Miracle-dz/UniFAR-FTUs huggingface dataset:
The pre-glacial landscape of Antarctica

ABSTRACT The geomorphology of the hidden subglacial landscape of Antarctica is relevant to our understanding of the stability of the Antarctic Ice Sheet and also to that of global interactions between plate tectonics and surface processes. We believe that geomorphology has much to contribute, but that the lack of coherent hypotheses about the origins of the subglacial landscape is holding back understanding. This paper approaches the problem by using southern hemisphere land masses in Africa and Madagascar as analogues. We find that the Antarctic landscape evolved in a similar way to passive margin evolution in southern Africa. Rifting associated with the breakup of Gondwana changed river base levels and caused rapid erosion on the flanks of rifts and was accompanied by the uplift of rift-margin mountains. Rift-margin plains, often coastal or extending inland along large rivers, are backed by an escarpment, while low-gradient continental river basins characterised the interior of Antarctica. In East Antarctica ice has removed pre-existing regolith from lowlands and excavated 2–3 km troughs below sea level along the course of major trunk rivers. The micro-continents of West Antarctica are comparable to Madagascar and apparently share a similar topography with coastal plains, backing escarpments and interior plateaux.
The desirability of a corpus of online book responses

This position paper argues the need for a comprehensive corpus of online book responses. Responses to books (in traditional reviews, book blogs, on booksellers’ sites, etc.) are important for understanding how readers understand literature and how literary works become popular. A sufficiently large, varied and representative corpus of online responses to books will facilitate research into these processes. This corpus should include context information about the responses and should remain open to additional material. Based on a pilot study for the creation of a corpus of Dutch online book response, the paper shows how linguistic tools can find differences in word usage between responses from various sites. They can also reveal response type by clustering responses based on usage of either words or their POS-tags, and can show the sentiments expressed in the responses. LSA-based similarity between book fragments and response may be able to reveal the book fragments that most affected readers. The paper argues that a corpus of book responses can be an important instrument for research into reading behavior, reader response, book reviewing and literary appreciation.
Identification of Diversity-Generating Retroelements in Human Microbiomes

Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by accelerating the evolution of target genes through a specialized, error-prone, reverse transcription process. First identified in a Bordetella phage (BPP-1), which mediates the phage tropism specificity by generating variability in an involved gene, DGRs were predicted to be present in a larger collection of viral and bacterial species. A minimal DGR system is comprised of a reverse transcriptase (RTase) gene, a template sequence (TR) and a variable region (VR) within a target gene. We developed a computational tool, DGRscan, to allow either de novo identification (based on the prediction of potential template-variable region pairs) or similarity-based searches of DGR systems using known template sequences as the reference. The application of DGRscan to the human microbiome project (HMP) datasets resulted in the identification of 271 non-redundant DGR systems, doubling the size of the collection of known DGR systems. We further identified a large number of putative target genes (651, which share no more than 90% sequence identity at the amino acid level) that are potentially under diversification by the DGR systems. Our study provides the first survey of the DGR systems in the human microbiome, showing that the DGR systems are frequently found in human-associated bacterial communities, although they are of low incidence in individual genomes. Our study also provides functional clues for a large number of genes (reverse transcriptases and target genes) that were previously annotated as proteins of unknown functions or nonspecific functions.
The Redshift-Space Two-Point Correlation Functions of Galaxies and Groups in the Nearby Optical Galaxy Sample

We use the two-point correlation function in redshift space, ξ(s), to study the clustering of the galaxies and groups of the Nearby Optical Galaxy (NOG) sample, which is a nearly all-sky (|b| > 20°), complete, magnitude-limited sample of ~7000 bright and nearby optical galaxies (cz ≤ 6000 km s-1). The correlation function of galaxies is well described by a power law, ξ(s) = (s/s0)-γ, with slope γ ~ 1.5 and s0 ~ 6.4 h-1 Mpc (on scales 2.7-12 h-1 Mpc), in substantial agreement with previous results of several redshift surveys of optical galaxies. Splitting NOG into different morphological subsamples, we confirm the existence of morphological segregation between early- and late-type galaxies (out to 20 h-1 Mpc), and, in particular, we find a gradual decreasing of the strength of clustering from the S0 galaxies to the late-type spirals on intermediate scales (around 5 h-1 Mpc). The relative bias factor between early- and late-type galaxies appears to be substantially constant with scale. Furthermore, luminous galaxies turn out to be more clustered than dim galaxies. The luminosity segregation, which is significant for both early- and late-type objects, starts to become appreciable only for galaxies brighter than MB ~ -19.5 + 5 log h (~0.6L*) and is independent of scale. The NOG groups identified with the hierarchical and percolation algorithms show similar clustering properties, with a degree of clustering that is intermediate between galaxies and clusters. The group correlation functions are characterized by s0-values ranging from ~8 h-1 Mpc (for groups with at least three members) to ~10 h-1 Mpc (for groups with at least five members). The degree of group clustering depends on the physical properties of groups. Specifically, groups with greater velocity dispersions, sizes, and masses tend to be more clustered than those with lower values of these quantities.
Temporal trends in invasive pneumococcal disease and pneumococcal serotypes over 7 decades.

BACKGROUND Pneumococcal infections have historically played a major role in terms of morbidity and mortality. We explored historical trends of invasive pneumococcal disease (IPD) and pneumococcal serotypes in a population exposed to limited antibiotic selective pressure and conjugate pneumococcal vaccination (PCV). METHODS Retrospective cohort study based on nationwide laboratory surveillance data on IPD collected uninterruptedly in Denmark during 1938-2007. Changes in the reported incidence and trends of pneumococcal serotypes were explored using nonlinear regression analysis. RESULTS There were 25,502 IPD cases included in our study. The median incidence of IPD increased from 2.8 cases per 100,000 population (interquartile range [IQR], 1.5-2.6) during the first 4 decades to 15.7 cases per 100,000 population (IQR, 7-20.4) during the 1980s and 1990s, mainly attributed to an increase in the number of bacteremia cases. The incidence of meningitis remained relatively stable, with a median of 1.3 cases per 100,000 population (IQR, 0.9-1.6). The proportions of serotypes/groups 4 and 9 increased; the proportion of serotype 18C decreased; the proportions of serotypes 6, 7F, 14, and 23F remained stable; and serotype 2 nearly disappeared. Before the 1960s, serotypes 1, 2, 3, and 5 presented peaks every 2-3 years, becoming less frequent during the 1970s with peaks every 7-10 years. Between 20% and 90% of IPD in children <5 years were caused by PCV serotypes during the last 4 decades. Cases of IPD caused by serotype 19A increased before introduction of PCV. Between 1993 and 2007, the level of resistance to macrolides and beta-lactams was 6%. CONCLUSIONS The epidemiology of IPD and single serotypes has constantly changed over the past 7 decades. PCV serotypes appeared to dominate the pneumococcal population.
Meta-analysis of nitrogen balance studies for estimating protein requirements in healthy adults.

BACKGROUND The most recent international dietary protein recommendations for healthy adults are those developed and proposed by the 1985 FAO/WHO/UNU Joint Expert Consultation. OBJECTIVE The objective was to analyze available nitrogen balance data to establish new recommendations for the protein required by healthy adults. DESIGN Data were gathered from published nitrogen balance studies that had as their primary objective either the estimation of basal or maintenance requirements or the testing of the adequacy of specific nitrogen intakes in healthy adults. These data were synthesized to characterize the distribution of individual protein requirements; the effects of climate of the study site, adult age, sex, and dietary protein source on individual requirements; and the midpoint of and the variability between the protein requirements of healthy persons. RESULTS Data for 235 individual subjects, each studied at >or= 3 test protein intakes, were gathered from 19 studies. The median estimated average requirement (EAR) of nitrogen from these data was 105 mg N x kg(-1) x d(-1). Individual requirements were found to fit a log-normal distribution. The median EAR was estimated as the median of this distribution, 105 mg N x kg(-1) x d(-1), whereas the 97.5th percentile (the recommended dietary allowance; RDA) was estimated from the distribution of the log of the requirement (after correction of the total observed variability to remove within-individual variability) as 132 mg N x kg(-1) x d(-1). No significant differences between the climate of the study site, adult age class, sex, or source of dietary protein were observed, although there was an indication that women might have a lower requirement than do men. CONCLUSION This meta-analysis provides new recommendations for dietary reference values, ie, an EAR (median) and RDA (97.5th percentile) for healthy adults of 105 and 132 mg N x kg(-1) x d(-1) (0.65 and 0.83 g good-quality protein x kg(-1) x d(-1)), respectively.
Glaucoma and Driving: On-Road Driving Characteristics

Purpose To comprehensively investigate the types of driving errors and locations that are most problematic for older drivers with glaucoma compared to those without glaucoma using a standardized on-road assessment. Methods Participants included 75 drivers with glaucoma (mean = 73.2±6.0 years) with mild to moderate field loss (better-eye MD = -1.21 dB; worse-eye MD = -7.75 dB) and 70 age-matched controls without glaucoma (mean = 72.6 ± 5.0 years). On-road driving performance was assessed in a dual-brake vehicle by an occupational therapist using a standardized scoring system which assessed the types of driving errors and the locations where they were made and the number of critical errors that required an instructor intervention. Driving safety was rated on a 10-point scale. Self-reported driving ability and difficulties were recorded using the Driving Habits Questionnaire. Results Drivers with glaucoma were rated as significantly less safe, made more driving errors, and had almost double the rate of critical errors than those without glaucoma. Driving errors involved lane positioning and planning/approach, and were significantly more likely to occur at traffic lights and yield/give-way intersections. There were few between group differences in self-reported driving ability. Conclusions Older drivers with glaucoma with even mild to moderate field loss exhibit impairments in driving ability, particularly during complex driving situations that involve tactical problems with lane-position, planning ahead and observation. These results, together with the fact that these drivers self-report their driving to be relatively good, reinforce the need for evidence-based on-road assessments for evaluating driving fitness.
Inhibition of Herpesvirus Replication by 5-Substituted 4′-Thiopyrimidine Nucleosides

ABSTRACT A series of 4′-thionucleosides were synthesized and evaluated for activities against orthopoxviruses and herpesviruses. We reported previously that one analog, 5-iodo-4′-thio-2′-deoxyuridine (4′-thioIDU), exhibits good activity both in vitro and in vivo against two orthopoxviruses. This compound also has good activity in cell culture against many of the herpesviruses. It inhibited the replication of herpes simplex virus type 1 (HSV-1), HSV-2, and varicella-zoster virus with 50% effective concentrations (EC50s) of 0.1, 0.5, and 2 μM, respectively. It also inhibited the replication of human cytomegalovirus (HCMV) with an EC50 of 5.9 μM but did not selectively inhibit Epstein-Barr virus, human herpesvirus 6, or human herpesvirus 8. While acyclovir-resistant strains of HSV-1 and HSV-2 were comparatively resistant to 4′-thioIDU, it retained modest activity (EC50s of 4 to 12 μM) against these strains. Some ganciclovir-resistant strains of HCMV also exhibited reduced susceptibilities to the compound, which appeared to be related to the specific mutations in the DNA polymerase, consistent with the observed incorporation of the compound into viral DNA. The activity of 4′-thioIDU was also evaluated using mice infected intranasally with the MS strain of HSV-2. Although there was no decrease in final mortality rates, the mean length of survival after inoculation increased significantly (P < 0.05) for all animals receiving 4′-thioIDU. The findings from the studies presented here suggest that 4′-thioIDU is a good inhibitor of some herpesviruses, as well as orthopoxviruses, and this class of compounds warrants further study as a therapy for infections with these viruses.
Improvement in visual function and quality of life following a blindness prevention surgery program in a rural area of Eastern China

The aim of this study was to assess the changes in visual function (VF) and quality of life (QOL) among patients following blindness prevention surgery in a rural area of Eastern China. The prospective study selected cataract patients via mobile eye screening camps. VF and QOL questionnaires originally developed by Fletcher et al were completed prior to and 6 months after surgery. Small-incision cataract surgery (SICS) with posterior chamber intraocular lens (IOL) implantation was performed on patients by a blindness prevention surgery group. The VF and QOL scores of 178 cataract patients preoperatively were 48.58±31.18 and 65.97±26.77, respectively. The scores decreased in proportion to decreasing vision status. The VF and QOL scale scores were significantly correlated with the vision grade of the patient (rVF=−17.2093, t=−10.87, P<0.001, rQOL=−13.1399, t=−8.87, P<0.001) and age (rVF=−0.6505, t=−3.87, P<0.001, rQOL=− 0.3309, t=−2.10, P=0.037). A total of 131 patients responded to the second survey, VF and QOL scores increased significantly over a six-month postoperative period (VF=83.21±16.40, P<0.001; QOL=86.53±16.33, P<0.001). The VF scale scores were correlated with the grade of vision and residence area, the QOL scale scores were correlated with the grade of vision and gender. The VF and QOL of patients were significantly improved by performing SICS with posterior chamber IOL implantation collectively in a short period in rural areas of Eastern China. It is important to follow-up cataract patients postoperatively as untreated complications of the surgery may affect the stability of VF and QOL postoperatively.
Navigating healthcare: a qualitative study exploring prostate cancer patients' and doctors' experience of consultations using a decision‐support intervention

Men with prostate cancer face preference‐sensitive decisions when choosing among treatments with similar survival outcomes but different procedures, risks and potential complications. A decision‐support intervention, ‘Decision Navigation’ assists men with prostate cancer to prepare a question list (consultation plan) for their doctors and provides them with a consultation summary and audio recording. A randomised controlled trial of Decision Navigation showed advantages over usual care on quantitative measures including confidence in decision‐making and regret.
Nonsense-mediated decay as a terminating mechanism for antisense oligonucleotides

Antisense oligonucleotides (ASOs) are synthetic oligonucleotides that alter expression of disease-associated transcripts via Watson–Crick hybridization. ASOs that function through RNase H or the RNA-induced silencing complex (RISC) result in enzymatic degradation of target RNA. ASOs designed to sterically block access of proteins to the RNA modulate mRNA metabolism but do not typically cause degradation. Here, we rationally design steric blocking ASOs to promote mRNA reduction and characterize the terminating mechanism. Transfection of ASOs complementary to constitutive exons in STAT3 and Sod1 results in greater than 70% reduction of mRNA and protein. The ASOs promote aberrant exon skipping and generation of premature termination codon (PTC)-containing mRNAs. We inhibit the nonsense-mediated mRNA decay (NMD) pathway and show that the PTC-containing mRNAs are recognized by the UPF1 ATPase, cleaved by the SMG6 endonuclease and degraded by the XRN1 cytoplasmic exonuclease. NMD surveillance, however, does not entirely explain the mechanism of decreased STAT3 expression. In addition to exon skipping, ASO treatment causes intron retention and reduction of chromatin-associated STAT3 mRNA. The application of steric blocking ASOs to promote RNA degradation allows one to explore more nucleotide modifications than tolerated by RNase H or RISC-dependent ASOs, with the goal of improving ASO drug properties.
Beta‐amyloid peptides stimulate endozepine biosynthesis in cultured rat astrocytes

Accumulation of β‐amyloid peptide (Aβ), which is a landmark of Alzheimer's disease, may alter astrocyte functions before any visible symptoms of the disease occur. Here, we examined the effects of Aβ on biosynthesis and release of diazepam‐binding inhibitor (DBI), a polypeptide primarily expressed by astroglial cells in the CNS. Quantitative RT–PCR and specific radioimmunoassay demonstrated that aggregated Aβ25−35, at concentrations up to 10−4 m, induced a dose‐dependent increase in DBI mRNA expression and DBI‐related peptide release from cultured rat astrocytes. These effects were totally suppressed when aggregation of Aβ25−35 was prevented by Congo red. Measurement of the number of living cells revealed that Aβ25−35 induced a trophic rather than a toxic effect on astrocytes. Administration of cycloheximide blocked Aβ25−35‐induced increase of DBI gene expression and endozepine accumulation in astrocytes, indicating that protein synthesis is required for DBI gene expression. Altogether, the present data suggest that Aβ‐induced activation of endozepine biosynthesis and release may contribute to astrocyte proliferation associated with Alzheimer's disease.
Channel, Phase Noise, and Frequency Offset in OFDM Systems: Joint Estimation, Data Detection, and Hybrid Cramér-Rao Lower Bound

Oscillator phase noise (PHN) and carrier frequency offset (CFO) can adversely impact the performance of orthogonal frequency division multiplexing (OFDM) systems, since they can result in inter carrier interference and rotation of the signal constellation. In this paper, we propose an expectation conditional maximization (ECM) based algorithm for joint estimation of channel, PHN, and CFO in OFDM systems. We present the signal model for the estimation problem and derive the hybrid Cramér-Rao lower bound (HCRB) for the joint estimation problem. Next, we propose an iterative receiver based on an extended Kalman filter for joint data detection and PHN tracking. Numerical results show that, compared to existing algorithms, the performance of the proposed ECM-based estimator is closer to the derived HCRB and outperforms the existing estimation algorithms at moderate-to-high signal-to-noise ratio (SNR). In addition, the combined estimation algorithm and iterative receiver are more computationally efficient than existing algorithms and result in improved average uncoded and coded bit error rate (BER) performance.
Classification of Histologic Lesions in Primary Pulmonary Hypertension Group Medial lesions Intimal lesions Medial hypertrophy Increased smooth muscle

The use of pharmacologic agents in the treatment of pulmonary hypertension has not proved to be uniformly successful or predictable. One possible reason for the vagaries in response is that the pulmonary vascular lesions are not consistent. We examined the relation between the structure of the pulmonary resistance vessels in unexplained (primary) pulmonary hypertension and the response to pulmonary vasodilators. Our study involved 19 patients with clinically unexplained pulmonary hypertension (mean pressure, 59±14 mm Hg). After characterizing them clinically and performing control hemodynamic measurements, we determined the acute effects of a series of vasodilator agents that have different mechanisms of action. In 16 patients, lung biopsy material was related to the hemodynamic studies; in nine patients, including six who had undergone open lung biopsy, the hemodynamic studies were related to the pathologic changes found at autopsy. Histologic specimens from all 19 patients were evaluated qualitatively and sorted into three subsets of hypertensive pulmonary arteriopathy: medial hypertrophy (with minimal intimal proliferation), arteriopathy with plexiform lesions (associated predominantly with concentric laminar intimal proliferation and fibrosis), and arteriopathy with microthrombotic lesions (associated predominantly with eccentric intimal proliferation and fibrosis). The 16 lung biopsies were also quantitated by morphometric techniques. Using a decrease in calculated pulmonary vascular resistance of more than 30% accompanied by a decrease in mean pulmonary arterial pressure of at least 10% to define vasodilation, only four patients were responders. The patients varied considerably in their responses to different vasodilator agents. Patients with similar clinical and hemodynamic profiles differed considerably with respect to the nature of their pulmonary vascular obstructive lesions and their responses to vasodilator agents. Qualitative histologic examination of lung tissue did not provide a basis for predicting how individual patients would respond to vasodilator agents. However, quantitative morphologic analysis of the initial open lung biopsy specimens did prove helpful in predicting acute responsiveness to vasodilator agents and the subsequent clinical course of these patients with unexplained (primary) pulmonary hypertension. An intimal area of more than 18% of the vascular cross-sectional area had an 85% predictive value for identifying the patients who did poorly during the first 36 months of follow-up. (Circulation 1989;80:1207-1221)
Exploration of Friendship Experiences, before and after Illness Onset in Females with Anorexia Nervosa: A Qualitative Study

Background Difficulties with social relationships have been implicated in both the development and maintenance of Anorexia Nervosa (AN) but the friendship experiences of individuals with AN have not been explored in depth. Method Ten adults with AN took part in a semi-structured interview about their friendship experiences both before and since the onset of their illness. Results Five principle themes were identified through thematic analysis: Social Concern; Impact of AN; Social Connectedness; Inflexibility and Preferred Social Activity. Difficulties with friendship were present prior to the onset of AN in all cases, with participants experiencing anxiety in relation to various aspects of their friendships. Participants described mixed experiences of how their AN has affected their friendships but most participants described having less contact with their friends since becoming unwell. Conclusion This research highlights the role that social difficulties may play in the development of AN, whilst also emphasising the importance of addressing problems with friendship in the course of inpatient treatment.