Miracle-dz/UniFAR-FTUs huggingface dataset:
Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red alga Galdieria sulphuraria to its hot, acid, toxic‐metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice‐binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism.
Prefrontal Activity and Diagnostic Monitoring of Memory Retrieval: fMRI of the Criterial Recollection Task

According to the distinctiveness heuristic, subjects rely more on detailed recollections (and less on familiarity) when memory is tested for pictures relative to words, leading to reduced false recognition. If so, then neural regions that have been implicated in effortful postretrieval monitoring (e.g., dorsolateral prefrontal cortex) might be recruited less heavily when trying to remember pictures. We tested this prediction with the criterial recollection task. Subjects studied black words, paired with either the same word in red font or a corresponding colored picture. Red words were repeated at study to equate recognition hits for red words and pictures. During fMRI scanning, alternating red word memory tests and picture memory tests were given, using only white words as test stimuli (say yes only if you recollect a corresponding red word or picture, respectively). These tests were designed so that subjects had to rely on memory for the criterial information. Replicating prior behavioral work, we found enhanced rejection of lures on the picture test compared to the red word test, indicating that subjects had used a distinctiveness heuristic. Critically, dorsolateral prefrontal activity was reduced when rejecting familiar lures on the picture test, relative to the red word test. These findings indicate that reducing false recognition via the distinctiveness heuristic is not heavily dependent on frontally mediated postretrieval monitoring processes.
Trends in Employment and Earnings of Allowed and Rejected Applicants to the Social Security Disability Insurance Program.

3308 Since the early 1980s, changes in the economic environment and in the process for determining eligibility for the Social Security Disability Insurance (DI) program have had significant effects on the program. First, the economic situation and labor force opportunities for lower-skilled people continued to decline, leading to lower rates of participation in the labor force for less-educated men. Second, changes in the eligibility process made it easier to obtain DI benefits based on conditions difficult to clearly identify on medical terms alone, such as back pain or depression. Those two factors have likely contributed to a substantial increase in the number of individuals receiving DI, as well as a significant change in the characteristics of applicants and new beneficiaries over the same period. Both applicants and new beneficiaries have become younger, longer-lived, more likely to apply because of nonterminal conditions such as back pain or mental health, and more likely to be female. As a result, recent work projects a rapid increase in program costs as greater numbers of beneficiaries stay on the program for more years (e.g., David H. Autor and Duggan 2006). The concurrent developments in the economy and eligibility rules have also fueled the concern that the generosity of DI increasingly induces low-income workers to apply for and sometimes receive benefits, and that some of those beneficiaries would be able to work in the absence of the program. Indeed, a growing body of research suggests that some workers in difficult economic conditions exit the labor force to
Immunoglobulin G1 Allotype Influences Antibody Subclass Distribution in Response to HIV gp140 Vaccination

Antibody subclasses exhibit extensive polymorphisms (allotypes) that could potentially impact the quality of HIV-vaccine induced B cell responses. Allotypes of immunoglobulin (Ig) G1, the most abundant serum antibody, have been shown to display altered functional properties in regard to serum half-life, Fc-receptor binding and FcRn-mediated mucosal transcytosis. To investigate the potential link between allotypic IgG1-variants and vaccine-generated humoral responses in a cohort of 14 HIV vaccine recipients, we developed a novel protocol for rapid IgG1-allotyping. We combined PCR and ELISA assays in a dual approach to determine the IgG1 allotype identity (G1m3 and/or G1m1) of trial participants, using human plasma and RNA isolated from PBMC. The IgG1-allotype distribution of our participants mirrored previously reported results for caucasoid populations. We observed elevated levels of HIV gp140-specific IgG1 and decreased IgG2 levels associated with the G1m1-allele, in contrast to G1m3 carriers. These data suggest that vaccinees homozygous for G1m1 are predisposed to develop elevated Ag-specific IgG1:IgG2 ratios compared to G1m3-carriers. This elevated IgG1:IgG2 ratio was further associated with higher FcγR-dimer engagement, a surrogate for potential antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) function. Although preliminary, these results suggest that IgG1 allotype may have a significant impact on IgG subclass distribution in response to vaccination and associated Fc-mediated effector functions. These results have important implications for ongoing HIV vaccine efficacy studies predicated on engagement of FcγR-mediated cellular functions including ADCC and ADCP, and warrant further investigation. Our novel allotyping protocol provides new tools to determine the potential impact of IgG1 allotypes on vaccine efficacy.
Intrageneric Variability Between the Chloroplast Genomes of Trachelomonas grandis and Trachelomonas volvocina and Phylogenomic Analysis of Phototrophic Euglenoids

The latest studies of chloroplast genomes of phototrophic euglenoids yielded different results according to intrageneric variability such as cluster arrangement or diversity of introns. Although the genera Euglena and Monomorphina in those studies show high syntenic arrangements at the intrageneric level, the two investigated Eutreptiella species comprise low synteny. Furthermore Trachelomonas volvocina show low synteny to the chloroplast genomes of the sister genera Monomorphina aenigmatica, M. parapyrum, Cryptoglena skujae, Euglenaria anabaena, Strombomonas acuminata, all of which were highly syntenic. Consequently, this study aims at the analysis of the cpGenome of Trachelomonas grandis and a comparative examination of T. volvocina to investigate whether the cpGenomes are of such resemblance as could be expected for a genus within the Euglenaceae. Although these analyses resulted in almost identical gene content to other Euglenaceae, the chloroplast genome showed significant novelties: In the rRNA operon, we detected group II introns, not yet found in any other cpGenome of Euglenaceae and a substantially heterogeneous cluster arrangement in the genus Trachelomonas. The phylogenomic analysis with 84 genes of 19 phototrophic euglenoids and 18 cpGenome sequences from Chlorophyta and Streptophyta resulted in a well‐supported cpGenome phylogeny, which is in accordance to former phylogenetic analyses.
The ties that bind: Maternal kin bias in a multilevel primate society despite natal dispersal by both sexes

In many social animals, individuals derive fitness benefits from close social bonds, which are often formed among kin of the philopatric sex. Hamadryas baboons, however, exhibit a hierarchical, multilevel social system where both sexes disperse from their natal one‐male‐unit (OMU). Although this would seem to hinder maintenance of kin ties, both sexes appear largely philopatric at the higher order band and clan levels, possibly allowing for bonds with same sex kin by both males and females. In order to investigate the possibility of kin bonds in hamadryas baboons, we identified kin dyads in a band without known pedigree information using a large panel of genetic markers: 1 Y‐linked, 4 X‐linked, and 23 autosomal microsatellites and part of the mitochondrial hypervariable region I. With these data, we performed a kinship analysis while accounting for misclassification rates through simulations and determined kinship among two types of dyads: leader and follower males and female dyads within OMUs. Leader and follower males were maternal relatives more often than expected by chance, suggesting that kinship plays a role in the formation of these relationships. Moreover, maternal female relatives were found in the same OMU more often than expected by chance, indicating that females may be motivated to maintain post‐dispersal contact with maternal female kin. Our results suggest that hamadryas baboons can recognize maternal kin and that kin selection has contributed to shaping their complex social system. This implies that an ancestral maternal kin bias has been retained in hamadryas society. Am. J. Primatol. 78:731–744, 2016. © 2016 Wiley Periodicals, Inc.
A Novel Imaging Algorithm for Focusing High-Resolution Spaceborne SAR Data in Squinted Sliding-Spotlight Mode

To process squinted sliding-spotlight synthetic aperture radar data, the azimuth preprocessing step based on the linear range walk correction (LRWC) and derotation operations is implemented to eliminate the effect of 2-D spectrum skew and azimuth spectral aliasing. However, two key issues arise from the azimuth preprocessing. First, the traditional chirp scaling (CS) kernel is not suitable for data focusing because the property of the 2-D spectrum is changed significantly; second, the spatial variation of the targets' Doppler rates along the azimuth direction due to the LRWC operation limits the depth-of-azimuth-focus (DOAF) seriously. In this letter, a modified accurate CS kernel is derived to realize range compensation. Then, an azimuth spatial variation removing method based on the principle of nonlinear CS is proposed to equalize the Doppler rates of the targets located at the same range cell, which can extend the DOAF and improve processing efficiency. Finally, a novel imaging algorithm is proposed, with its effectiveness demonstrated by simulation results.
Increased arterial stiffness in childhood onset diabetes: a cardiovascular magnetic resonance study

Aims Arterial stiffness is a strong predictor of cardiovascular events. We aimed to assess the impact of type 1 diabetes (T1D) on arterial stiffness and cardiac function in young adults. Methods and results Aortic pulse wave velocity (PWV), distensibility, left ventricular (LV) function and LV mass were measured by cardiovascular magnetic resonance imaging (CMR) in 47 T1D patients and 33 healthy controls. All were participants in the Atherosclerosis and Childhood Diabetes study, with baseline values registered 5 years previously. The patients had a mean age of 20.8 years and a median duration of diabetes of 10.0 years. PWV was significantly higher in the diabetes group compared with controls, mean 4.10 (SD = 4.58) vs. 3.90 (SD = 4.04) m/s, P = 0.045. In the diabetes group, insulin pump users at baseline had lower PWV than multiple injection users, mean 3.94 (SD = 0.38) vs. 4.23 (SD = 0.48) m/s, P = 0.028. Also in the diabetes group, multiple regression analysis identified C-reactive protein (CRP), female gender and insulin pump use as independent baseline risk factors for PWV 5 years later. There was no difference in cardiac function or LV mass between the diabetes and control groups. Conclusion In this prospective study, we found increased PWV assessed by CMR in young adults with T1D compared with controls. Also, CRP, female gender and insulin pump use emerged as independent baseline risk factors for PWV 5 years later.
Standardized Attending Rounds to Improve the Patient Experience: A Pragmatic Cluster Randomized Controlled Trial

BACKGROUND: At academic medical centers, attending rounds (AR) serve to coordinate patient care and educate trainees, yet variably involve patients. OBJECTIVE: To determine the impact of standardized bedside AR on patient satisfaction with rounds. DESIGN: Cluster randomized controlled trial. SETTING: 500‐bed urban, quaternary care hospital. PATIENTS: 1200 patients admitted to the medicine service. INTERVENTION: Teams in the intervention arm received training to adhere to 5 AR practices: 1) pre‐rounds huddle; 2) bedside rounds; 3) nurse integration; 4) real‐time order entry; 5) whiteboard updates. Control arm teams continued usual rounding practices. MEASUREMENTS: Trained observers audited rounds to assess adherence to recommended AR practices and surveyed patients following AR. The primary outcome was patient satisfaction with AR. Secondary outcomes were perceived and actual AR duration, and attending and trainee satisfaction. RESULTS: We observed 241 (70.1%) and 264 (76.7%) AR in the intervention and control arms, respectively, which included 1855 and 1903 patient rounding encounters. Using a 5‐point Likert scale, patients in the intervention arm reported increased satisfaction with AR (4.49 vs 4.25; P = 0.01) and felt more cared for by their medicine team (4.54 vs 4.36; P = 0.03). Although the intervention shortened the duration of AR by 8 minutes on average (143 vs 151 minutes; P = 0.052), trainees perceived intervention AR as lasting longer and reported lower satisfaction with intervention AR. CONCLUSIONS: Medicine teams can adopt a standardized, patient‐centered, time‐saving rounding model that leads to increased patient satisfaction with AR and the perception that patients are more cared for by their medicine team.
Program Synthesis from Natural Language Using Recurrent Neural Networks

Oftentimes, a programmer may have difficulty implementing a desired operation. Even when the programmer can describe the goal in English, it can be difficult to translate into code. Existing resources, such as question-and-answer websites, tabulate specific operations that someone has wanted to perform in the past, but they are not effective in generalizing to new tasks, to compound tasks that require combining previous questions, or sometimes even to variations of listed tasks. Our goal is to make programming easier and more productive by letting programmers use their own words and concepts to express the intended operation, rather than forcing them to accommodate the machine by memorizing its grammar. We have built a system that lets a programmer describe a desired operation in natural language, then automatically translates it to a programming language for review and approval by the programmer. Our system, Tellina, does the translation using recurrent neural networks (RNNs), a state-of-the-art natural language processing technique that we augmented with slot (argument) filling and other enhancements. We evaluated Tellina in the context of shell scripting. We trained Tellina’s RNNs on textual descriptions of file system operations and bash one-liners, scraped from the web. Although recovering completely correct commands is challenging, Tellina achieves top-3 accuracy of 80% for producing the correct command structure. In a controlled study, programmers who had access to Tellina outper-formed those who did not, even when Tellina’s predictions were not completely correct, to a statistically significant
Complete Synchronous Vibration Suppression for a Variable-Speed Magnetically Suspended Flywheel Using Phase Lead Compensation

The synchronous vibration rising from the magnetically suspended flywheel (MSFW) will drastically reduce the pointing precision of the satellites. In this paper, the high precision suppression for the frequency-varying synchronous vibration forces in the permanent-magnet-biased hybrid MSFW is investigated. First, the synchronous vibration forces generated in the permanent-magnet-biased hybrid magnetic bearing are modeled and analyzed. Then, a practical and effective synchronous vibration suppression method is proposed to plug into the baseline magnetic suspension system. The proposed method ascertains the overall system stability over the entire speed range by an adjustable phase angle. Moreover, it eliminates the residual synchronous vibration forces in the negative displacement stiffness by considering phase-lag influence of the power amplifier. The direct testing for the synchronous vibration forces proves the feasibility of the proposed suppression method.
RUNNING HEAD : Status conflict in groups Status Conflict in Groups

We introduce status conflicts-defined as attempts to defend or elevate one's own relative status (i.e., prominence or respect)-as a key group process that affects task group performance. Using mixed research methods, we qualitatively identify the characteristics of status conflicts, validate a four-item survey scale that distinctly measures status conflict, and investigate the relationship between status conflict and group performance. We determine that status conflict exerts a significant, negative main effect and moderates the effects of task conflict on group performance. A significant volume of research has analyzed the relationship between various types of conflict and task group performance (e.g., De Dreu & Weingart 2003b). Scholars have distinguished among task conflict, which is disagreement over ideas, viewpoints and opinions pertaining to the group's task, relationship conflict, which is disagreement resulting from interpersonal incompatibilities, including affective components such as feeling tension and process conflict, which is conflict about dividing and delegating responsibilities and deciding how to get work done (Jehn 1997). As we read ethnographies of organizational conflicts, however, we found numerous examples that did not fit one of those three categories. Instead, they seemed to involve conflicts over status, which is the prominence and respect conferred upon an individual by others & Correll 2006). For example, consider the description of " Black Friday " in Roy's (1959) classic Banana Time article. In this example, low status Ike publically insulted high status George. George perceived this as a challenge to his superior status, and responded by giving Ike the " silent treatment " for thirteen days. To the author, George said, " Ike acts like a five-year old, not a man! … He's always fooling around! I'm going to stop that! I'm going to show him his place! " (p. 165, italics added). In the end, the relationship between George and Ike returned to normal only once the status order had been clearly restored. The symbolic power one derives from positions of high status depends on the acceptance and deference of low status group members (Goffman 1967). Given the benefits of status, including greater influence, credit for contributing more to the group than others, rewards such as information and resources that contribute to individuals' performance (Friedkin 1999; Ridgeway & Correll 2006), and more positive evaluations than those with low status in groups (Berger, Rosenholtz & Zelditch 1980), it Status conflicts in groups 3 seems logical that individuals would compete for status and …
A Second Actin-Like MamK Protein in Magnetospirillum magneticum AMB-1 Encoded Outside the Genomic Magnetosome Island

Magnetotactic bacteria are able to swim navigating along geomagnetic field lines. They synthesize ferromagnetic nanocrystals that are embedded in cytoplasmic membrane invaginations forming magnetosomes. Regularly aligned in the cytoplasm along cytoskeleton filaments, the magnetosome chain effectively forms a compass needle bestowing on bacteria their magnetotactic behaviour. A large genomic island, conserved among magnetotactic bacteria, contains the genes potentially involved in magnetosome formation. One of the genes, mamK has been described as encoding a prokaryotic actin-like protein which when it polymerizes forms in the cytoplasm filamentous structures that provide the scaffold for magnetosome alignment. Here, we have identified a series of genes highly similar to the mam genes in the genome of Magnetospirillum magneticum AMB-1. The newly annotated genes are clustered in a genomic islet distinct and distant from the known magnetosome genomic island and most probably acquired by lateral gene transfer rather than duplication. We focused on a mamK-like gene whose product shares 54.5% identity with the actin-like MamK. Filament bundles of polymerized MamK-like protein were observed in vitro with electron microscopy and in vivo in E. coli cells expressing MamK-like-Venus fusions by fluorescence microscopy. In addition, we demonstrate that mamK-like is transcribed in AMB-1 wild-type and ΔmamK mutant cells and that the actin-like filamentous structures observed in the ΔmamK strain are probably MamK-like polymers. Thus MamK-like is a new member of the prokaryotic actin-like family. This is the first evidence of a functional mam gene encoded outside the magnetosome genomic island.
Users' relevance criteria for video in leisure contexts

Purpose The purpose of this paper is to understand how typical users of YouTube judge the relevance of videos in leisure contexts; what are the reasons users give when judging video material as relevant or not relevant? Design/methodology/approach A naturalistic diary was performed in which 30 participants completed diaries providing details on their video relevance criteria. The analysis revealed 28 relevance criteria grouped into eight categories. Findings In total, 28 relevance criteria were identified through the analyses of the diaries’ content and they were grouped into eight categories. The findings revealed that criteria related to the content of the video are the most dominant group of criteria with topicality being the most dominant criterion. There is a considerable overlap between leisure relevance criteria and previous relevance criteria studies, but the importance of these criteria varies among different contexts. New criteria, e.g. habit emerged from the data which tend to be more related to leisure contexts. Research limitations/implications The decision to follow a naturalistic approach reduced the level of control on the study. A further limitation can be found in the participants’ sample used in this study, all the participants of the main study were university or college students. Practical implications This study attempted to enrich the current literature by investigating users’ video relevance criteria in leisure contexts. This investigation might have implications on the design of video search systems. Originality/value Previous relevance criteria studies focussed on work contexts and the information judged was mainly in text format. This paper outlines new insights by investigating video relevance criteria in leisure context.