Miracle-dz/UniFAR-FTUs huggingface dataset:
Donor CD4 T Cell Diversity Determines Virus Reactivation in Patients After HLA-Matched Allogeneic Stem Cell Transplantation

Delayed reconstitution of the T cell compartment in recipients of allogeneic stem cell grafts is associated with an increase of reactivation of latent viruses. Thereby, the transplanted T cell repertoire appears to be one of the factors that affect T cell reconstitution. Therefore, we studied the T cell receptor beta (TCRβ) gene rearrangements of flow cytometry–sorted CD4+ and CD8+ T cells from the peripheral blood of 23 allogeneic donors before G‐CSF administration and on the day of apheresis. For this purpose, TCRβ rearrangements were amplified by multiplex PCR followed by high‐throughput amplicon sequencing. Overall, CD4+ T cells displayed a significantly higher TCRβ diversity compared to CD8+ T cells irrespective of G‐CSF administration. In line, no significant impact of G‐CSF treatment on the TCR Vβ repertoire usage was found. However, correlation of the donor T cell repertoire with clinical outcomes of the recipient revealed that a higher CD4+ TCRβ diversity after G‐CSF treatment is associated with lower reactivation of cytomegalovirus and Epstein–Barr virus. By contrast, no protecting correlation was observed for CD8+ T cells. In essence, our deep TCRβ analysis identifies the importance of the CD4+ T cell compartment for the control of latent viruses after allogeneic stem cell transplantation.
Rhetorical Framing in Planning: An Empirical Investigation of How Planners Discuss Density

Planning departments can frame a policy by citing some of its presumed benefits over others. However, there is limited understanding of framing’s frequency within planning and why planning departments pursue it. Using a nationwide mail survey, we examined how planning departments (n = 197; 40.1% response rate) frame discussions of proposals to increase allowed residential density. We found that departments air fewer presumed benefits of these proposals than respondents perceive to exist, demonstrating that departments selectively frame these proposals. Using logistic regression modeling, we found a number of demographic and political factors associated with departments’ framing, suggesting that this framing is rhetorical.
Detection and characterization of a 500 μm dust emissivity excess in the Galactic plane using Herschel/Hi-GAL observations

Context. Past and recent observations have revealed unexpected variations in the far-infrared – millimeter (FIR-mm) dust emissivity in the interstellar medium. In the Herschel spectral range, those are often referred to as a 500 μm emission excess. Several dust emission models have been developed to interpret astrophysical data in the FIR-mm domain. However, these are commonly unable to fully reconcile theoretical predictions with observations. In contrast, the recently revised two level system (TLS) model, based on the disordered internal structure of amorphous dust grains, seems to provide a promising way of interpreting existing data. Aims. The newly available Herschel infrared GALactic (Hi-GAL) data, which covers most of the inner Milky Way, offers a unique opportunity to investigate possible variations in the dust emission properties both with wavelength and environment. The goal of our analysis is to constrain the internal structure of the largest dust grains on Galactic scales, in the framework of the TLS model. Methods. By combining the IRIS (Improved Reprocessing of the IRAS Survey) 100 μm with the Hi-GAL 160, 250, 350, and 500 μm data, we model the dust emission spectra in each pixel of the Hi-GAL maps, using both the TLS model and, for comparison, a single modified black-body fit. The effect of temperature mixing along the line of sight is investigated to test the robustness of our results. Results. We find a slight decrease in the dust temperature with distance from the Galactic center, confirming previous results. We also report the detection of a significant 500 μm emissivity excess in the peripheral regions of the plane (35° < |l| < 70°) of about 13–15% of the emissivity, which can reach up to 20% in some HII regions. We present the spatial distributions of the best-fit values for the two main parameters of the TLS model, i.e. the charge correlation length, lc, used to characterize the disordered charge distribution (DCD) part of the model, and the amplitude A of the TLS processes with respect to the DCD effect. These distributions illustrate the variations in the dust properties with environment, in particular the plausible existence of an overall gradient with distance to the Galactic center. A comparison with previous findings in the solar neighborhood shows that the local value of the excess is less than expected from the Galactic gradient observed here.
Classical and Mg II-selected damped Lyman α absorbers: impact on ΩH I at z < 1.7

The Damped Lyman-alpha systems (DLAs), seen in absorption in the spectrum of quasars, are believed to contain a large fraction of the neutral gas in the Universe. Paradoxically, these systems are more difficult to observe at z_abs 21.0 than seen otherwise at low redshift. If confirmed, this property will in turn affect estimates of Omega_HI which is dominated by the highest HI column densities. We find that log N(HI) does not correlate significantly with metal equivalent widths. Similarly, we find no evidence that gravitational lensing, the fraction of associated systems or redshift evolution affect the absorber samples in a different way. We conclude that the hint of discrepancies in N(HI) distributions most likely arises from small number statistics. Therefore, further observations are required to better clarify the impact of this discrepancy on estimates of Omega_HI at low redshift.
A Global Perspective On The Significance of Violent Imagery in Relation To Other Variables Of Interest Within Computer Games

This study explores the significance of explicit violence in computer games as a mechanism for entertaining the player. Twenty-Two participants played a violent and non-violent version of the same computer game and then rated each one in relation to how much they enjoyed the experience. To provide effective analysis of the research data purpose built stimuli was used in this study to ensure that every aspect of their construction, other than the presence or absence of violent imagery, was standardised to eliminate alternative variables of interest. Through analysis of counter-balanced quantitative and qualitative data it was found that increased realism and violent intensity had little effect on the samples overall arousal and surprisingly the majority of participants preferred the non-violent alternative. Although there was some evidence to suggest that increased violence correlated with intensified immersed emotional reactivity, the results showed that the fundamental gameplay mechanics were the primary contributor to player behaviour such as excitement, aggression and competitiveness. The findings of this study suggest that gory violence had little effect on player emotional reactivity which raises doubts as to whether violence in computer games is as significant of a stimulant as previous researchers have suggested.
Chapter 2 . 2 Altered GABAA receptor density and unaltered blood-brain barrier [ 11 C ] fl umazenil transport in drug-resistant epilepsy patients with mesial temporal sclerosis

Studies in rodents suggest that fl umazenil is a P-glycoprotein (P-gp) substrate at the blood-brain barrier (BBB). This study aimed to assess whether [C]fl umazenil is a P-gp substrate in humans and to what extent increased P-gp function in epilepsy may confound interpretation of clinical [C]fl umazenil studies used to assess GABAA receptors. Nine drug-resistant patients with epilepsy and mesial temporal sclerosis (MTS) were scanned twice using [C]fl umazenil before and after partial P-gp blockade with tariquidar. Volume of distribution (VT), non-displaceable binding potential (BPND), and the ratio of rate constants (K1/k2) of [C]fl umazenil transport across the BBB were derived for whole brain and several regions. All parameters were compared between pre and post tariquidar scans. Regional results were compared between MTS and contralateral sides. Tariquidar signifi cantly increased global K1/k2 (+23%) and VT (+10%), but not BPND. At the MTS side VT and BPND were lower in hippocampus (both ~-19%) and amygdala (both ~-16%), but K1/k2 did not diff er, suggesting that only regional GABAA receptor density is altered in epilepsy. In conclusion, although [C]fl umazenil appears to be a (weak) P-gp substrate in humans, this does not seem to aff ect its role as a tracer for assessing GABAA receptor density. 47 [C]Flumazenil brain effl ux by P-gp in epilepsy patients
Kemampuan Berpikir Kritis Siswa dengan Inkuiri Terbimbing dipadu Carousel Feedback pada Materi Sifat-sifat Cahaya di Sekolah Dasar

The purpose of this study was to determine differences in critical thinking skills of students learning with guided inquiry learning model combined carousel feedback and student learning by inquiry learning model. This study is a quasi-experimental research design with posttest-only nonequivalent control group. The subjects were students of class as an experimental class Va and Vb grade students as a control group. Students in the experimental class was learned with model guided inquiry combined carousel feedback while students in the control class was learned with model guided inquiry. The instrument used to measure the success of this study is the essay to measure students' critical thinking skills. The results showed that the critical thinking skills of students in the experimental class and control class differ statistically through the achievements obtained by the difference T test critical thinking skills both classes, namely 0.029 <0.05. Thus, it can be said combined carousel guided inquiry learning feedback significantly affect the ability of students' critical thinking on the material properties of the light. Tujuan penelitian ini adalah untuk mengetahui perbedaan kemampuan berpikir kritis siswa yang belajar dengan model pembelajaran inkuiri terbimbing dipadu carousel feedback dan siswa yang belajar dengan model pembelajaran inkuiri. Penelitian ini merupakan penelitian eksperimen semu dengan desain posttest only nonequivalent control group . Subjek penelitian ini adalah siswa kelas VA sebagai kelas eksperimen dan siswa kelas VB sebagai kelas kontrol. Siswa pada kelas eksperimen dibelajarkan dengan model inkuiri terbimbing dipadu carousel feedback sedangkan siswa di kelas kontrol dibelajarkan dengan model inkuiri terbimbing. Instrumen yang digunakan untuk mengukur keberhasilan penelitian ini adalah soal esai untuk mengukur kemampuan berpikir kritis siswa. Hasil penelitian menunjukkan bahwa kemampuan berpikir kritis siswa pada kelas eksperimen dan kelas kontrol berbeda secara statistik melalui uji T diperoleh selisih capaian kemampuan berpikir kritis kedua kelas yaitu 0,029 < 0,05. Dengan demikian, dapat dikatakan pembelajaran inkuiri terbimbing dipadu carousel feedback berpengaruh secara signifikan terhadap kemampuan berpikir kritis siswa pada materi sifat-sifat cahaya.
Researcher

This study offers foundational insights into the ways in which perceptions of different interview media – principally, face-to-face, telephone and videoconferencing channels of communication – may influence researcher choices and practices. Informed by the reflections of 23 senior accounting researchers, our evidence identifies a duality of practices in the usage of different interviewing media, influenced primarily through the role played by experience, which informs perceptions upon which practices are based. We discuss this duality of practices in terms of Information Richness Theory and Channel Expansion Theory, and offer further insights into the factors that influence and shape researchers’ perceptions of the contextual suitability of particular media available to interview-based accounting research. Paper classification
Land Constraints and Agricultural Intensification in Ethiopia: A Village-Level Analysis of High-Potential Areas

Highland Ethiopia is one of the most densely populated regions of Africa and has long been associated with both Malthusian disasters and Boserupian agricultural intensification. This paper explores the race between these two countervailing forces, with the goal of inform two important policy questions. First, how do rural Ethiopians adapt to land constraints? And second, do land constraints significantly influence welfare outcomes in rural Ethiopia? To answer these questions we use a recent household survey of high-potential areas. We first show that farm sizes are generally very small in the Ethiopian highlands and declining over time, with young rural households facing particularly severe land constraints. We then ask whether smaller and declining farm sizes are inducing agricultural intensification, and if so, how. We find strong evidence in favor of the Boserupian hypothesis that land-constrained villages typically use significantly more purchased input costs per hectare and more family labor, and achieve higher maize and teff yields and higher gross income per hectare. However, although these higher inputs raise gross revenue, we find no substantial impact of greater land constraints on net farm income per hectare once family labor costs are accounted for. Moreover, farm sizes are strongly positively correlated with net farm income, suggesting that land constraints are an important cause of rural poverty. We conclude with some broad policy implications of our results.
Albumin-Associated Lipids Regulate Human Embryonic Stem Cell Self-Renewal

Background Although human embryonic stem cells (hESCs) hold great promise as a source of differentiated cells to treat several human diseases, many obstacles still need to be surmounted before this can become a reality. First among these, a robust chemically-defined system to expand hESCs in culture is still unavailable despite recent advances in the understanding of factors controlling hESC self-renewal. Methodology/Principal Findings In this study, we attempted to find new molecules that stimulate long term hESC self-renewal. In order to do this, we started from the observation that a commercially available serum replacement product has a strong positive effect on the expansion of undifferentiated hESCs when added to a previously reported chemically-defined medium. Subsequent experiments demonstrated that the active ingredient within the serum replacement is lipid-rich albumin. Furthermore, we show that this activity is trypsin-resistant, strongly suggesting that lipids and not albumin are responsible for the effect. Consistent with this, lipid-poor albumin shows no detectable activity. Finally, we identified the major lipids bound to the lipid-rich albumin and tested several lipid candidates for the effect. Conclusions/Significance Our discovery of the role played by albumin-associated lipids in stimulating hESC self-renewal constitutes a significant advance in the knowledge of how hESC pluripotency is maintained by extracellular factors and has important applications in the development of increasingly chemically defined hESC culture systems.
Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element

Previously, we described a novel pH-responsive RNA element in Escherichia coli that resides in the 5′ untranslated region of the alx gene and controls its translation in a pH-dependent manner. Under normal growth conditions, this RNA region forms a translationally inactive structure, but when transcribed under alkaline conditions, it forms an active structure producing the Alx protein. We identified two distinct transcriptional pause sites and proposed that pausing at these sites interfered with the formation of the inactive structure while facilitating folding of the active one. Alkali increases the longevity of pausing at these sites, thereby promoting folding of the translationally active form of alx RNA. We show here that mutations that modify the extent and/or position of pausing, although silent with regard to structure stability per se, greatly influence the dynamics of folding and thereby translation. Our data illustrate the mechanistic design of alx regulation, relying on precise temporal and spatial characteristics. We propose that this unique design provides an opportunity for environmental signals such as pH to introduce structural changes in the RNA and thereby modulate expression.
Near-Infrared and Mid-Infrared Spectroscopy with the Infrared Camera (IRC) for AKARI

The Infrared Camera (IRC) is one of the two instruments on board the AKARI satellite. In addition to deep imaging from 1.8-26.5um for the pointed observation mode of the AKARI, it has a spectroscopic capability in its spectral range. By replacing the imaging filters by transmission-type dispersers on the filter wheels, it provides low-resolution (lambda/d_lambda ~ 20-120) spectroscopy with slits or in a wide imaging field-of-view (approximately 10'X10'). The IRC spectroscopic mode is unique in space infrared missions in that it has the capability to perform sensitive wide-field spectroscopic surveys in the near- and mid-infrared wavelength ranges. This paper describes specifications of the IRC spectrograph and its in-orbit performance.
Copper‐induced release of complexing ligands similar to thiols by Emiliania huxleyi in
seawater cultures

Marine microalgae (Emiliania huxleyi) were grown in seawater enriched only with nitrogen and phosphorus, without control of free metal concentrations using synthetic chelators. Complexing ligands and thiol compounds were determined by cathodic stripping volt–ammetry. Copper was added to these cultures, and ligands were produced in response to the copper addition. Parallel measurements of thiols showed that glutathione and other unidentified thiols (electrochemically similar to thioacetamide) were produced by the algae at rates and concentrations similar to those of the complexing ligands. Smaller amounts of thiols were produced when ligands including thiols were added to the culture. The results indicate that thiols can account for a major part or most of the copper–complexing ligands produced by these algae. Furthermore, a feedback mechanism exists in which the production of thiol–type complexing ligands is controlled by the free copper concentration, production already being stimulated by an increase of [Cu2+] from 0.4 to 1.5 pM. Incubations with added exudates, thiols, and salicylaldoxime (SA) showed much reduced copper toxicity even though copper uptake was increased by the exudates and the SA.
A review of marine mammal deterrents and their possible applications to limit killer whale (Orcinus orca) predation on Steller sea lions (Eumetopias jubatus)

This report does not constitute a publication and is for information only. All data herein are to be considered provisional. Abstract The population of Steller sea lions (Eumetopias jubatus) in the western Aleutian Islands has declined significantly and is currently listed as an endangered species. Among the possible limiting factors for this population is predation by transient killer whales (Orcinus orca). The purpose of this report is to provide some analysis of the feasibility of limiting killer whale predation on Steller sea lions in the western Aleutian Islands using marine mammal deterrents. This report provides a review of various marine mammal deterrents, used primarily in fisheries, to either prevent marine mammal entanglement or predation. Deterrent methods are evaluated based upon various factors including effectiveness, particularly with killer whales, potential impacts on non-target species, including Steller sea lions, and feasibility of use in the western Aleutian Islands. Possible deterrent options are considered, however, all would require significant research before implementation. Based upon a thorough review of the literature, lack of previous long-term success and high degrees of uncertainty, it is unlikely that deterrents would be successful in this application.
Bristol Centre for Complexity Sciences Exploring methods for analysing trajectories of long-scale Molecular Dynamics simulations on the example of the 150-loop in Neuraminidase September 2013

The development of ever more efficient hardware and software has allowed for the simulation of complex biological systems, such as that of a large protein, in atomistic detail on the timescale of up to around a microsecond. This is enough to observe biologically significant conformational changes driven by complex combinations of thermally induced perturbations to single atoms that make up the protein. Neuraminidase (NA) is a major protein of influenza (commonly known as flu), the causative agent of many recent pandemics. Recent studies have revealed complex functional dynamics of the protein’s 150-loop, which leads to drug unbinding and confers drug resistance. This project involved running simulations of 7 types of NA (including wild-type and mutated structures of the free protein, as well as bound with Oseltamivir) in order to find out what underpins the mechanism of drug resistance and explore data mining and machine learning methods for identifying biologically significant events in the simulations and quantitatively defining the conformational states of the 150-loop. The simulations confirmed previously observed behaviour of the 150-loop that can be mechanistically related to drug resistance. Reducing the dimensionality of the system down to only the states that are defined by distinct peaks in the time occupancy of the secondary structure dihedral angle histograms and constructing a network of transitions between states provides a new method for comparing the phase space explored by simulation trajectories and quantifying activation energy barriers between conformational states.
A Case Study of Urban Particle Acidity and Its Influence on Secondary Organic Aerosol

Atmospheric Sciences Research Center (ASRC) and Department of Environmental Health Sciences, 251 Fuller Road, CESTM L110, University at Albany, State University of New York, Albany, New York 12203, Cooperative Institute for Research in Environmental Sciences (CIRES) and Department of Chemistry and Biochemistry, 216 UCB, University of Colorado-Boulder, Boulder, Colorado 80309, and Aerodyne Research Inc., Billerica, Massachusetts 01821
Emergence of Sensory Patterns during Sleep Highlights Differential Dynamics of REM and Non-REM Sleep Stages

Despite the profound reduction in conscious awareness associated with sleep, sensory cortex remains highly active during the different sleep stages, exhibiting complex interactions between different cortical sites. The potential functional significance of such spatial patterns and how they change between different sleep stages is presently unknown. In this electrocorticography study of human patients, we examined this question by studying spatial patterns of activity (broadband gamma power) that emerge during sleep (sleep patterns) and comparing them to the functional organization of sensory cortex that is activated by naturalistic stimuli during the awake state. Our results show a high correlation (p < 10−4, permutation test) between the sleep spatial patterns and the functional organization found during wakefulness. Examining how the sleep patterns changed through the night highlighted a stage-specific difference, whereby the repertoire of such patterns was significantly larger during rapid eye movement (REM) sleep compared with non-REM stages. These results reveal that intricate spatial patterns of sensory functional organization emerge in a stage-specific manner during sleep.