Miracle-dz/UniFAR-FTUs huggingface dataset:
Aged Mice Exhibit a Severely Diminished CD8 T Cell Response following Respiratory Syncytial Virus Infection

ABSTRACT Respiratory virus infections in the elderly result in increased rates of hospitalization and death. Respiratory syncytial virus (RSV) is a leading cause of severe virus-induced respiratory disease in individuals over the age of 65. CD8 T cells play a critical role in mediating RSV clearance. While it is clear that T cell immunity declines with age, it is not clear to what extent the CD8 T cell response to RSV is altered. Using aged BALB/c mice, we demonstrated that RSV-specific CD8 T cell responses were significantly reduced in the lungs of aged mice at the peak of the T cell response and that this decrease correlated with delayed viral clearance. Despite a decrease in the overall numbers of RSV-specific CD8 T cells during acute infection, their capacity to produce effector cytokines was not impaired. Following viral clearance, the RSV-specific memory CD8 T cells were similar in total number and phenotype in young and aged mice. Furthermore, following infection with a heterologous pathogen expressing an RSV epitope, RSV-specific memory CD8 T cells exhibited similar activation and ability to provide early control of the infection in young and aged mice. These data demonstrate a decrease in the capacity of aged mice to induce a high-magnitude acute CD8 T cell response, leading to prolonged viral replication, which may contribute to the increased disease severity of RSV infection observed for aged individuals.
On the skewness of vorticity in the upper ocean

Conservation of potential vorticity suggests that when the magnitude of relative vorticity approaches the planetary vorticity, cyclonic vorticity should be preferred. Small‐scale, 3‐km relative vorticity is examined using shipboard Acoustic Doppler Current Profiler (ADCP) velocity measurements and P‐code Global Positioning System (GPS) navigation from a cruise in the North Pacific. The skewness of relative vorticity in the mixed layer is positive, consistent with theory. The probability density function of vorticity reveals that positive skewness occurs because large vorticities are more likely to be cyclonic than anticyclonic. The skewness is shown to be significant relative to measurement and random errors. In contrast, skewness in the thermocline has no preferred sign. The skewness peaks at the surface and decays to zero at the base of the mixed layer.
ESO imaging survey: optical follow-up of 12 selected XMM-Newton fields

This paper presents the data recently released for the XMM-Newton/WFI survey carried out as part of the ESO Imaging Survey (EIS) project. The aim of this survey is to provide optical imaging follow-up data in BVRI for identification of serendipitously detected X-ray sources in selected XMM-Newton fields. In this paper, fully calibrated individual and stacked images of 12 fields as well as science-grade catalogs for the 8 fields located at high-galactic latitude are presented. These products were created, calibrated and released using the infrastructure provided by the EIS Data Reduction system and its associated EIS/MVM image processing engine, both of which are briefly described here. The data covers an area of ∼3 square degrees for each of the four passbands. The median seeing as measured in the final stacked images is 0. �� 94, ranging from 0. �� 60 and 1. �� 51. The median limiting magnitudes (AB system, 2 �� aperture, 5σ detection limit) are 25.20, 24.92, 24.66, and 24.39 mag for B-, V-, R-, and I-band, respectively. When only the 8 high-galactic latitude fields are included these become 25.33, 25.05, 25.36, and 24.58 mag, in good agreement with the planned depth of the survey. Visual inspection of images and catalogs, comparison of statistics derived from the present data with those obtained by other authors and model predictions, as well as direct comparison of the results obtained from independent reductions of the same data, demonstrate the science-grade quality of the automatically produced final images and catalogs. These survey products, together with their logs, are available to the community for science exploitation in conjunction with their X-ray counterparts. Preliminary results from the X-ray/optical cross-correlation analysis show that about 61% of the detected X-ray point sources in deep XMM-Newton exposures have at least one optical counterpart within 2 �� radius down to R � 25 mag, 50% of which are so faint as to require VLT observations thereby meeting one of the top requirements of the survey, namely to produce large samples for spectroscopic follow-up with the VLT, whereas only 15% of the objects have counterparts down to the DSS limiting magnitude.
Cross-domain sentiment classification via spectral feature alignment

Sentiment classification aims to automatically predict sentiment polarity (e.g., positive or negative) of users publishing sentiment data (e.g., reviews, blogs). Although traditional classification algorithms can be used to train sentiment classifiers from manually labeled text data, the labeling work can be time-consuming and expensive. Meanwhile, users often use some different words when they express sentiment in different domains. If we directly apply a classifier trained in one domain to other domains, the performance will be very low due to the differences between these domains. In this work, we develop a general solution to sentiment classification when we do not have any labels in a target domain but have some labeled data in a different domain, regarded as source domain. In this cross-domain sentiment classification setting, to bridge the gap between the domains, we propose a spectral feature alignment (SFA) algorithm to align domain-specific words from different domains into unified clusters, with the help of domain-independent words as a bridge. In this way, the clusters can be used to reduce the gap between domain-specific words of the two domains, which can be used to train sentiment classifiers in the target domain accurately. Compared to previous approaches, SFA can discover a robust representation for cross-domain data by fully exploiting the relationship between the domain-specific and domain-independent words via simultaneously co-clustering them in a common latent space. We perform extensive experiments on two real world datasets, and demonstrate that SFA significantly outperforms previous approaches to cross-domain sentiment classification.
Rapid scale-up of a community-based HIV treatment service: programme performance over 3 consecutive years in Guguletu, South Africa.

BACKGROUND Despite rapid expansion of antiretroviral therapy (ART) in sub-Saharan Africa there are few longitudinal data describing programme performance during rapid scale-up. METHODS We compared mortality, viral suppression and programme retention in 3 consecutive years of a public sector community-based ART clinic in a South African township. Data were collected prospectively from establishment of services in October 2002 to the censoring date in September 2005. Viral load and CD4 counts were monitored at 4-monthly intervals. Community-based counsellors provided adherence and programme support. RESULTS During the study period 1139 ART-naïve patients received ART (161, 280 and 698 in the 1st, 2nd and 3rd years respectively). The median CD4 cell counts were 84 cells/microl (interquartile range (IQR) 42-139), 89 cells/microl (IQR 490-149), and 110 cells/microl (IQR 55-172), and the proportions of patients with World Health Organization (WHO) clinical stages 3 and 4 were 90%, 79% and 76% in each sequential year respectively. The number of counsellors increased from 6 to 28 and the median number of clients allocated to each counsellor increased from 13 to 33. The overall loss to follow-up was . 9%. At the date of censoring, the Kaplan-Meier estimates of the proportion of patients still on the programme were 82%, 86% and 91%, and the proportion who were virally suppressed (< 400 copies/ml) were 100%, 92% and 98% for the 2002, 2003 and 2004 cohorts respectively. CONCLUSIONS While further operational research is required into optimal models of care in different populations across sub-Saharan Africa, these results demonstrate that a single community-based public sector ART clinic can extend care to over 1000 patients in an urban setting without compromising programme performance.
A Case Study of the Adequacy of GCM Simulations for Input to Regional Climate Change Assessments.

Abstract The Sacramento Basin is used as the focus for a case study testing whether general circulation models (GCMS) are capable of simulating the large-scale and synoptic-scale processes important in studies of regional water resources. Output from a variety of GCMs developed at GISS and NCAR were examined, but only results from Community Climate Model (CCM) simulations are presented since they are typical. The stationary waves, jet streams, and storm tracks in the North Pacific-North America region in the CCM simulators show major differences from the observations, both in the mean and in their interannual variations. In addition, although the stationary wave and jet stream patterns associated with individual storms in the basin exhibit robust differences from mean fields in the observations, these differences are not captured in the models. Consequently, the larger-scale fields necessary for driving nested models and impact models for the basin, or for western North America in general, are problematic.
Birkeland currents and charged particles in the high-latitude prenoon region: A new interpretation

Simultaneous, conjugate measurements of magnetic fields and charged particles at low altitude in the high-latitude prenoon sector and the magnetosheath were made with the DMSP F7, HILAT, and Active Magnetospheric Particle Tracer Explorers (AMPTE) CCE satellites on November 1, 1984. These data show that the low-latitude portion of the traditional “cusp” particle signature is coincident with the prenoon region 1 current system in both hemispheres and for both northward and southward interplanetary magnetic fields (IMF). The traditional “cusp” Birkeland currents are associated with the dispersion region of cusp ions when the IMF is directed southward and with electron fluxes that are slightly enhanced over polar rain intensities. Finally, electron spectra measured by AMPTE CCE in the magnetosheath near 1000 MLT are similar in shape and energy to those acquired at low altitude by both DMSP F7 and HILAT. These observations indicate that for both northward and southward IMF, the traditional “cusp particle” signature is coincident with the region 1 Birkeland current system and maps to low altitude along field lines that thread the dayside boundary layer. The traditional “cusp” Birkeland current system flows along field lines that lie poleward of the region of cusp particles and the region 1 current system. These field lines thread the plasma mantle. Thus, we suggest that the traditional “cusp” current system might be appropriately renamed the “mantle” Birkeland current system.
Sociodemographic differences in depressed mood: results from a nationally representative sample of high school adolescents.

BACKGROUND Research on adolescent mental health suggests that prevalence rates for depressed mood are not uniformly distributed across all populations. This study examined demographic difference in depressed mood among a nationally representative sample of high school adolescents. METHODS The 2003 National Youth Risk Behavior Survey was utilized to examine the association between depressed mood and demographic variables. To examine demographic associations, chi-square and follow-up logistic regression models were created for the sample of high school adolescents (N = 15,214). RESULTS Caucasians and African Americans were significantly less likely to report depressed mood when compared to Hispanics and Others. Women were also more likely than men to report depressed mood. No significant differences were observed among levels of urbanicity and age. CONCLUSIONS An understanding of the difference in the prevalence and correlates of depressed mood among adolescents of various ethnic/racial and gender groups deserves increased attention. Given the fact that challenges with depressed mood in adolescents can be substantial and relatively unrecognized, there is an increased need to identify these adolescents early and intervene with culturally appropriate interventions.
Experimental Study of Flow in a Vortex Drop Shaft

Model experiments were conducted to investigate the performance of a vortex drop structure with a relatively small height to diameter ratio. Detailed measurements of wall pressure and water thickness of annular jet flow were obtained along the vertical drop shaft, and the rate of air entrainment was measured. The results confirmed the high efficiency of energy dissipation in the vortex drop structure even for a relatively small drop height. The air entrainment rate was found to be significant, and good correlation was observed between the rate of air entrainment and the water jet velocity. The one-dimensional frictional free-vortex flow model was extended to include the effects of pressure forces. While the energy loss in the drop shaft can be simulated by correcting the friction factor, both the frictional model and the extended model significantly underpredict the wall pressure.
Symmetry breaking for suffix tree construction

There are several serial algorithms for suffix tree construction which run in linear time, but the number of operations in the only parallel algorithm available, due to Apostolic, Iliopoulos, Landau, Schieber and VLshkin, is proportional to n log n. The algorithm is based on labeling substringsj similar to a classical serial algorithm, with the same operations bound, by Karp, Miller and Rosenberg. We show how to break symmetries that occur in the process of assigning labels using the Deterministic Coin Tossing (DCT) technique, and thereby reduce the number of labeled substrings to linear. We give several algorithms for suffix tree construction. One of them runs in 0(log2 n) parallel time and O(n) work for input strings whose characters are drawn from a constant size alphabet.
Combined effects of environmental factors and regulation on macrophyte vegetation along three rivers in western France

The longitudinal changes of richness and composition of aquatic plants have been studied from headwaters to the fifth stream order in three rivers in western Brittany (France), the Orne, Sélune and Rance. All rivers are regulated by dams along their lower reaches. The total macrophyte richness differed between the rivers (61 to 150 taxa); it was lowest in the Sélune, which flows over a granite substratum throughout its basin. Absolute richness per site varied greatly between rivers, and between groups of sites either upstream or downstream of the dams, though consistently higher values were observed downstream. In contrast, the relative richness at the river basin scale was similar for the group of upstream (average 20 taxa) and downstream sites (average 28) of all rivers. At the site level, richness increased along all there rivers. Several sites below the dams had the highest richness per site, with more than 40 taxa. A shifting evolution of the macrophyte richness was revealed along the river axis, related to habitat heterogeneity and geological changes.
Characterization of teleost insulin receptor family members. II. Developmental expression of insulin-like growth factor type I receptor messenger RNAs in rainbow trout.

The insulin-like growth factor (IGF) system in teleosts consists of two ligands, IGF-I and IGF-II, multiple binding proteins, and high-affinity transmembrane receptors. There exists a large gap in our knowledge of the structure and expression of receptors mediating the biological effects of the IGFs in teleosts. For example, nucleotide sequence data other than those from the kinase domain, evidence of multiple genes, mRNA expression pattern and polyadenylation status in multiple tissues at different developmental stages, and quantitation of mRNA levels in multiple tissues are not known for any teleost. In the study described here, two rainbow trout IGF type I receptor cDNAs (rtIGFR Ia and rtIGFR Ib) were isolated by a 5' rapid amplification of cDNA ends method and confirmed as separate genes by genomic Southern blot hybridization. The predicted amino acid sequences are 85% identical to each other in the tyrosine kinase domain. Both cDNAs are more homologous to mammalian IGF type I receptors than to insulin receptors. Reverse transcription-polymerase chain reaction from total RNA using either oligo(dT) or random hexamers as primers resulted in a diminished ability to detect IGF receptor mRNAs when oligo(dT) was used, suggesting developmental and tissue-specific polyadenylation. The highest steady-state mRNA levels of rtIGFR Ia were found in juvenile gill and adult heart, while the highest levels of rtIGFR Ib were found in adult pyloric caeca, which also contained diffuse pancreatic and adipose tissue. The lowest steady-state mRNA levels of both rtIGFR Ia and rtIGFR Ib were found in juvenile heart, liver, muscle, and spleen, and adult liver. Significant differences in steady-state mRNA levels were also found between juveniles and adults. These results suggest a complex expression pattern of IGF type I receptor mRNAs in partial tetraploid fish.
Convectively induced mesoscale weather systems in the tropical and warm‐season midlatitude atmosphere

As anticipated by Nelson [1991] in the last U.S. National Report, mesoscale meteorology has continued to be an area of vigorous research activity. Progress is evinced by a growing number of process-oriented studies capitalizing on expanded observational capabilities, as well as more theoretical treatments employing numerical simulations of increasing sophistication. While the majority of papers within the scope of this review fall into the category of basic research, the field's maturation is evident in the emergence of a growing number of applications to operational weather forecasting. Even as our ability to anticipate shifts in synoptic scale upper-air patterns and associated baroclinic developments has steadily improved, lagging skill with regard to quantitative forecasts of precipitation—particularly in situations where deep moist convection is prevalent—has sustained research in warm-season mesoscale meteorology. Each spring and summer midlatitude populations are exposed to life-threatening natural weather phenomena in the form of lightning, tornadoes, straight-line winds, hail, and flash floods. This point was driven home during the summer of 1993, when an extraordinarily persistent series of mesoscale convective systems (MCSs) led to unusually severe and widespread flooding throughout the Mississippi and Missouri river basins. In addition to this obvious impact on regional climate, the 1990's have brought an increased appreciation for the less direct yet potentially significant role that tropical convection may play in shaping global climate through phenomena such as the El Nino-Southern Oscillation (ENSO).
Neuroimaging endophenotypes: Strategies for finding genes influencing brain structure and function

It is vitally important to identify the genetic determinants of complex brain‐related disorders such as autism, dementia, mood disorders, and schizophrenia. However, the search for genes predisposing individuals to these illnesses has been hampered by their genetic and phenotypic complexity and by reliance upon phenomenologically based qualitative diagnostic systems. Neuroimaging endophenotypes are quantitative indicators of brain structure or function that index genetic liability for an illness. These indices will significantly improve gene discovery and help us to understand the functional consequences of specific genes at the level of systems neuroscience. Here, we review the feasibility of using neuroanatomic and neuropsychological measures as endophenotypes for brain‐related disorders. Specifically, we examine specific indices of brain structure or function that are genetically influenced and associated with neurological and psychiatric illness. In addition, we review genetic approaches that capitalize on the use of quantitative traits, including those derived from brain images. Hum Brain Mapp, 2007. © 2007 Wiley‐Liss, Inc.
Improvement of systolic and diastolic heart function after physical training in sedentary women

The present study examined the cardiac effects of football training and running for inactive pre‐menopausal women by standard echocardiography and tissue Doppler imaging. Thirty‐seven subjects were randomized to two training groups (football: FG; n=19; running; RG; n=18) training 1 h with equal average heart rates twice a week for 16 weeks and compared with a matched inactive control group (CG; n=10). During the training period, left ventricular end‐diastolic volume increased by 13% in FG and 11% in RG (P<0.05). Left ventricular posterior wall thickness increased in FG from 8.5±1.4 to 9.0±1.3 mm (P<0.05). Right ventricle diameter increased by 12% in FG and 10% in RG (P<0.05). Tissue Doppler imaging demonstrated increased left ventricular systolic and diastolic performances in both training groups. Peak systolic velocity increased by 26% in FG and 17% in RG (P<0.05) and left ventricular longitudinal displacement increased in both groups by 13% (P<0.05). Isovolumetric relaxation time decreased significantly more in FG than in RG (26% vs 14%, respectively P<0.05). In conclusion, 16 weeks of football and running exercise training induced significant changes of cardiac dimensions and had favorable effects on both left ventricular systolic and diastolic function. These training‐induced cardiac adaptations appeared to be more consistent after football training compared with running.
High‐pressure elasticity of stishovite and the P42/mnm ⇌ Pnnm phase transition

A Landau free energy expansion has been developed to describe the elastic constant variations of stishovite (SiO2) associated with the P42/mnm (rutile-type) ⇌ Pnnm (CaCl2-type) phase transition as a function of pressure. The transition appears to display classical second-order character, with an equilibrium transition pressure which is renormalized by coupling of the soft optic mode with spontaneous strain. Lattice parameter data from the literature show that the symmetry breaking strain is large, while the nonsymmetry breaking strains are small. These have been used to constrain the numerical values of the strain/order parameter coupling coefficients, which in turn have been used to constrain values for the Landau coefficients. When substituted into expressions for all the individual elastic constants, taking values for experimental and calculated values of the bare elastic constants from the literature, a clear view of the pattern of elastic constant variations is produced. Variations of P and S wave velocities derived from the calculated elastic constants for a second-order transition show a dip as the transition point is approached from high pressure and from low pressure but do not show a discontinuity. The velocity anomaly provides a signature for the presence of free silica in the lower mantle.