, optimal protocols are still not entirely set. Objective/hypothesis The current study aimed to investigate the effects of four different anodal tDCS (a-tDCS) current densities on corticospinal excitability. Methods Four current intensities of 0.3, 0.7, 1.4 and 2 mA resulting in current densities (CDs) of 0.013, 0.029, 0.058 and 0.083 mA/cm2 were applied on twelve right-handed (mean age 34.5±10.32 yrs) healthy individuals in different sessions at least 48 hours apart. a-tDCS was applied continuously for 10 minute, with constant active and reference electrode sizes of 24 and 35 cm2 respectively. The corticospinal excitability of the extensor carpi radialis muscle (ECR) was measured before and immediately after the intervention and at 10, 20 and 30 minutes thereafter. Results Post hoc comparisons showed significant differences in corticospinal excitability changes for CDs of 0.013 mA/cm2 and 0.029 mA/cm2 (P = 0.003). There were no significant differences between excitability changes for the 0.013 mA/cm2 and 0.058 mA/cm2 (P = 0.080) or 0.013 mA/cm2 and 0.083 mA/cm2 (P = 0.484) conditions. Conclusion This study found that a-tDCS with a current density of 0.013 mA/cm2 induces significantly larger corticospinal excitability changes than CDs of 0.029 mA/cm2. The implication is that might help to avoid applying unwanted amount of current to the cortical areas.
Generalizing Adversarial Reinforcement

Reinforcement Learning has been used for a number of years in single agent environments. This article reports on our investigation of Reinforcement Learning techniques in a multi-agent and adversarial environment with continuous observable state information. Our framework for evaluating algorithms is two-player hexagonal grid soccer. We introduce an extension to Prioritized Sweeping that allows generalization of learnt knowledge over neighboring states in the domain and we introduce an extension to the U Tree generalizing algorithm that allows the handling of continuous state spaces.
Impaired CXCL4 expression in tumor-associated macrophages (TAMs) of ovarian cancers arising in endometriosis

Inflammatory cells play important roles in progression of solid neoplasms including ovarian cancers. Tumor-associated macrophages (TAMs) contribute to angiogenesis and immune suppression by modulating microenvironment. Ovarian cancer develops occasionally on the bases of endometriosis, a chronic inflammatory disease. We have recently demonstrated differential expressions of CXCR3 variants in endometriosis and ovarian cancers. In this study, we showed impaired CXCL4 expression in TAMs of ovarian cancers arising in endometriosis. The expressions of CXCL4 and its variant CXCL4L1 were investigated among normal ovaries (n = 26), endometriosis (n = 18) and endometriosis-associated ovarian cancers (EAOCs) composed of clear cell (n = 13) and endometrioid (n = 11) types. In addition, four cases of EAOCs that contained both benign and cancer lesions contiguously in single cysts were investigated in the study. Western blot and quantitative RT-PCR analyses revealed significant downregulation of CXCL4 and CXCL4L1 in EAOCs compared with those in endometriosis. In all EAOCs coexisting with endometriosis in the single cyst, the expression levels of CXCL4 and CXCL4L1 were significantly lower in cancer lesions than in corresponding endometriosis. Histopathological study revealed that CXCL4 was strongly expressed in CD68+ infiltrating macrophages of endometriosis. In microscopically transitional zone between endometriosis and EAOC, CD68+ macrophages often demonstrated CXCL4− pattern. The majority of CD68+ TAMs in overt cancer lesions were negative for CXCL4. Collective data indicate that that CXCL4 insufficiency may be involved in specific inflammatory microenvironment of ovarian cancers arising in endometriosis. Suppression of CXCL4 in cancer lesions is likely to be attributable to TAMs in part.
Extragonadal germ cell tumors.

Germ cell cancer is the most common malignancy in men aged 15–35 years; 5% of the malignant germ cell tumors are of extragonadal origin [1]. An extragonadal germ cell tumor (EGGCT) is by definition a germ cell neoplasm displaying one of the histologies associated with gonadal origin, but located outside of the gonads. This specific clinical entity was first described in the 19th century [2, 3]. Histological, serological and cytogenetic characteristics of EGGCTs are similar to those of primary testicular germ cell tumors, but major differences in clinical behavior suggest that gonadal and extragonadal tumors are biologically different (Table 1). In particular, this is true of primary mediastinal EGGCTs and tumors originating in the sacrococcygeal or pineal region; in contrast, tumors arising in the retroperitoneum are more often associated with premalignant lesions in one of the testes and behave clinically in a manner very similar to that of the primary testis counterpart. Also male patients with carcinoma of unknown primary (CUP syndrome) with undifferentiated histology and typical germ cell tumor serum markers, as well as presentation in the midline structures, belong to the group of EGGCT. However, in practice it may be difficult to distinguish extragonadal tumors from metastatic tumors where the primary testis lesion has regressed, e.g. in some cases a scar is found in the testis probably representing a ‘burn-out’ or ‘autoinfarcted’ primary [4]. Furthermore, it is unclear whether the presence of a carcinoma in situ or intraepithelial germ cell neoplasia represents a primary tumor lesion resulting in metastatic deposits e.g. in the mediastinum or retroperitoneum, or whether this testicular lesion represents a general premalignant or malignant change of germ cells at any location distributed in the body, leading to an extragonadal malignant tumor.
A Broadband 220-320 GHz Medium Power Amplifier Module

In this paper, we present the development of an ultra-broadband H-band (220 - 325 GHz) submillimeter-wave monolithic integrated circuit (S-MMIC) medium power amplifier (MPA) module for use in next generation high-resolution imaging systems and communication links operating around 300 GHz. Therefore, a variety of compact amplifier circuits has been developed by using an advanced 35 nm InAlAs/InGaAs based depletion-type metamorphic high electron mobility transistor (mHEMT) technology in combination with grounded coplanar waveguide (GCPW) circuit topology. A three-stage amplifier S-MMIC based on compact cascode devices was realized, demonstrating a maximum gain of 22.2 dB at 294 GHz and a small-signal gain of more than 16 dB over the frequency range from 184 to 312 GHz. Finally, mounting and packaging of the monolithic amplifier chip into a WR-3.4 waveguide module was accomplished with only minor reduction in circuit performance.
How to find the optimal paths in stochastic time-dependent transportation networks?

This paper conducted a theoretical study on finding optimal paths in stochastic time-dependent (STD) transportation networks. A stochastic consistent network with STD link travel times was built. The methodology of robust optimization was applied to evaluate the paths for a priori optimization without requiring the probability distribution of travel times. The paths with greatest robustness, namely minimum upper bounds of travel times were defined as the optimal path. Under the stochastic consistent condition, the STD robust optimal path model can be converted into solving a time-dependent shortest path problem in a FIFO network. Then extended Dijkstra's algorithm can be applied to solve the simplified STD problem with computation complexity O(n2). In the field experiment, several tests were conducted on finding robust optimal paths in a sampled STD transportation network of Shanghai, China. The numerical results confirmed the validity of the proposed approach and verified that the natural extension of conventional Dijkstra's algorithm can solve the STD robust optimal path problem as efficiently as a static network problem.