Miracle-dz/UniFAR-FTUs huggingface dataset:
Atomic contact vectors in protein‐protein recognition

The ability to analyze and compare protein‐protein interactions on the structural level is critical to our understanding of various aspects of molecular recognition and the functional interplay of components of biochemical networks. In this study, we introduce atomic contact vectors (ACVs) as an intuitive way to represent the physico‐chemical characteristics of a protein‐protein interface as well as a way to compare interfaces to each other. We test the utility of ACVs in classification by using them to distinguish between homodimers and crystal contacts. Our results compare favorably with those reported by other authors. We then apply ACVs to mine the PDB for all known protein‐protein complexes and separate transient recognition complexes from permanent oligomeric ones. Getting at the basis of this difference is important for our understanding of recognition and we achieved a success rate of 91% for distinguishing these two classes of complexes. Although accessible surface area of the interface is a major discriminating feature, we also show that there are distinct differences in the contact preferences between the two kinds of complexes. Illustrating the superiority of ACVs as a basic comparison measure over a sequence‐based approach, we derive a general rule of thumb to determine whether two protein‐protein interfaces are redundant. With this method, we arrive at a nonredundant set of 209 recognition complexes—the largest set reported so far. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Characterization of Microcirculation in Multiple Sclerosis Lesions by Dynamic Texture Parameter Analysis (DTPA)

Objective Texture analysis is an alternative method to quantitatively assess MR-images. In this study, we introduce dynamic texture parameter analysis (DTPA), a novel technique to investigate the temporal evolution of texture parameters using dynamic susceptibility contrast enhanced (DSCE) imaging. Here, we aim to introduce the method and its application on enhancing lesions (EL), non-enhancing lesions (NEL) and normal appearing white matter (NAWM) in multiple sclerosis (MS). Methods We investigated 18 patients with MS and clinical isolated syndrome (CIS), according to the 2010 McDonald's criteria using DSCE imaging at different field strengths (1.5 and 3 Tesla). Tissues of interest (TOIs) were defined within 27 EL, 29 NEL and 37 NAWM areas after normalization and eight histogram-based texture parameter maps (TPMs) were computed. TPMs quantify the heterogeneity of the TOI. For every TOI, the average, variance, skewness, kurtosis and variance-of-the-variance statistical parameters were calculated. These TOI parameters were further analyzed using one-way ANOVA followed by multiple Wilcoxon sum rank testing corrected for multiple comparisons. Results Tissue- and time-dependent differences were observed in the dynamics of computed texture parameters. Sixteen parameters discriminated between EL, NEL and NAWM (pAVG = 0.0005). Significant differences in the DTPA texture maps were found during inflow (52 parameters), outflow (40 parameters) and reperfusion (62 parameters). The strongest discriminators among the TPMs were observed in the variance-related parameters, while skewness and kurtosis TPMs were in general less sensitive to detect differences between the tissues. Conclusion DTPA of DSCE image time series revealed characteristic time responses for ELs, NELs and NAWM. This may be further used for a refined quantitative grading of MS lesions during their evolution from acute to chronic state. DTPA discriminates lesions beyond features of enhancement or T2-hypersignal, on a numeric scale allowing for a more subtle grading of MS-lesions.
Effect of Dopamine Therapy on Nonverbal Affect Burst Recognition in Parkinson's Disease

Background Parkinson's disease (PD) provides a model for investigating the involvement of the basal ganglia and mesolimbic dopaminergic system in the recognition of emotions from voices (i.e., emotional prosody). Although previous studies of emotional prosody recognition in PD have reported evidence of impairment, none of them compared PD patients at different stages of the disease, or ON and OFF dopamine replacement therapy, making it difficult to determine whether their impairment was due to general cognitive deterioration or to a more specific dopaminergic deficit. Methods We explored the involvement of the dopaminergic pathways in the recognition of nonverbal affect bursts (onomatopoeias) in 15 newly diagnosed PD patients in the early stages of the disease, 15 PD patients in the advanced stages of the disease and 15 healthy controls. The early PD group was studied in two conditions: ON and OFF dopaminergic therapy. Results Results showed that the early PD patients performed more poorly in the ON condition than in the OFF one, for overall emotion recognition, as well as for the recognition of anger, disgust and fear. Additionally, for anger, the early PD ON patients performed more poorly than controls. For overall emotion recognition, both advanced PD patients and early PD ON patients performed more poorly than controls. Analysis of continuous ratings on target and nontarget visual analog scales confirmed these patterns of results, showing a systematic emotional bias in both the advanced PD and early PD ON (but not OFF) patients compared with controls. Conclusions These results i) confirm the involvement of the dopaminergic pathways and basal ganglia in emotional prosody recognition, and ii) suggest a possibly deleterious effect of dopatherapy on affective abilities in the early stages of PD.
Coronal Heating by Nanoflares and the Variability of the Occurrence Frequency in Solar Flares

It has been proposed that flares in the solar corona may well be a result of an internal self-organized critical (SOC) process in active regions. We have developed a cellular automaton SOC model that simulates flaring activity extending over an active subflaring background. In the resulting frequency distributions we obtain two distinct power laws. That of the weaker events is shorter and much steeper (power law with index ≃-3.26) than that of the intermediate and large events (power law with index ≃-1.73). The flatter power law is in close agreement with observations of flares. Weaker events are responsible for ≃90% of the total magnetic energy released, indicating a possible connection of nanoflares with coronal heating. Moreover, certain mechanisms cause the variability of the resulting indices and may provide answers to the problem of the variability of flares' occurrence frequency during the solar cycle.
Biomarkers in Chronic Fatigue Syndrome: Evaluation of Natural Killer Cell Function and Dipeptidyl Peptidase IV/CD26

Background Chronic Fatigue Syndrome (CFS) studies from our laboratory and others described decreased natural killer cell cytotoxicity (NKCC) and elevated proportion of lymphocytes expressing the activation marker, dipeptidyl peptidase IV (DPPIV) also known as CD26. However, neither these assays nor other laboratory tests are widely accepted for the diagnosis or prognosis of CFS. This study sought to determine if NKCC or DPPIV/CD26 have diagnostic accuracy for CFS. Methods/Results Subjects included female and male CFS cases and healthy controls. NK cell function was measured with a bioassay, using K562 cells and 51Cr release. Lymphocyte associated DPPIV/CD26 was assayed by qualitative and quantitative flow cytometry. Serum DPPIV/CD26 was measured by ELISA. Analysis by receiver operating characteristic (ROC) curve assessed biomarker potential. Cytotoxic function of NK cells for 176 CFS subjects was significantly lower than in the 230 controls. According to ROC analysis, NKCC was a good predictor of CFS status. There was no significant difference in NK cell counts between cases and controls. Percent CD2+ lymphocytes (T cells and NK cells) positive for DPPIV/C26 was elevated in CFS cases, but there was a decrease in the number of molecules (rMol) of DPPIV/C26 expressed on T cells and NK cells and a decrease in the soluble form of the enzyme in serum. Analyses by ROC curves indicated that all three measurements of DPPIV/CD26 demonstrated potential as biomarkers for CFS. None of the DPPIV/C26 assays were significantly correlated with NKCC. Conclusions By ROC analysis, NKCC and three methods of measuring DPPIV/C26 examined in this study had potential as biomarkers for CFS. Of these, NKCC, %CD2+CD26+ lymphocytes and rMol CD26/CD2+ lymphocyte, required flow cytometry, fresh blood and access to a high complexity laboratory. Soluble DPPIV/C26 in serum is done with a standard ELISA assay, or with other soluble factors in a multiplex type of ELISA. Dipeptidyl peptidase IV on lymphocytes or in serum was not predictive of NKCC suggesting that these should be considered as non-redundant biomarkers. Abnormalities in DPPIV/CD26 and in NK cell function have particular relevance to the possible role of infection in the initiation and/or the persistence of CFS.
Making sense of co-operative governance: competing models and tensions

This paper focuses on how cooperatives and mutual associations are governed. At the heart of these arrangements is an organisation's governing body or board. Paralleling developments in the private sector, the quality of governance of co-operatives has been questioned. Serious concerns have been raised both about the democratic legitimacy of boards and their effectiveness, for example the ability of lay board members to effectively supervise senior managers, ensure probity and protect the interests of members and other relevant stakeholders.
Control of Feedforward Dendritic Inhibition by NMDA Receptor-Dependent Spike Timing in Hippocampal Interneurons

Two putative functional populations of feedforward interneurons with distinct spike-timing properties were identified in stratum radiatum of the CA1 rat hippocampus. Interneurons with fast (half width, <100 msec) EPSPs fired after short EPSP-spike latencies and with a high degree of temporal precision compared with cells with slow (half width, >100 msec) EPSPs. Spike timing in fast and slow interneurons occurred at different phases of the EPSPs of simultaneously activated pyramidal cells. In addition, firing of fast interneurons preceded action potentials in principal neurons, whereas action potentials in slow interneurons could either precede or follow firing in pyramidal cells. Temporal integration of separate inputs leading to synaptically evoked firing was more prominent in slow than fast interneurons. Functional diversity between the two putative populations was abolished by the NMDA receptor (NMDAR) antagonist d-(-)-2-amino-5-phosphonopentanoic acid (d-AP-5). The axon of both cell types was primarily restricted to striatum radiatum or to striatum lacunosum-moleculare in the case of slow cells, suggesting targeting of principal cell dendrites for the majority of the cells of this study. Indeed, firing of slow and fast interneurons generated similar unitary IPSCs (uIPSCs) in pyramidal neurons. uIPSCs were mediated by GABAAreceptors and had in most cases small amplitudes and slow kinetics. Our results suggest that functionally heterogeneous interneurons encode the temporal properties of dendritic feedforward inhibition, and that NMDARs play an essential role in shaping the integrative properties of interneurons and in setting the timing of GABA release.
Spinal Cord Atrophy and Early Motor Recovery following Transverse Myelitis in Pediatric Patients

Objective To compare the motor recovery following transverse myelitis in pediatric patients with and without spinal cord atrophy. Method From January 1995 through December 2009, twenty children (8 boys and 12 girls with an onset at 5.7±3.8 years) that were diagnosed with transverse myelitis at a Children's Hospital in Korea, and undertaken an initial and follow-up spine magnetic resonance image (MRI) were included. Medical records and spine MRI scans were reviewed retrospectively. An initial MRI was taken 5.1±8.7 days after the onset. The interval between an initial and follow-up MRIs was 33.4±23.0 days. The motor recovery differences between subjects with and without spinal cord atrophy on follow-up MRIs were determined. Motor recovery was defined as the elevation of one or more grades of manual muscle tests of the Medical Research Council. Results Eight patients had developed spinal cord atrophies and 12 patients had not. Of the 8 patients with spinal cord atrophy, 7 showed no motor improvement. Among the 12 patients without atrophy, 11 had motor improvement. Spinal cord atrophy on follow-up MRIs were related to the risk of no motor improvement (odds ratio=77.0, 95% confidence interval [4.114-1441.049], p-value=0.001). Conclusion Children with transverse myelitis who had developed spinal cord atrophy on follow-up MRIs had poor motor recovery than those who had not. The appearance of spinal cord atrophy on follow-up MRI could be an indicator of poor prognosis in pediatric transverse myelitis.
Picomolar Dichotomous Activity of Gnidimacrin Against HIV-1

Highly active antiretroviral therapy (HAART) has offered a promising approach for controlling HIV-1 replication in infected individuals. However, with HARRT, HIV-1 is suppressed rather than eradicated due to persistence of HIV-1 in latent viral reservoirs. Thus, purging the virus from latent reservoirs is an important strategy toward eradicating HIV-1 infection. In this study, we discovered that the daphnane diterpene gnidimacrin, which was previously reported to have potent anti-cancer cell activity, activated HIV-1 replication and killed persistently-infected cells at picomolar concentrations. In addition to its potential to purge HIV-1 from latently infected cells, gnidimacrin potently inhibited a panel of HIV-1 R5 virus infection of peripheral blood mononuclear cells (PBMCs) at an average concentration lower than 10 pM. In contrast, gnidimacrin only partially inhibited HIV-1 ×4 virus infection of PBMCs. The strong anti-HIV-1 R5 virus activity of gnidimacrin was correlated with its effect on down-regulation of the HIV-1 coreceptor CCR5. The anti-R5 virus activity of gnidimacrin was completely abrogated by a selective protein kinase C beta inhibitor enzastaurin, which suggests that protein kinase C beta plays a key role in the potent anti-HIV-1 activity of gnidimacrin in PBMCs. In summary, these results suggest that gnidimacrin could activate latent HIV-1, specifically kill HIV-1 persistently infected cells, and inhibit R5 viruses at picomolar concentrations.
Cosmological constraints from the X-ray gas mass fraction in relaxed lensing clusters observed with Chandra

We present precise measurements of the X-ray gas mass fraction for a sample of luminous, relatively relaxed clusters of galaxies observed with the Chandra Observatory, for which independent confirmation of the mass results is available from gravitational lensing studies. Parameterizing the total (luminous plus dark matter) mass profiles using the model of Navarro, Frenk & White (1997), we show that the X-ray gas mass fractions in the clusters asymptote towards an approximately constant value at a radius r_2500, where the mean interior density is 2500 times the critical density of the Universe at the redshifts of the clusters. Combining the Chandra results on the X-ray gas mass fraction and its apparent redshift dependence with recent measurements of the mean baryonic matter density in the Universe and the Hubble Constant determined from the Hubble Key Project, we obtain a tight constraint on the mean total matter density of the Universe, Omega_m = 0.30^{+0.04}_{-0.03}, and measure a positive cosmological constant, Omega_Lambda = 0.95^{+0.48}_{-0.72}. Our results are in good agreement with recent, independent findings based on analyses of anisotropies in the cosmic microwave background radiation, the properties of distant supernovae, and the large-scale distribution of galaxies.
Extensive Bone Marrow Necrosis in a Case of Acute Myeloid Leukemia Transformed from a Myeloproliferative Neoplasm

Extensive necrosis affecting more than 50% of the bone marrow is an extremely rare histopathological finding. Relatively little is known about its clinical significance because it is most commonly identified at autopsy - whether it is an independent prognostic marker or whether it is a surrogate marker of underlying disease burden remains unclear. We describe herein a case of a 66-year-old patient with acute myeloid leukemia who presented with acute bone marrow failure and was found to have extensive necrosis. We include presenting clinical features, pathology attained at biopsy, and the challenge of treatment. Bone marrow necrosis is a rare but important clinicopathological entity whose recognition may herald the way for more effective prognostication of underlying disease.
Implementation of an additional monitoring device to prevent failures of the cooling systems

Computer systems in a datacenter are designed to work best when the ambient temperature is around 20 Celsius degree. These requirements ensure that the datacenter has to be equipped with automatic ventilation and thermostatic systems. The systems keep temperature around equipment and components to a specified level, regardless of the amount of heat generation and variation of external temperature. The thermostatic process is achieved by automatic controlled of fans and chillers. This paper presents a device that trigger an alarm for the user because of the possible damaged that could arise if the system is not stopped or if the user is not intervening. The system is helping us in monitoring the datacenter in which we have installed a Grid system and the network system of the National Institute for Research and Development of Isotopic and Molecular Technologies, which is an important datacenter in the Nord-West part of Transilvania.
WITH RESPECT TO WALSH – LIKE SYSTEMS AND THE DYADIC DERIVATIVE

In this paper we present some results on summability of oneand multi-dimensional Walsh-, Walsh-Kaczmarzand Vilenkin-Fourier series and on the dyadic and Vilenkin derivative. The Fejér and Cesàro summability methods are investigated. We will prove that the maximal operator of the summability means is bounded from the martingale Hardy space Hp to Lp (p > p0). For p = 1 we obtain a weak type inequality by interpolation, which ensures the a.e. convergence of the summability means. Similar results are formulated for the oneand multi-dimensional dyadic and Vilenkin derivative. The dyadic version of the classical theorem of Lebesgue is proved, more exactly, the dyadic derivative of the dyadic integral of a function f is a.e. f . This research was supported by the Hungarian Scientific Research Funds (OTKA) K67642. Mathematics Subject Classifications: Primary 42C10, 43A75; Secondary 60G42, 42B30.
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum

Identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-specific RNA-seq (ssRNA-seq) datasets collected under two experimental conditions to derive the genomic TU organization of Clostridium thermocellum using a machine-learning approach. Our method accurately predicted the genomic boundaries of individual TUs based on two sets of parameters measuring the RNA-seq expression patterns across the genome: expression-level continuity and variance. A total of 2590 distinct TUs are predicted based on the four RNA-seq datasets. Among the predicted TUs, 44% have multiple genes. We assessed our prediction method on an independent set of RNA-seq data with longer reads. The evaluation confirmed the high quality of the predicted TUs. Functional enrichment analyses on a selected subset of the predicted TUs revealed interesting biology. To demonstrate the generality of the prediction method, we have also applied the method to RNA-seq data collected on Escherichia coli and achieved high prediction accuracies. The TU prediction program named SeqTU is publicly available at https://code.google. com/p/seqtu/. We expect that the predicted TUs can serve as the baseline information for studying transcriptional and post-transcriptional regulation in C. thermocellum and other bacteria.
Calibration of quartz tuning fork spring constants for non-contact atomic force microscopy: direct mechanical measurements and simulations

Summary Quartz tuning forks are being increasingly employed as sensors in non-contact atomic force microscopy especially in the “qPlus” design. In this study a new and easily applicable setup has been used to determine the static spring constant at several positions along the prong of the tuning fork. The results show a significant deviation from values calculated with the beam formula. In order to understand this discrepancy the complete sensor set-up has been digitally rebuilt and analyzed by using finite element method simulations. These simulations provide a detailed view of the strain/stress distribution inside the tuning fork. The simulations show quantitative agreement with the beam formula if the beam origin is shifted to the position of zero stress onset inside the tuning fork base and torsional effects are also included. We further found significant discrepancies between experimental calibration values and predictions from the shifted beam formula, which are related to a large variance in tip misalignment during the tuning fork assembling process.
Blurring the boundaries between midwifery and obstetrics : an exploration of the role of midwife practitioner in a maternity unit in Wales

This thesis explores the newly established role of midwife practitioner (MP) and its impact on midwives and obstetricians in a maternity unit in Wales. MPs manage the care of women at high obstetric risk and carry out aspects of care, such as assessment, diagnosis and the development of management plans, which in the past were predominantly performed by obstetricians. This qualitative study employs a focused ethnographic approach and uses a purposive sample. Phase one consisted of seven focus groups, which were held between May and August 2004, with midwives (n=48) from maternity units in Mid and South Wales. In Phase two, participant observation was undertaken with MPs (n=3) over a two-week period encompassing eight 12-hour night shifts, during November and December 2004. For Phase three, semi-structured interviews were conducted with midwives (n=10), clients (n=10) and obstetricians (n=7), between July and December 2005. Phases two and three were carried out in a maternity unit in South Wales. The key findings of this study demonstrate that the lack of planning for the MP role inadvertently resulted in the creation of a distinct health care role, which encompasses positive aspects of both midwives' and obstetricians' work to provide safe and acceptable care for clients. The MPs in this study are committed to providing holistic care that takes into consideration the emotional and social needs of women and their families. In addition, these MPs are developing confidence and analytical skills, normally demonstrated by medical staff. However, further initiatives such as allowing MPs to prescribe, or to refer to other specialties, have not yet been adapted to support these new roles. It is too early to see the full impact of this role, but it is argued that it will have no significant effect on the work of the other midwives. MPs, however, do have the potential to impact upon the work of the obstetricians. This study contributes to the current body of knowledge concerning policy and practice for maternity care by examining a new role early in its genesis. This study makes a number of recommendations, including extending the number of MPs employed in Wales, the need for careful planning of future extensions to the midwives' role and further research into the safety and effectiveness of the MP role.