Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic profiles reveal evolutionary relationships within the “twilight zone” of sequence similarity

Inferring evolutionary relationships among highly divergent protein sequences is a daunting task. In particular, when pairwise sequence alignments between protein sequences fall <25% identity, the phylogenetic relationships among sequences cannot be estimated with statistical certainty. Here, we show that phylogenetic profiles generated with the Gestalt Domain Detection Algorithm–Basic Local Alignment Tool (GDDA-BLAST) are capable of deriving, ab initio, phylogenetic relationships for highly divergent proteins in a quantifiable and robust manner. Notably, the results from our computational case study of the highly divergent family of retroelements accord with previous estimates of their evolutionary relationships. Taken together, these data demonstrate that GDDA-BLAST provides an independent and powerful measure of evolutionary relationships that does not rely on potentially subjective sequence alignment. We demonstrate that evolutionary relationships can be measured with phylogenetic profiles, and therefore propose that these measurements can provide key insights into relationships among distantly related and/or rapidly evolving proteins.
Tail Behavior and Limit Distribution of Maximum of Logarithmic General Error Distribution

Logarithmic general error distribution, an extension of the log-normal distribution, is proposed. Some interesting properties of the log GED are derived. These properties are applied to establish the asymptotic behavior of the ratio of probability densities and the ratio of the tails of the logarithmic general error and log-normal distributions, and to derive the asymptotic distribution of the partial maximum of an independent and identically distributed sequence obeying the log GED.
Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron-ion interaction pseudopotential features

The identification of hot spots, a small subset of protein interfaces that accounts for the majority of binding free energy, is becoming more important for the research of drug design and cancer development. Based on our previous methods (APIS and KFC2), here we proposed a novel hot spot prediction method. For each hot spot residue, we firstly constructed a wide variety of 108 sequence, structural, and neighborhood features to characterize potential hot spot residues, including conventional ones and new one (pseudo hydrophobicity) exploited in this study. We then selected 3 top-ranking features that contribute the most in the classification by a two-step feature selection process consisting of minimal-redundancy-maximal-relevance algorithm and an exhaustive search method. We used support vector machines to build our final prediction model. When testing our model on an independent test set, our method showed the highest F1-score of 0.70 and MCC of 0.46 comparing with the existing state-of-the-art hot spot prediction methods. Our results indicate that these features are more effective than the conventional features considered previously, and that the combination of our and traditional features may support the creation of a discriminative feature set for efficient prediction of hot spots in protein interfaces.
Deaf Ni-Vanuatu and their signs: A sociolinguistic study

This thesis provides the first documentation and description of the signs created and used by deaf individuals in Vanuatu. The specific aims of this research were as follows: to establish the sociolinguistic context experienced by deaf people in Vanuatu; to identify the repertoire and characteristics of signs used by the deaf participants; to compare features of participants’ individual signs with the characteristics of home signs and emerging sign languages; and to consider the degree of similarity and potential similarity of signs between participants and how this reflects individuals’ opportunities for contact with other deaf people and signing interlocutors. The limitations of this study are that field methodology for data collection was developed in situ as conditions allowed. The sociolinguistic context for deaf Ni-Vanuatu confirms that language isolation leads to marginalisation from community and society. The study established that these home sign lexicons were limited in quantity and conceptual range, and that shared background knowledge was essential for comprehension. Overall, 22 handshapes were documented, and the predominant handshapes unmarked. Most participants preferred handling strategy for depicting signs. Some evidence of noun-verb distinction was noted in the repertoire of some participants. However, across this range of formational characteristics, results showed significant individual variations. Furthermore, multiple barriers have precluded development of a shared sign language and any form of deaf community.
Genetic Polymorphisms of Transcription Factor NRF2 and of its Host Gene Sulfiredoxin (SRXN1) are Associated with Cerebrovascular Disease in a Finnish Cohort, the TAMRISK Study

Oxidative stress is involved in the pathophysiology of many cardiovascular disorders, such as hypertension and atherosclerosis. NRF2 is the primary transcriptional regulator of several antioxidant genes, including that of sulfiredoxin (SRXN1). The association of genotypes of NRF2 and SRXN1 with cardiovascular conditions was studied in a Finnish cohort of 336 subjects with diagnosed hypertension and 480 normotensive controls from the Tampere adult population cardiovascular risk study (TAMRISK). Samples were genotyped for four SNPs (rs1962142, rs2706110, rs6721961 and rs6706649) in the NRF2 gene region and four SNPs (rs6053666, rs6116929, rs2008022, rs6085283) in the SRXN1 gene region using Competitive Allele Specific PCR (KASP) technique. Cardiovascular diseases were followed up from 2005 to 2014 using the Finnish National Hospital Discharge Registry (HILMO). Four out of eight studied polymorphisms: rs6721961, rs1962142, rs2706110 of NRF2, and rs6053666 of SRXN1 were associated with cerebrovascular disease. NRF2 polymorphism rs6721961 showed association with hypertension. NRF2 and SRXN1 polymorphisms, previously thought to be associated with human disease, appear to be associated particularly with cerebrovascular disease.
OH main line masers in the M 82 starburst

Abstract A study of the distribution of OH gas in the central region of the nearby active starburst galaxy M82 has confirmed two previously known bright masers and revealed several new main line masers. Three of these are seen only at 1665 MHz, one is detected only at 1667 MHz, while the rest are detected in both lines. Observations covering both the 1665 and 1667 MHz lines, conducted with both the Very Large Array (VLA) and the Multi-Element Radio Linked Interferometer Network (MERLIN), have been used to accurately measure the positions and velocities of these features. This has allowed a comparison with catalogued continuum features in the starburst such as HII regions and supernova remnants, as well as known water and satellite line OH masers. Most of the main line masers appear to be associated with known HII regions although the two detected only at 1665 MHz are seen along the same line of sight as known supernova remnants.
The effect of community-oriented policing on police use of force: does community matter?

Purpose The purpose of this paper is to examine whether community-oriented policing (COP) influences rates of police use of force across communities, and whether the impact of COP varies according to the level of violent crime in communities. Design/methodology/approach A range of data sources including police use of force reports, online surveys of Officers-in-Charge and recorded crime data was used to examine the association between formal and informal community consultation and the frequency of police use of force, across 64 socially challenged communities in Australia. Findings Poisson multilevel modelling indicated no overall association between informal or formal community engagement and rates of police use of force. However, significant interaction terms for both informal and formal community consultation with violent crime rates indicated that higher levels of informal and formal community consultation were associated with lower rates of police use of force in communities with higher levels of violent crime. This relationship was not evident in low violent crime areas. Research limitations/implications Communities were purposively sampled to have a high propensity for police use of force, on the basis that they had high rates of violent crime, or high levels of socio-economic disadvantage, or both. This research should be replicated with a representative sample of communities. Practical implications The findings extend the potential benefits of COP to reducing the use of coercive policing tactics in high violent crime communities. Originality/value This study finds that COP can reduce the frequency of violent encounters between police and community members in high violent crime communities.
The role of dopamine in planning

Planen, welches eine wichtige kognitive Fertigkeit darstellt, wurde in der Vergangenheit mehrfach mit dem Neurotransmitter Dopamin in Zusammenhang gebracht. Da vorherige Studien, in Bezug auf die Richtung dieses Zusammenhangs, zu unterschiedlichen Ergebnissen gelangt sind bedarf dieses Thema weiterer Forschung. In der vorliegenden Studie wurde der Zusammenhang von Dopamin und Planen in einem Between-Subject, Placebo-kontrollierten Design untersucht. 77 mannlichen Teilnehmern wurde entweder eine hohe Dosis des Dopamin D2/D3 Antagonisten Sulpiride (800 mg) oder ein Placebo verabreicht. Zusatzlich wurden alle Teilnehmer im Hinblick auf einen Genpolymorphismus, welcher im Zusammenhang steht mit der striatalen Dichte von Dopamin D2 Rezeptoren, stratifiziert. Die Planungsfahigkeit wurde erhoben mit dem One-Touch Stockings of Cambridge (OTSOC), welches eine modifizierte Version des Tower of London task darstellt. Wie hypothesiert wurde, fuhrte die Verabreichung des Dopamin D2/D3 Antagonisten Sulpiride zu einer verminderten Leistung in der Planungsaufgabe. Des Weiteren, wurden keine Effekte bezogen auf den Genpolymorphismus gefunden. Dies bedeutet, dass Probanden sich nicht in Abhangigkeit von ihrer striatalen Dopamin D2 Rezeptor Dichte unterschieden. Die Ergebnisse der vorliegenden Studie zeigen die Moglichkeit auf, dass Sulpiride nicht nur an striatalen Dopamin D2/D3 Rezeptoren wirkt, sondern ebenfalls kortikale Dopamin Rezeptoren blockiert. Die vorliegenden Ergebnisse stellen zudem die prominente Rolle striataler Dopamin D2 Rezeptoren in Frage. In zukunftigen Studien, sollte eine mogliche wichtige Rolle von Dopamin D3 Rezeptoren, beim Planen untersucht werden.
Photon triplets and bound entanglement

Entanglement is central to quantum information technologies. In this talk, I will describe recent experimental results in generation of novel entangled photon states using photons. I will show that a single-photon can be split into three using a cascade of spontaneous down-conversion processes. Further I will present a demonstration of bound entanglement, entangled states which cannot be distilled, by applying random polarization rotations on highly entangled pure states.
Cyanidin-3-O-glucoside: Physical-Chemistry, Foodomics and Health Effects

Anthocyanins (ACNs) are plant secondary metabolites from the flavonoid family. Red to blue fruits are major dietary sources of ACNs (up to 1 g/100 g FW), being cyanidin-3-O-glucoside (Cy3G) one of the most widely distributed. Cy3G confers a red hue to fruits, but its content in raspberries and strawberries is low. It has a good radical scavenging capacity (RSC) against superoxide but not hydroxyl radicals, and its oxidative potential is pH-dependent (58 mV/pH unit). After intake, Cy3G can be metabolized (phases I, II) by oral epithelial cells, absorbed by the gastric epithelium (1%–10%) and it is gut-transformed (phase II & microbial metabolism), reaching the bloodstream (<1%) and urine (about 0.02%) in low amounts. In humans and Caco-2 cells, Cy3G’s major metabolites are protocatechuic acid and phloroglucinaldehyde which are also subjected to entero-hepatic recycling, although caffeic acid and peonidin-3-glucoside seem to be strictly produced in the large bowel and renal tissues. Solid evidence supports Cy3G’s bioactivity as DNA-RSC, gastro protective, anti-inflammatory, anti-thrombotic chemo-preventive and as an epigenetic factor, exerting protection against Helicobacter pylori infection, age-related diseases, type 2 diabetes, cardiovascular disease, metabolic syndrome and oral cancer. Most relevant mechanisms include RSC, epigenetic action, competitive protein-binding and enzyme inhibition. These and other novel aspects on Cy3G’s physical-chemistry, foodomics, and health effects are discussed.
Stratos: A Network-Aware Orchestration Layer for Virtual Middleboxes in Clouds

Enterprises want their in-cloud services to leverage the performance and security benefits that middleboxes offer in traditional deployments. Such virtualized deployments create new opportunities (e.g., flexible scaling) as well as new challenges (e.g., dynamics, multiplexing) for middlebox management tasks such as service composition and provisioning. Unfortunately, enterprises lack systematic tools to efficiently compose and provision in-the-cloud middleboxes and thus fall short of achieving the benefits that cloud-based deployments can offer. To this end, we present the design and implementation of Stratos, an orchestration layer for virtual middleboxes. Stratos provides efficient and correct composition in the presence of dynamic scaling via software-defined networking mechanisms. It ensures efficient and scalable provisioning by combining middlebox-specific traffic engineering, placement, and horizontal scaling strategies. We demonstrate the effectiveness of Stratos using an experimental prototype testbed and large-scale simulations.
Rethinking the Mechanisms of Gang Desistance in a Developing Country

ABSTRACT Most academic literature is based on experiences of gang members in developed countries. This article explores the mechanisms of desistance among street gangs in El Salvador. Gangs in this Central American nation, which include MS-13 and the 18th Street gang, are known for complex structures and their transnational reach. Based on a survey with nearly 1,200 gang members and former gang members in El Salvador and 24 in-depth interviews with former gang members in rehabilitation programs, this study finds that the characteristics of the gang organization play a more significant role in the ways individuals exit the gangs in extremely violent contexts. It also shows that a religious experience is the most frequent mechanism to leave the group because it provides a safer alternative in those contexts.
Application of PTR-MS for Measuring Odorant Emissions from Soil Application of Manure Slurry

Odorous volatile organic compounds (VOC) and hydrogen sulfide (H2S) are emitted together with ammonia (NH3) from manure slurry applied as a fertilizer, but little is known about the composition and temporal variation of the emissions. In this work, a laboratory method based on dynamic flux chambers packed with soil has been used to measure emissions from untreated pig slurry and slurry treated by solid-liquid separation and ozonation. Proton-transfer-reaction mass spectrometry (PTR-MS) was used to provide time resolved data for a range of VOC, NH3 and H2S. VOC included organic sulfur compounds, carboxylic acids, phenols, indoles, alcohols, ketones and aldehydes. H2S emission was remarkably observed to take place only in the initial minutes after slurry application, which is explained by its high partitioning into the air phase. Long-term odor effects are therefore assessed to be mainly due to other volatile compounds with low odor threshold values, such as 4-methylphenol. PTR-MS signal assignment was verified by comparison to a photo-acoustic analyzer (NH3) and to thermal desorption GC/MS (VOC). Due to initial rapid changes in odorant emissions and low concentrations of odorants, PTR-MS is assessed to be a very useful method for assessing odor following field application of slurry. The effects of treatments on odorant emissions are discussed.
The Intentional Basis of Presence

Presence is the experience of being somewhere arising from the interplay of technological, psychological and bodily factors. Experiences, generally – though there are exceptionsTPPT, are a consequence of interactions with things and events in the world. Thus to experience is to experience something. Ordinarily these somethings are objects and events in the world but in presence research these are presented by way of technology. Either way, to understand an experience is to understand both the psychological and bodily states of the experiencer and the objects and events which give rise to the experience. Most, if not all, of these psychological and bodily factors are intentional. Intentionality refers to the about-ness or directed-ness of these states rather than the sense of being deliberate. The experience of presence is intentional. However, intentionality is better thought of as an arc connecting us with the world and consequentially giving rise to a range of experiences including the sense of presence. In order to understand this we must include both the embodied, psychological being at one end of the arc and the things, events and people at the other end. It is proposed that this external aspect of presence can be thought of as a meshwork of affordances. Thus the sense of presence is the product of an intentionality-affordance dynamic. Keywords--intentionality, affordance, experience.
The theory and practice of group psychotherapy, 5th ed.

IRVIN D. YALOM with MOLYN LESZCZ IRVIN D. YALOM, M.D. , is professor emeritus of psychiatry at the Stanford University School of Medicine. He was the recipient of the 1974 Edward Strecker Award and the 1979 Foundations’ Fund Prize in Psychiatry. He is the author of When Nietzsche Wept (winner of the 1993 Commonwealth Club gold medal for fiction), Love’s Executioner, and the classic textbooks Inpatient Group Psychotherapy and Existential Psychotherapy. His latest novel is The Schopenhauer Cure. He lives in Palo Alto, California.
Daylight availability in top-lit atria: prediction of skylight transmittance and daylight factor

Atrium and skylight shapes are important architectural design elements that influence daylight availability within the space and, therefore, lighting energy consumption. There is a lack of prediction models for skylight transmittance. and daylight availability in atria. A new concept was developed to predict the diffuse transmittance of skylights. A skylight shape is converted into a representative shape through a shape parameter. Generic formulae for the skylight diffuse transmittance were developed under different sky conditions. A zonal model combined with the flux transfer method was developed to predict daylight availability in top-lit atria through the predictions of the average daylight factor (DF) at the atrium floor and ceiling (non-glazed portion of the roof), and the local DF normal to walls. The DF model was compared with currently available models derived from theory and experiments under artificial skies. The results showed that the computed e transmittance for translucent skylights. under real partly cloudy or dear skies may reach up to 33% in summer and 56% in winter higher than that under CIE overcast skies. The developed zonal model yielded very dose results to the models based on the nnite-dement method. However, models based on physical scale measurements lack general consensus among themselves, and may produce average DF values at floor level up to 43% higher than those produced by the zonal model. Physical scale models may also yield local DF values normal to walls up to 50% lower than those predicted by the zonal model.
A Possibility to Square the Circle? Youth Uncertainty and the Imagination of Late Adulthood

Youth transitions literature has traditionally devoted great attention to identifying and analysing events that are considered crucial to young people regarding their (short term) orientation to the future and wider narratives of the self. Such categories as ‘turning points’, ‘critical moments’, and ‘crossroads’ have been used to identify and explain the events around which young people take important decisions in order to realise the so-called transition to adulthood, each suggesting a sense of rupture. This focus sits within a central interest of youth transition literature, namely to investigate what hinders or facilitates independence. When looking more broadly at how young people imagine their future, however, taking a longer perspective opens insights not only in terms of ruptures, which these categories tend to refer to, but also in terms of the continuities that might also be very important in these narratives. Despite the methodological difficulties in getting young people to speak about their long future, this article seeks to discuss how they see their late adulthood through reflecting on how their narratives play out across different temporal horizons in order to establish their current priorities. Empirically, it is substantiated by essays on the future written by 18-year-old students based in Sardinia, and discusses in particular an emphasis which they put on the long as a term of fulfilment of their values.
Splenic siderotic nodules in patients with liver cirrhosis

The aim of this study was to investigate the interrelation between splenic siderotic nodules, hypersplenism and liver function in patients with liver cirrhosis. The splenic enhanced susceptibility-weighted angiography (ESWAN) and conventional magnetic resonance images of 33 patients with liver cirrhosis were retrospectively studied and the ESWAN images were graded. The distribution and prevalence of the image grades for patients with and without hypersplenism were evaluated. In addition, the splenic volume and the distribution of Child-Pugh and albumin scores were compared between patients with and without siderotic nodules, and the correlation between splenic volume and the ESWAN image grades were evaluated in the patients with siderotic nodules. The ESWAN images revealed splenic siderotic nodules in 24 patients. The distribution and prevalence of the ESWAN image grades were demonstrated to be significantly different (P<0.001) between patients with and without hypersplenism. Furthermore, significant differences were observed between patients with and without siderotic nodules with regard to splenic volume and the distribution of Child-Pugh and serum albumin scores (P<0.001). No significant correlation was demonstrated between splenic volume and the ESWAN image grades (P>0.05). In conclusion, a higher prevalence of splenic siderotic nodules (72.7%) was observed using the ESWAN sequence, in comparison with results from previous studies, obtained using the T1-spoiled gradient echo sequence. The presence of splenic siderotic nodules was consistent with the occurrence of hypersplenism and was interrelated with reserved liver function.