Miracle-dz/UniFAR-FTUs huggingface dataset:
Requirement for Yeast RAD26, a Homolog of the HumanCSB Gene, in Elongation by RNA Polymerase II

ABSTRACT Mutations in the human CSB gene cause Cockayne syndrome (CS). In addition to increased photosensitivity, CS patients suffer from severe developmental abnormalities, including growth retardation and mental retardation. Whereas a deficiency in the preferential repair of UV lesions from the transcribed strand accounts for the increased photosensitivity of CS patients, the reason for developmental defects in these individuals has remained unclear. Here we provide in vivo evidence for a role of RAD26, the counterpart of the CSB gene in Saccharomyces cerevisiae, in transcription elongation by RNA polymerase II, and in addition we show that under conditions requiring rapid synthesis of new mRNAs, growth is considerably reduced in cells lackingRAD26. These findings implicate a role for CSB in transcription elongation, and they strongly suggest that impaired transcription elongation is the underlying cause of the developmental problems in CS patients.
Terson hemorrhage in patients suffering aneurysmal subarachnoid hemorrhage: predisposing factors and prognostic significance.

OBJECT The association of vitreous and/or subhyaloid hemorrhage with aneurysmal subarachnoid hemorrhage (SAH) has been frequently identified since the original description by Terson in 1900. In this prospective clinical study the authors examined the actual incidence of Terson hemorrhage in patients suffering aneurysmal SAH, they attempted to identify those parameters that could predispose its development, and they evaluated its prognostic significance in the overall patients' outcome. METHODS A total of 174 patients suffering aneurysmal SAH were included in this study. The admitting Glasgow Coma Scale scores (GCS), World Federation of Neurological Societies (WFNS) scale scores, Hunt and Hess grades, and Fisher grades were recorded. A careful ophthalmological evaluation was performed in all participants. The exact anatomical locations and the largest diameter of the dome of the ruptured aneurysms were also recorded. Surgical clipping or endovascular coiling was used in 165 patients. Clinical outcome was evaluated at discharge from the hospital by using the Glasgow Outcome Scale and the modified Rankin Scale. Periodic ophthalmological evaluations were performed for 2 years. RESULTS In this series, the observed incidence of Terson hemorrhage was 12.1%. Statistical analysis of our data demonstrated that patients with low GCS scores and high WFNS scores, Hunt and Hess grades, and Fisher grades had an increased incidence of Terson hemorrhage. The mortality rate for patients with Terson hemorrhage was 28.6%, whereas that for patients without Terson hemorrhage was 2.0%. Moreover, patients with Terson hemorrhage who survived had significantly worse outcomes than those in patients without Terson hemorrhage. CONCLUSIONS Terson hemorrhage constitutes a common SAH-associated complication. Its incidence is increased in patients with low GCS and high WFNS scores, and high Hunt and Hess and Fisher grades. Its presence is associated with increased mortality and morbidity rates.
Optimizing Relative Transformations in Graph-Based SLAM

Traditional back-end optimization in graph-based SLAM is focused on improving global pose estimates. The object of the optimization is to find the most likely configuration of global poses given fixed relative transformation constraints produced in the front-end. However, the relative transformations delivered by the front-end are themselves only estimates. In this paper we show how making relative transformations the focus of the back-end optimization leads to a novel algorithm that iteratively improves the joint estimate of global poses and relative transformations. We test the algorithm on frontend data from a 225 meter closed-loop trajectory. Our results show the algorithm provides the same global pose estimates in slightly less computational time when compared to go, a state-of-the-art back-end optimization tool. But the optimized relative transformations produced by go require several iterations before they become more accurate than their initial values. The algorithm presented in this paper offers advantages over traditional back-end optimization in at least two ways. It uses the covariance instead of the information form, allowing ready access to marginal covariance elements needed by the front-end. It also improves both global pose and relative transformation estimates at each iteration, making the end result of the optimization suitable to a wider variety of applications.
Educational Readiness of Survivors of Neonatal Encephalopathy Associated with Birth Asphyxia at Term

Standardized individual psychoeducational school-readiness tests were completed by 127 non-disabled survivors of moderate (lethargy, hypotonia, and suppressed primitive reflexes) or mild (hyperalertness, hyperexcitibility) neonatal encephalopathy associated with term birth asphyxia. Application of the readiness test battery to the children with moderate or mild encephalopathy and to children of two other populations, term neonatal intensive care unit (ICU) graduates without encephalopathy and a peer population, revealed that children with moderate encephalopathy had significantly lower scores for many tests than those in the other groups. Children with mild encephalopathy performed well. We found no significant differences due to social variables. For the moderate group, we found an increased number of types of anticonvulsants and abnormal findings on the neurologic examination at neonatal intensive care unit (NICU) discharge to be predictors of low achievement on school-readiness tests. Also for the nondisabled moderate group, multiple regression analysis of the independent variables with the 5.5-year scores added variables suggestive of intrauterine growth retardation to the prediction of lower scores on many school-readiness tests. We conclude that clinical categorizing of moderate neonatal encephalopathy associated with birth asphyxia in term infants selects a group of children with an increased percentage of school-readiness delay, and could be a useful indicator for clinicians and educators in defining those neonates who may need special preschool evaluation and benefit from a modified early school program.
[Psychological development of the child].

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Cloning of a Clostridium thermocellum DNA fragment encoding polypeptides that bind the catalytic components of the cellulosome.

A test based on the binding of 125I-labelled endoglucanase CelD was used to clone a DNA region encoding at least two different polypeptides that interact with the conserved reiterated segment present in many catalytic components of the Clostridium thermocellum cellulosome. One of the polypeptides corresponds to the COOH-terminal region of the SL (or S1) component of the cellulosome (U.T. Gerngross and A.L. Demain, personal communication). It comprises repeated domains that are responsible for binding 125I-labelled CelD, and presumably represent anchoring sites for the various catalytic components of the cellulosome. The other polypeptide is encoded by a gene that has not yet been described.
The reaction of first-born children to the birth of a sibling: mothers' reports.

SUMMARY The reactions of first-born children to the birth of a sibling, as reported by their mothers, were studied in 40 families. Increased clinging, withdrawal and tearfulness were negatively related to positive interest in the baby, but other aspects of disturbed behaviour were not significantly associated with each other, or with positive interest. Differences in temperament, in the quality of the mother-first-born relationship, in age and in the mothers' State in the post partum weeks were found to be associated with differences in the reaction of the first-born children.
Use of the factorized form for the collision strength in exploration of the effect of the generalized Breit interaction.

Expressions are given for the convenient factorized form [Bar-Shalom, Klapisch, and Oreg, Phys. Rev. A 38, 1773 (1988)] for the collision strength with inclusion of the generalized Breit interaction. This is used to explore further the importance of the inclusion of the generalized Breit interaction in calculating electron-impact excitation cross sections or collision strengths, by considering the inner-shell excitation of Be-like uranium and the [ital n]=2 to [ital n]=3 transitions in neonlike xenon and uranium.
Management of therapeutic hypothermia for neonatal hypoxic ischaemic encephalopathy in a tertiary centre in South Africa

Aim Therapeutic hypothermia (TH), shown in developed countries to improve outcome in infants with hypoxic-ischaemic encephalopathy (HIE), was introduced into standard care at Tygerberg Children's Hospital in 2008. We aimed to describe the management and characteristics of infants treated with TH at this tertiary centre as well as the logistical challenges encountered. Methods Infants admitted for TH between 2008 and 2011 were included. They fulfilled TOBY study entry criteria and were cooled using a whole-body cooling system. A retrospective analysis of the cooling process and clinical findings was made using data collected during treatment. Results 100 infants with mild (32%), moderate (45%) and severe (23%) HIE were treated over 3 years. Mean time to admission was 4.87 (±1.63) hours, median time from delivery to target temperature was 7.5 h (range 2.5–15.5 h). Mean temperature on admission was 35.5°C (±1.5°C). Overall, rectal temperature was within target temperature for 82.8% of the time. Complications noted were clinically suspected/proven infection (45%), abnormal coagulation tests (48%), thrombocytopenia (34%), need for inotropic support (17%), hypoglycaemia (4%) and hyperglycaemia (10%). Rate of follow-up at 1 year among survivors was 57%. Infants not attending 1-year follow-up were more likely to have HIV-infected mothers, but there were no other demographic or clinical differences when compared with those who attended follow-up. Conclusions Cooling is feasible in a resource-limited setting, within a strict protocol. With close monitoring, the known and common complications occur as frequently as in less resource-limited settings. Surrogate markers of later outcome need to be explored where follow-up is problematic.
Towards HMD-based Immersive Analytics

Advances in 3D hardware and software have led to increasingly cheaper and simple-to-use immersive virtual reality systems that can provide real-time interactive 3D data representation. The immersive analytics field is developing as the newest avatar of 3D visual analyt- ics, which may relaunch the long enduring 2D vs 3D visualization debate. However, the terms of the debate have changed: leveraging 3D human perception within virtual environments is now easier, and the immersive quality of today’s rendering is sufficient enough for researchers to concentrate on testing and designing immersive data representation and interaction rather than on technological problems. In this position paper we propose a short historical perspective on the use of immersive technologies for visual analytics and on the 2D vs 3D debate. We stress out five principles that we think should be followed to explore the HMD-based visual analytics design space, before introducing ongoing work within the IDEA project.
60-GHz Substrate Integrated Waveguide Fed Cavity-Backed Aperture-Coupled Microstrip Patch Antenna Arrays

Cavity-backed patch antenna arrays with full corporate substrate integrated waveguide (SIW) feed networks are demonstrated at V-band for applications with the needs of highgain antennas. A prototype of 16 × 16 radiating elements with a waveguide transition is fabricated by applying standard printed circuit board (PCB) facilities. A gain up to 30.1 dBi with a 3-dB gain bandwidth of 16.1%, an impedance bandwidth of 15.3% for SWR <; 2, and symmetrically broadside radiation patterns with -40 dB cross-polarizations are achieved. The performance of the proposed antenna array is also systematically evaluated. The result serves as a reference for designing large antenna arrays operating at millimeter-wave frequencies.
Histological examination of the rat ovarian follicle wall prior to ovulation.

The histological changes occurring in rat ovarian follicle walls prior to ovulation were studied by light and electron microscopy. Follicles were collected at 0, 5, 10, and 11 h after the administratin of HCG to stimulate ovulation, and al’o at what was judged to be the instant before rupture from ovaries that were exteriorized in a plastic chamber for direct observation. The earliest morphological change detected was the leakage of crythrocytes from blood vessels, and thus their presence, presumably along with plasma, in the intercellular spaces of the follicle walls. Somewhat later, occasional theca cells died and degenerated, and slight signs of cytolysis appeared at the surface of all cell types. The tunica albuginea often became loose, with a large increase in the extent of extracellular space between cells. A conspicuous feature of follicle walls near the time of ovulation was the rounding up and detachment from the follicle wall of apparently healthy granulosa and theca cells; at ovulation the granulosa layer was absent from the stigma. Clumps of fibrin were commonly found in the extracellular space of the follicle wall and in follicular fluid, as was debris from degenerating cells. The final change noted before ovulation was the degeneration and loss of peritoneal epithelial cells. No collagen could be detected in follicle walls at any time. The early leakage of erythrocytes from blood vessels and the common occurrence of fibnn in the intercellular space and follicular fluid suggested that an acute inflammatory reaction may be involved in the formation and rupture of the stigma. The anti-inflammatory drugs aspirin, salicylate, and indomethacin inhibited ovulation in immature rats when administered in anti-inflammatory dosages shortly before the expected time of ovulation. The inhibition was observed in animals superovulated by exogenous PMS and HCG, as well as in animals ovulating spontaneously after a small dose of PMS. It is concluded that a process which involves prostaglandin synthesis is involved in follicle rupture, and that this step may possibly be the early vascular phase of an inflammatory response.
Molecular analyses of the phase-2 antigen complex 1,2,.. of Salmonella spp

The nucleotide sequences of the structural genes (fljB) for salmonellar flagellins representative of the phase-2 flagellar antigens 1,2. , 1,5. , 1,6. , and 1,7. were determined. The results did not indicate linear epitopes for the antigen 1 subfactors, suggesting that conformational aspects are involved in determining these antigenic specificities.
A novel eukaryotic factor for cytosolic Fe–S cluster assembly

Iron regulatory protein 1 (IRP1) is regulated through the assembly/disassembly of a [4Fe–4S] cluster, which interconverts IRP1 with cytosolic aconitase. A genetic screen to isolate Saccharomyces cerevisiae strains bearing mutations in genes required for the conversion of IRP1 to c‐aconitase led to the identification of a previously uncharacterized, essential gene, which we call CFD1 (cytosolic Fe–S cluster deficient). CFD1 encodes a highly conserved, putative P‐loop ATPase. A non‐lethal mutation of CFD1 (cfd1‐1) reduced c‐aconitase specific activity in IRP1‐transformed yeast by >90%, although IRP1 in these cells could be readily converted to c‐aconitase in vitro upon incubation with iron alone. IRP1‐transformed cfd1‐1 yeast lacked EPR‐detectable Fe–S clusters in c‐aconitase, pointing to a defect in Fe–S cluster assembly. The specific activity of another cytosolic Fe–S protein, Leu1p, was also inhibited by >90% in cfd1‐1 yeast, whereas activity of mitochondrial Fe–S proteins was not inhibited. Consistent with a cytosolic site of activity, Cfd1p was localized in the cytoplasm. To our knowledge, Cfd1p is the first cytoplasmic Fe–S cluster assembly factor described in eukaryotes.
In situ estrogen production and its regulation in human breast carcinoma: From endocrinology to intracrinology

The great majority of breast carcinomas arising in postmenopausal women are estrogen dependent or positive for estrogen receptor (ER) in carcinoma cells despite markedly low plasma or circulating estrogen concentrations. In these patients, biologically active estrogens are locally produced from circulating inactive steroids including adrenal androgens in an intracrine mechanism in the breast cancer tissues and confer estrogenic activities on carcinoma cells. A series of enzymes are involved in this intra‐tumoral or in situ production of estrogens in breast carcinoma tissues but aromatase, a member of the cytochrome P450 family, is a key enzyme of estrogen production through conversion from circulating adrenal androgens in estrogen‐dependent postmenopausal breast cancer. It then becomes important to identify the sites of this estrogen production. There has been, however, controversy regarding intra‐tumoral localization of aromatase in breast carcinoma, especially whether intra‐tumoral production of estrogens through aromatase occurs in carcinoma or stromal cells. The enzyme was demonstrated to be expressed in both carcinoma and stromal cells in breast carcinoma tissues on immunohistochemistry with a well‐characterized mAb 677 and combined laser capture microdissection/qualitative reverse transcriptase–polymerase chain reaction. Intra‐tumoral aromatase in both of these cell types was subsequently demonstrated to be induced by carcinoma–stromal interactions associated with carcinoma invasion in breast tissue. The signals through various nuclear receptors, especially estrogen‐related receptor‐α in carcinoma cells and liver receptor homologue‐1 in adipocytes adjacent to carcinoma invasion, in conjunction with various cytokines and/or growth factors, play pivotal roles in this induction of intra‐tumoral aromatase. This increased aromatase subsequently results in increased in situ estrogen concentrations of breast cancer. Aromatase inhibitors are currently established as the gold standard for the treatment for ER‐positive breast carcinoma but resistance to the therapy still remains to be solved by other modes of suppression of intra‐tumoral estrogen production.
Parallel Variable Distribution

An approach is presented here for solving optimization problems in which the variables are distributed among p processors. Each processor has primary responsibility for updating its own block of variables in parallel while allowing the remaining variables to change in a restricted fashion, e.g., along a steepest descent, quasi-Newton, or any arbitrary direction. This “forget-me-not” approach is a distinctive feature of the algorithm that has not been analyzed before. The parallelization step is followed by a fast synchronization step wherein the affine hull of the points computed by the parallel processors and the current point is searched for an optimal point. Convergence to a stationary point under continuous differentiability is established for the unconstrained case, as well as a linear convergence rate under the additional assumption of a Lipschitzian gradient and strong convexity. For problems constrained to lie in the Cartesian product of closed convex sets, convergence is established to a point sa.
Transforming research and clinical knowledge in traumatic brain injury pilot: multicenter implementation of the common data elements for traumatic brain injury.

Traumatic brain injury (TBI) is among the leading causes of death and disability worldwide, with enormous negative social and economic impacts. The heterogeneity of TBI combined with the lack of precise outcome measures have been central to the discouraging results from clinical trials. Current approaches to the characterization of disease severity and outcome have not changed in more than three decades. This prospective multicenter observational pilot study aimed to validate the feasibility of implementing the TBI Common Data Elements (TBI-CDEs). A total of 650 subjects who underwent computed tomography (CT) scans in the emergency department within 24 h of injury were enrolled at three level I trauma centers and one rehabilitation center. The TBI-CDE components collected included: 1) demographic, social and clinical data; 2) biospecimens from blood drawn for genetic and proteomic biomarker analyses; 3) neuroimaging studies at 2 weeks using 3T magnetic resonance imaging (MRI); and 4) outcome assessments at 3 and 6 months. We describe how the infrastructure was established for building data repositories for clinical data, plasma biomarkers, genetics, neuroimaging, and multidimensional outcome measures to create a high quality and accessible information commons for TBI research. Risk factors for poor follow-up, TBI-CDE limitations, and implementation strategies are described. Having demonstrated the feasibility of implementing the TBI-CDEs through successful recruitment and multidimensional data collection, we aim to expand to additional study sites. Furthermore, interested researchers will be provided early access to the Transforming Research and Clinical Knowledge in TBI (TRACK-TBI) data set for collaborative opportunities to more precisely characterize TBI and improve the design of future clinical treatment trials. (ClinicalTrials.gov Identifier NCT01565551.).
Radiographic results from the Minocycline in Rheumatoid Arthritis (MIRA) Trial.

OBJECTIVE To assess radiographically determined disease progression in patients in the Minocycline in Rheumatoid Arthritis (MIRA) Trial. METHODS A double blind, randomized, multicenter, 48 week trial of oral minocycline (200 mg/day) or placebo in 6 clinical centers in the United States. Patients include 219 adults with active RA previously receiving limited treatment with disease modifying drugs. Posteroanterior films of the hands from baseline and final visits, blinded for sequence, were read for erosions and joint space narrowing by trained observers. Outcomes included rate of disease progression (change/month) and percentage of patients with progression from baseline, newly involved joints, and newly erosive disease. RESULTS Using intent-to-treat analyses, progression rates for erosions (0.11 +/- 0.42 minocycline, 0.17 +/- 0.41 placebo; p = 0.47) and joint space narrowing (0.16 +/- 0.55 minocycline and 0.23 +/- 0.71 placebo; p = 0.14) were similar. (Power 43% to detect a 50% difference.) Newly erosive joints occurred more frequently in the placebo group (44 vs 32%; p = 0.08), not a statistically significant difference. CONCLUSION Radiographic measurement of disease progression using 4 measures failed to show a significant difference between minocycline and placebo treatment, although for all methods there was a trend toward treatment benefit, consistent with reported clinical results. A one year trial duration, high measurement variability, and slow rate of radiographic progression in this cohort may explain the low power to detect a treatment effect. The measurement that denoted "newly involved" joints was most sensitive in detecting change. In future trials longer term assessment (minimum 2 years) of radiographic changes and further comparison of measures of disease progression are warranted.