Miracle-dz/UniFAR-FTUs huggingface dataset:
Using technology to improve longitudinal studies: self-reporting with ChronoRecord in bipolar disorder.

OBJECTIVES Longitudinal studies are an optimal approach to investigating the highly variable course and outcome associated with bipolar disorder, but are expensive and often have missing data. This study validates patient self-reported mood ratings using a home computer-based system (ChronoRecord) with clinician mood ratings on the Hamilton Depression Rating scale (HAMD) and Young Mania Rating scale (YMRS), and investigates the patient acceptance of the technology. METHODS After brief training, outpatients with bipolar disorder were given the software version of an established paper based self-reporting form (ChronoSheet) to install on a home computer. Every day for 3 months, patients entered mood, medications, sleep, life events, and menstrual data. Weight was entered weekly. RESULTS Eighty of 96 (83%) patients returned 8662 days of data. The mean days of data returned was 114.7 +/- 32.3 SD The mean percentage of days missing for mood data was 6.1% +/- 9.3 SD, equivalent to missing 7.3 day of the 114.7 days. Self-reported ratings were strongly correlated with clinician HAMD ratings (-0.683, p < 0.001). CONCLUSIONS This study demonstrates concurrent validity between ChronoRecord and HAMD. Patients with bipolar disorder showed high acceptance of a computer-based system for self-reporting of daily data. Automation of data collection can reduce missing data and eliminate errors associated with data entry. This technology also enables on-going feedback for both patient and researcher during a long-term study.
Turning back from the brink: Detecting an impending regime shift in time to avert it

Ecological regime shifts are large, abrupt, long-lasting changes in ecosystems that often have considerable impacts on human economies and societies. Avoiding unintentional regime shifts is widely regarded as desirable, but prediction of ecological regime shifts is notoriously difficult. Recent research indicates that changes in ecological time series (e.g., increased variability and autocorrelation) could potentially serve as early warning indicators of impending shifts. A critical question, however, is whether such indicators provide sufficient warning to adapt management to avert regime shifts. We examine this question using a fisheries model, with regime shifts driven by angling (amenable to rapid reduction) or shoreline development (only gradual restoration is possible). The model represents key features of a broad class of ecological regime shifts. We find that if drivers can only be manipulated gradually management action is needed substantially before a regime shift to avert it; if drivers can be rapidly altered aversive action may be delayed until a shift is underway. Large increases in the indicators only occur once a regime shift is initiated, often too late for management to avert a shift. To improve usefulness in averting regime shifts, we suggest that research focus on defining critical indicator levels rather than detecting change in the indicators. Ideally, critical indicator levels should be related to switches in ecosystem attractors; we present a new spectral density ratio indicator to this end. Averting ecological regime shifts is also dependent on developing policy processes that enable society to respond more rapidly to information about impending regime shifts.
The ntrBC genes of Rhizobium leguminosarum are part of a complex operon subject to negative regulation

We report here that ntrB and ntrC genes of Rhizobium leguminosarum biovar phaseoli are cotranscribed with an open reading frame (called 0RF1) of unknown Unction. The promoter region of the 0RF1‐ntrB‐ntrC operon was mapped immediately upstream of ORF1 and two in vivo transcription initiation sites were identified, both preceded by −35/−10 promoter consensus sequences. Some major aspects differentiate ft leguminosarum from the enteric nitrogen regulatory system: the ntrBC genes are cotranscribed with 0RF1 which is homologous to an ORF located upstream of ntrBC of R. capsulatus and to the 0RF1 located upstream of the fis gene of Escherichia coir, ntrBC are not transcribed from a −24/−12 promoter and are only autogenously repressed. Moreover, the intracellular concentration of the NtrC protein increases when the bacterium is grown on ammonium salts, white under the same conditions the promoter of one of its target genes, glnII, is 12 times less active.
Adults with Rubinstein–Taybi syndrome

Information in the medical literature regarding adults with genetic syndromes is limited, making the care of these patients challenging. We conducted a questionnaire study of adults with Rubinstein–Taybi syndrome that addressed medical problems, education, independence, and behavior. The most common medical problems included short stature, obesity, visual difficulties, keloids, eating problems, spine curvature, and joint problems. The adults had typically moderate mental retardation, but most achieved some independence in self‐care and communication; many participated in supported work situations. However, approximately one‐third were said to have some decreased abilities over time. Behavior problems were common and often worsened with age. Very few of the study participants were seeing a geneticist as an adult. Long‐term involvement of geneticists and education of adult primary care providers may help with many of the challenges facing adults with RTS and their families. © 2011 Wiley‐Liss, Inc.
Geometric Algorithms for Trajectory Analysis

Technology such as the Global Positing System (GPS) has made tracking moving entities easy and cheap. As a result there is a large amount of trajectory data available, and an increasing demand on tools and techniques to analyze such data. We consider several analysis tasks for trajectory data, and develop efficient algorithms to perform them automatically. In particular, we study the following tasks: •Find a segmentation of a trajectory based on a non-monotone criterion. •Find hotspots; regions in which the entity spent a large amount of time. •Find all groups and the grouping structure. A group is a movement pattern in which sufficiently many entities move together during a sufficiently long time interval. In addition to the groups themselves we also find the relation between groups, e.g. a large group came into existence when two smaller groups merged. •Find a central trajectory: a representative for a set of trajectories. For each task, we formalize the problem, and analyze its geometric properties. We use these properties to obtain efficient algorithms to automatically perform the task at hand. In many cases, we also show that our analysis is tight, and that our algorithms are optimal.
Accurate Simulation of the Electron Density of Surrounding Gate Transistors

In this work we have studied the influence of the effective mass anisotropy on the Quantum Electron Density (QED) of surrounding gate transistors (SGTs). We show that, despite the cylindrical symmetry of the circular cross-section SGTs, the electron density is not symmetric due to the anisotropy of the silicon conduction band. We have compared the quantum electron densities obtained in devices with different orientations, showing interesting behaviors when combining effective mass anisotropy with nonhomogeneous electrostatics due to the presence of corners.
Magnetic Shielding Characteristics of Second Generation High Temperature Superconductors at Variable Temperatures Obtained by Cryogenic Helium Gas Circulation

Magnetic shielding characteristics of 40 mm wide second generation high temperature superconducting (2GHTS) materials were studied at variable temperatures. Shielding characteristics were measured in DC and variable frequency AC magnetic fields at a range of magnitudes up to 60 mT. Magnetic shields fabricated in the form of short cylinders were studied with magnetic field perpendicular to their axis. Shielding properties of single and double layer shields were compared at various temperatures between 50 and 80 K. Shielding factor up to 98% was achieved. The benefit of lower temperatures is particularly visible at higher magnetic fields. Trends of shielding characteristics modeled as a function of external magnetic field strength with finite element models using COMSOL match with those of the experimental observations.
ULTRASTRUCTURAL VARIATIONS IN N,N'-BIS(4-AMINOPHENYL)-N,N'-DIMETHYLETHYLENEDIAMINE (BED) OXIDASE LOCALIZATION IN RAT LIVER AND PAROTID GLAND WITH VARIATION IN LENGTH OF FIXATION

The localization and reactivity of a terminal oxidase which oxidizes N,N'-bis(4-amino-phenyl)-N,N'-dimethylethylenediamine (BED) were studied in rat liver and parotid gland after varying the concentration of formaldehyde fixative and the length of fixation. Reaction product was observed in mitochondrial outer compartments, smooth elements of rough endoplasmic reticulum, some Golgi lamellae, perinuclear membranes and cytoplasmic membranous structures often associated with mitochondria. A reaction also occurred in the limiting membrane and, to some degree, in the material comprising the secretory granules of the parotid. The reaction in the mitochondrial outer compartment was extremely formaldehyde-sensitive. Controls in which diaminobenzidine (DAB) was substituted for BED showed reaction only in mitochondrial cristae and outer compartments, whereas controls without either reagent showed no reactivity.
Control of poly(A) tail length

Poly(A) tails have long been known as stable 3′ modifications of eukaryotic mRNAs, added during nuclear pre‐mRNA processing. It is now appreciated that this modification is much more diverse: A whole new family of poly(A) polymerases has been discovered, and poly(A) tails occur as transient destabilizing additions to a wide range of different RNA substrates. We review the field from the perspective of poly(A) tail length. Length control is important because (1) poly(A) tail shortening from a defined starting point acts as a timer of mRNA stability, (2) changes in poly(A) tail length are used for the purpose of translational regulation, and (3) length may be the key feature distinguishing between the stabilizing poly(A) tails of mRNAs and the destabilizing oligo(A) tails of different unstable RNAs. The mechanism of length control during nuclear processing of pre‐mRNAs is relatively well understood and is based on the changes in the processivity of poly(A) polymerase induced by two RNA‐binding proteins. Developmentally regulated poly(A) tail extension also generates defined tails; however, although many of the proteins responsible are known, the reaction is not understood mechanistically. Finally, destabilizing oligoadenylation does not appear to have inherent length control. Rather, average tail length results from the balance between polyadenylation and deadenylation. WIREs RNA 2011 2 348–361 DOI: 10.1002/wrna.56
The Extended Welfare Assessment Grid: A Matrix for the Assessment of Welfare and Cumulative Suffering in Experimental Animals

Combining a range of assessment parameters into one usable entity has been identified as an important goal in providing a practical, objective and robust assessment of welfare, particularly in laboratory animals. This paper refines and extends one such previously published method. The proposed Extended Welfare Assessment Grid provides for the incorporation of changes in the state of an animal over time, allowing for predictive, retrospective, scheduled, or event monitoring. It enables the numeric, as well as visual, representation of the animal's welfare, placing this in the context of the careful and realistic justification for experimental use of the animal. This assessment method represents a valuable tool for those tasked with ensuring ethical oversight, as well as for those planning the use, or monitoring, of animals in research. It is particularly applicable to animals used in long-term studies, especially non-human primates. It is believed that this system will draw attention to the temporal component of suffering that is often overlooked in the planning of research schedules and allow an assessment of cumulative suffering imposed by the events that occur.
Hypervolemic hypertension in mice with systemic inactivation of the (floxed) guanylyl cyclase‐A gene by αMHC‐Cre‐mediated recombination

To dissect the tissue‐specific functions of atrial natriuretic peptide (ANP), we recently introduced loxP sites into the murine gene for its receptor, guanylyl cyclase‐A (GC‐A), by homologous recombination (tri‐lox GC‐A). For either smooth‐muscle or cardiomyocyte‐restricted deletion of GC‐A, floxed GC‐A mice were mated to transgenic mice expressing Cre‐recombinase under the control of the smooth‐muscle SM22 or the cardiac αMHC promoter. As shown in these studies, Cre‐mediated recombination of the floxed GC‐A gene fully inactivated GC‐A function in a cell‐restricted manner. In the present study we show that αMHC‐Cre, but not SM22‐Cre, with high frequency generates genomic recombinations of the floxed GC‐A gene segments which were transmitted to the germline. Alleles with partial or complete deletions were readily recovered from the next generation, after segregation of the Cre‐transgene. We took advantage of this strategy to generate a new mouse line with global, systemic deletion of GC‐A. Doppler‐echocardiographic and physiological studies in these mice demonstrate for the first time the tremendous impact of ANP/GC‐A dysfunction on chronic blood volume homeostasis. genesis 39:288–298, 2004. © 2004 Wiley‐Liss, Inc.
THE SPITZER MID-INFRARED ACTIVE GALACTIC NUCLEUS SURVEY. I. OPTICAL AND NEAR-INFRARED SPECTROSCOPY OF OBSCURED CANDIDATES AND NORMAL ACTIVE GALACTIC NUCLEI SELECTED IN THE MID-INFRARED

We present the results of a program of optical and near-infrared spectroscopic follow-up of candidate active galactic nuclei (AGNs) selected in the mid-infrared. This survey selects both normal and obscured AGNs closely matched in luminosity across a wide range, from Seyfert galaxies with bolometric luminosities Lbol ∼ 1010 L☉ to highly luminous quasars (Lbol ∼ 1014 L☉), all with redshifts ranging from 0 to 4.3. Samples of candidate AGNs were selected with mid-infrared color cuts at several different 24 μm flux density limits to ensure a range of luminosities at a given redshift. The survey consists of 786 candidate AGNs and quasars, of which 672 have spectroscopic redshifts and classifications. Of these, 137 (20%) are type 1 AGNs with blue continua, 294 (44%) are type 2 objects with extinctions AV ≳ 5 toward their AGNs, 96 (14%) are AGNs with lower extinctions (AV ∼ 1), and 145 (22%) have redshifts, but no clear signs of AGN activity in their spectra. Of the survey objects 50% have Lbol > 1012 L☉, in the quasar regime. We present composite spectra for type 2 quasars and objects with no signs of AGN activity in their spectra. We also discuss the mid-infrared—emission-line luminosity correlation and present the results of cross correlations with serendipitous X-ray and radio sources. The results show that: (1) obscured objects dominate the overall AGN population, (2) mid-infrared selected AGN candidates exist which lack AGN signatures in their optical spectra but have AGN-like X-ray or radio counterparts, and (3) X-ray and optical classifications of obscured and unobscured AGNs often differ.
CONSERVATIVE MULTIGRID METHODS FOR TERNARY CAHN-HILLIARD SYSTEMS ∗

We develop a conservative, second order accurate fully implicit discretization of ternary (three-phase) Cahn-Hilliard (CH) systems that has an associated discrete energy functional. This is an extension of our work for two-phase systems (13). We analyze and prove convergence of the scheme. To efficiently solve the discrete system at the implicit time-level, we use a nonlinear multigrid method. The resulting scheme is efficient, robust and there is at most a 1 st order time step constraint for stability. We demonstrate convergence of our scheme numerically and we present several simulations of phase transitions in ternary systems.
Using Data Visualisation to Tell Stories about Collections

The paper explores visualisation of "big data" from digitised museum collections and archives, focusing on the relationship between data, visualisation and narrative. A contrast is presented between visualisations that show "just the data" and those that present the information in such a way as to tell a story using visual rhetorical devices; such devices have historically included trees, streams, chains, geometric shapes and other forms. The contrast is explored through historical examples and a survey of current practice. A discussion centred on visualising datasets from the British Library, Science Museum and Wellcome Library is used to outline key research questions.
Structural Study of the Partially Disordered Full‐Length δ Subunit of RNA Polymerase from Bacillus subtilis

The partially disordered δ subunit of RNA polymerase was studied by various NMR techniques. The structure of the well‐folded N‐terminal domain was determined based on inter‐proton distances in NOESY spectra. The obtained structural model was compared to the previously determined structure of a truncated construct (lacking the C‐terminal domain). Only marginal differences were identified, thus indicating that the first structural model was not significantly compromised by the absence of the C‐terminal domain. Various 15N relaxation experiments were employed to describe the flexibility of both domains. The relaxation data revealed that the C‐terminal domain is more flexible, but its flexibility is not uniform. By using paramagnetic labels, transient contacts of the C‐terminal tail with the N‐terminal domain and with itself were identified. A propensity of the C‐terminal domain to form β‐type structures was obtained by chemical shift analysis. Comparison with the paramagnetic relaxation enhancement indicated a well‐balanced interplay of repulsive and attractive electrostatic interactions governing the conformational behavior of the C‐terminal domain. The results showed that the δ subunit consists of a well‐ordered N‐terminal domain and a flexible C‐terminal domain that exhibits a complex hierarchy of partial ordering.
Plant systematics in the next 50 years-re-mapping the new frontier

In the historical context of plant systematics over the last 50 years, systematics is examined in terms of where it is now, where it is headed, where it should be, and how it should get there. Issues and concerns of the past decades are still with us today. Molecular systematics has become the over-arching field in systematics, but each of eight other areas (genome, chromosomes, morphology and anatomy, development, population biology, speciation, floristics and monography, nomenclature and classification) are evaluated. A revolution in
Consolidation docetaxel after concurrent chemoradiotherapy in stage IIIB non-small-cell lung cancer: phase II Southwest Oncology Group Study S9504.

PURPOSE To test the concept of taxane sequencing in combined-modality therapy, this phase II trial (S9504) evaluated consolidation docetaxel after concurrent chemoradiotherapy in patients with pathologically documented stage IIIB non-small-cell lung cancer (NSCLC). Results were compared with those of the predecessor study (S9019) with identical eligibility, staging criteria, and treatment, excepting docetaxel consolidation. PATIENTS AND METHODS Treatment consisted of cisplatin 50 mg/m2 on days 1, 8, 29, and 36, etoposide 50 mg/m2 on days 1 through 5 and 29 through 33, and concurrent thoracic radiotherapy (total dose of 61 Gy). Consolidation docetaxel started 4 to 6 weeks after chemoradiotherapy at an initial dose of 75 mg/m2. RESULTS Stage subsets (tumor-node-metastasis system) in 83 eligible patients were as follows: T4N0/1, 31 patients (37%); T4N2, 22 patients (27%), and T1-3N3, 30 patients (36%). Concurrent chemoradiotherapy was generally well tolerated, but two patients died from probable radiation-associated pneumonitis. Neutropenia during consolidation docetaxel was common (57% with grade 4) and most frequent during escalation to 100 mg/m2. Median progression-free survival was 16 months, median survival was 26 months, and 1-, 2-, and 3-year survival rates were 76%, 54%, and 37%, respectively. Brain metastasis was the most common site of failure. In S9019, median survival was 15 months and 1-, 2-, and 3-year survival rates were 58%, 34%, and 17%, respectively. CONCLUSION Consolidation docetaxel after concurrent chemoradiotherapy in stage IIIB NSCLC is feasible and generally tolerable, and results compare favorably with the predecessor trial S9019. Nevertheless, this study remains hypothesis-generating and does not provide definitive evidence of the benefit of this approach. Phase III trials evaluating the S9504 regimen have been initiated to validate these results.
Relationship Between Serum Zinc Levels , Hormonal Profiles and Sexual Dysfunctions in Male Hemodialysis Patients

ÖZET Amaç: Erkek hemodiyaliz hastalar›nda seksüel bozukluklar›n s›kl›¤› ile serum çinko seviyesi, hormonal profil ve seksüel disfonksiyon aras›ndaki iliflkinin de¤erlendirilmesi. Materyal ve Metot: En az alt› ayd›r haftada 15 saat konvansiyonel bikarbonat tedavisi gören 41 erkek hasta de¤erlendirildi. Serum PRL, FSH, LH, progesteron, testosteron, TSH, serbest T4 ve çinko düzeyleri ölçüldü. Seksüel disfonksiyon kiflisel anketle de¤erlendirildi. Bulgular: Üç hastada düflük serum çinko düzeyi tespit edildi. 33 (%80.5) hastada PRL yüksekti. Hastalar›n 17’sinde (%41.5) prematür ejakülasyon, 10’unda (%24.4) erektil disfonksiyon, 7’sinde (%17) impotans ve 7’sinde (%17) azalm›fl libido saptand›. Yafl ile impotans aras›nda (r=0.594, p=0.000) ve hipozinkemi ile prematür ejakülasyon aras›nda (r=0.334, p=0.033) pozitif korelasyon bulundu. Hemodiyaliz süresi ile PRL düzeyi aras›nda negatif bir korelasyon saptand› (r=-0.363, p=0.020). Hipozinkemi ile hiperproloktinemi aras›nda anlaml› korelasyon bulunmad› (r=0.084, p=0.456). Sonuç: Hipozinkemi ve hiperprolaktinemi hemodiyaliz hastalar›nda yayg›nd›r. Hipozinkemi ile hiperprolaktinemi aras›nda iliflki bulunmad›. PRL düzeyi, hemodiyaliz süresine ba¤l› azalm›fl bulundu. Serum çinko düzeyi ile prematür ejakülasyon aras›nda pozitif korelasyon saptand›. Anahtar sözcükler: hipozinkemi, seksüel disfonksiyon, hiperprolaktinemi, HD patients ABSTRACT Objectives: To investigate the frequency of sexual disorders and the relationship between serum zinc levels, hormonal profiles and sexual dysfunctions in male HD patients. Materials and Methods: Forty-one male patients who were on chronic HD programme for at least six months, and treated by conventional bicarbonated HD 15 hours/week were evaluated. The serum levels of PRL, FSH, LH, progesterone, testosteron, TSH, free thyroxine and zinc were measured. A personal questionnaire was used to evaluate the sexual dysfunctions. Results: Three of the 41 patients had low serum zinc levels. Thirty-three (80.5%) of patients had elevated PRL levels. 17 (41.5%) of the patients had premature ejaculation, 10 (24.4%) had erectile dysfunction, 7 (17%) had impotence, and 7(17%) had decreased libido. A positive correlation was found between age and impotence (r=0.594, p=0.000) and between hypozincemia and premature ejaculation (r=0.334, p=0.033). A negative correlation was found between HD duration and PRL levels (r=-0.363, p=0.020). There was not any significant correlation between hypozincemia and hyperprolactinemia (r=0.084, p=0.456). Conclusion: Hypozincemia and hyperprolactinemia were prevalant among HD patients. No correlation was found between hypozincemia and hyperprolactinemia. PRL levels decreased due to HD duration. A correlation was found between serum Zn levels and premature ejaculation.