julilili42/papers huggingface dataset:
Functional neurological recovery after spinal cord injury is impaired in patients with infections
2012-10-23

Infections are a common threat to patients after spinal cord injury. Furthermore, infections might propagate neuronal death, and consequently contribute to the restriction of neurological recovery. We investigated the association of infections (i.e. pneumonia and/or postoperative wound infections) with functional neurological outcome after acute severe traumatic spinal cord injury. We screened data sets of 24 762 patients enrolled in a prospective cohort study (National Spinal Cord Injury Database, Birmingham, AL, USA). Patients were assessed according to the ASIA classification. ASIA impairment scale-classified A and B patients recruited within 24 h post-trauma (n = 1436) were selected as being a major recruitment population for interventional trials. Patients with documented pneumonia and/or postoperative wound infections (n = 581) were compared with control subjects (non-documented infections, n = 855). The functional neurological outcome parameters (i) upward ASIA impairment scale conversions; (ii) gain of ASIA motor scores; and (iii) gain of motor and sensory levels were consecutively analysed over time up to 1 year after spinal cord injury. The group with pneumonia and/or postoperative wound infections revealed less ASIA impairment scale upward conversions after 1 year than the control group (ASIA impairment scale A: 17.2 versus 23.9%, P = 0.03; ASIA impairment scale B: 57.1 versus 74.7%, P = 0.009). ASIA motor score gain [median (interquartile range)] was lower in patients with infections [ASIA impairment scale A: 8 (4-12) versus 10 (5-17), P = 0.01; ASIA impairment scale B: 19.5 (8-53.5) versus 42 (20.5-64), P = 0.03)]. Analysis of acquired motor/sensory levels supported these findings. In ASIA impairment scale A patients, the gain in motor levels (21.7 versus 33.3%, P = 0.04) and sensory levels (24.4 versus 38 of 102, 37.3%, P = 0.03) was significantly lower in the group with pneumonia and/or postoperative wound infections than in the control group. Multiple regression analysis identified pneumonia and/or postoperative wound infections as independent risk factors for impaired ASIA impairment scale upward conversion (odds ratio: 1.89, 95% confidence interval: 1.36-2.63, P < 0.0005) or lower gain in ASIA motor score (regression coefficient: -8.21, 95% confidence interval: -12.29 to -4.14, P < 0.0005). Infections associated with spinal cord injury, such as pneumonia and/or postoperative wound infections, qualify as independent risk factors for poor neurological outcome after motor complete spinal cord injury. Infections constitute a clinically relevant target for protecting the limited endogenous functional regeneration capacity. Upcoming interventional trials might gain in efficacy with improved patient stratification and might benefit from complementary protection of the intrinsic recovery potential after spinal cord injury.
Ion channels in genetic and acquired forms of epilepsy
2012-10-23

Abstract Genetic mutations causing dysfunction of both voltage‐ and ligand‐gated ion channels make a major contribution to the cause of many different types of familial epilepsy. Key mechanisms comprise defective Na + channels of inhibitory neurons, or GABA A receptors affecting pre‐ or postsynaptic GABAergic inhibition, or a dysfunction of different types of channels at axon initial segments. Many of these ion channel mutations have been modelled in mice, which has largely contributed to the understanding of where and how the ion channel defects lead to neuronal hyperexcitability. Animal models of febrile seizures or mesial temporal epilepsy have shown that dendritic K + channels, hyperpolarization‐activated cation channels and T‐type Ca 2+ channels play important roles in the generation of seizures. For the latter, it has been shown that suppression of their function by pharmacological mechanisms or in knock‐out mice can antagonize epileptogenesis. Defects of ion channel function are also associated with forms of acquired epilepsy. Autoantibodies directed against ion channels or associated proteins, such as K + channels, LGI1 or NMDA receptors, have been identified in epileptic disorders that can largely be included under the term limbic encephalitis which includes limbic seizures, status epilepticus and psychiatric symptoms. We conclude that ion channels and associated proteins are important players in different types of genetic and acquired epilepsies. Nevertheless, the molecular bases for most common forms of epilepsy are not yet clear, and evidence to be discussed indicates just how much more we need to understand about the complex mechanisms that underlie epileptogenesis.
Identification of HESS J1303−631 as a pulsar wind nebula throughγ-ray, X-ray, and radio observations
2012-10-23

The previously unidentified very high-energy (VHE; E &gt; 100 GeV) \\\\gamma-ray\\nsource HESS J1303-631, discovered in 2004, is re-examined including new data\\nfrom the H.E.S.S. Cherenkov telescope array. Archival data from the XMM-Newton\\nX-ray satellite and from the PMN radio survey are also examined. Detailed\\nmorphological and spectral studies of VHE \\\\gamma-ray emission as well as of the\\nXMM-Newton X-ray data are performed. Significant energy-dependent morphology of\\nthe \\\\gamma-ray source is detected with high-energy emission (E &gt; 10 TeV)\\npositionally coincident with the pulsar PSR J1301-6305 and lower energy\\nemission (E &lt;2 TeV) extending \\\\sim 0.4^{\\\\circ} to the South-East of the pulsar.\\nThe spectrum of the VHE source can be described with a power-law with an\\nexponential cut-off N_{0} = (5.6 \\\\pm 0.5) X 10^{-12} TeV^-1 cm^-2 s^-1, \\\\Gamma\\n= 1.5 \\\\pm 0.2) and E_{\\\\rm cut} = (7.7 \\\\pm 2.2) TeV. The PWN is also detected in\\nX-rays, extending \\\\sim 2-3' from the pulsar position towards the center of the\\n\\\\gamma-ray emission region. The spectral energy distribution (SED) is well\\ndescribed by a one zone leptonic scenario which, with its associated caveats,\\npredicts a very low average magnetic field for this source. Significant\\nenergy-dependent morphology of this source, as well as the identification of an\\nassociated X-ray PWN from XMM-Newton observations enable identification of the\\nVHE source as an evolved PWN associated to the pulsar PSR J1303-6305. However,\\nthe large discrepancy in emission region sizes and the low level of synchrotron\\nradiation suggest a multi-population leptonic nature. The low implied magnetic\\nfield suggests that the PWN has undergone significant expansion. This would\\nexplain the low level of synchrotron radiation and the difficulty in detecting\\ncounterparts at lower energies, the reason this source was originally\\nclassified as a "dark" VHE \\\\gamma-ray source.\\n
Modelling and predicting complex patterns of change using growth component models: An application to depression trajectories in cancer patients
2012-10-23

In this paper we present a general and flexible framework for constructively defining growth components to model complex change processes. Building on the concepts of the latent state-trait theory (LST theory; Steyer, Ferring, &amp; Schmitt, 1992), we develop structural equation models containing latent variables that represent latent growth (change) components of interest. We formulate these models based on an approach presented by Mayer, Steyer and Mueller (2012). We discuss an application to the longitudinal course of depression in 2,794 individuals from the Health and Retirement Study, who experienced cancer diagnosis over the course of the study. We found that (1) on average, the depression trajectories showed a steep increase after diagnosis as well as an adaptation phase where levels returned back to levels prior to diagnosis, and (2) individual differences in change were large and could be partly explained by marital status and cognitive functioning.
The PDZ-GEF protein Dizzy regulates the establishment of adherens junctions required for ventral furrow formation in Drosophila
2012-10-23

The PDZ-GEF protein Dizzy (Dzy) and its downstream GTPase Rap1 have pleiotropic roles during development of the Drosophila embryo. Here, we show that maternally provided Dzy and Rap1 first function during ventral furrow formation (VFF) where they are critical to guarantee rapid apical cell constrictions. Contraction of the apical actomyosin filament system occurs independently of Dzy and Rap1, but loss of Dzy results in a delayed establishment of the apical adherens junction (AJ) belt, whereas in the absence of Rap1 only a fragmentary apical AJ belt is formed in the epithelium. The timely establishment of apical AJs appears to be essential for coupling actomyosin contractions to cell shape change and to assure completion of the ventral furrow. Immediately after VFF, the downregulation of Dzy and Rap1 is necessary to allow normal mesodermal development to continue after the epithelial-to-mesenchymal transition, as overexpression of Dzy or of constitutively active Rap1 compromises mesodermal migration and monolayer formation. We propose that Dzy and Rap1 are crucial factors regulating the dynamics of AJs during gastrulation.
Mathematical Properties of the Deep Coalescence Cost
2012-10-24

In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has the minimal deep coalescence cost for reconciling a collection of gene trees is taken as an estimate of the species tree topology. The MDC method possesses the desirable Pareto property, and in practice it is quite accurate and computationally efficient. Here, in order to better understand the MDC method, we investigate some properties of the deep coalescence cost. We prove that the unit neighborhood of either a rooted species tree or a rooted gene tree under the deep coalescence cost is exactly the same as the tree's unit neighborhood under the rooted nearest-neighbor interchange (NNI) distance. Next, for a fixed species tree, we obtain the maximum deep coalescence cost across all gene trees as well as the number of gene trees that achieve the maximum cost. We also study corresponding problems for a fixed gene tree.
IL-4 Haplotype -590T, -34T and Intron-3 VNTR R2 Is Associated with Reduced Malaria Risk among Ancestral Indian Tribal Populations
2012-10-24

Our study suggests that the IL-4 polymorphisms regulate host susceptibility to malaria and disease progression. TTR2 haplotype, which gives protection against malaria, is high among ATPs. Since they inhabited in isolation and mainly practice hunter-gatherer lifestyles and exposed to various parasites, IL-4 TTR2 haplotype might be under positive selection.
Emergence of a Multidrug-ResistantHaemophilus influenzaeStrain Causing Chronic Pneumonia in a Patient with Common Variable Immunodeficiency
2012-10-24

We report the emergence of a multidrug-resistant Haemophilus influenzae strain in a patient with common variable immunodeficiency suffering from recurrent bronchopneumonia caused by H. influenzae. After the patient had received several antibiotic therapies, a strain was isolated showing resistance to ampicillin, ampicillin/sulbactam, cefazolin, cefuroxime, ciprofloxacin, and clarithromycin. Polymerase chain reaction analyses and sequencing revealed the presence of the beta-lactamase gene bla(TEM-1), two mutations (A502T and R517H) in the ftsI gene encoding the transpeptidase region of the penicillin-binding protein 3, and one mutation in the ribosomal protein gene L4 (G65D) conferring resistance to beta-lactams and macrolides, respectively. Additionally, the plasmid-encoded aac(6')-Ib-cr gene mediating slightly reduced susceptibility to quinolones and two mutations in the DNA gyrase gene gyrA and one mutation in the topoisomerase IV gene parC were identified leading to a high-level fluoroquinolone-resistant phenotype. In conclusion, the treatment of H. influenzae infections accompanied by high bacterial loads such as bronchopneumonia can be complicated by the selection of multidrug-resistant strains. Moreover, the emergence of aac(6')-Ib-cr in H. influenzae causing low fluoroquinolone resistance levels might have contributed to the selection of DNA gyrase and topoisomerase IV mutants.
The Frankencamera
2012-10-24

Although there has been much interest in computational photography within the research and photography communities, progress has been hampered by the lack of a portable, programmable camera with sufficient image quality and computing power. To address this problem, we have designed and implemented an open architecture and application programming interface (API) for such cameras: the Frankencamera. It consists of a base hardware specification, a software stack based on Linux, and an API for C++. Our architecture permits control and synchronization of the sensor and image processing pipeline at the microsecond timescale, as well as the ability to incorporate and synchronize external hardware like lenses and flashes. This paper specifies our architecture and API, and it describes two reference implementations we have built. Using these implementations, we demonstrate several computational photography applications: high dynamic range (HDR) viewfinding and capture, automated acquisition of extended dynamic range panoramas, foveal imaging, and inertial measurement unit (IMU)-based hand shake detection. Our goal is to standardize the architecture and distribute Frankencameras to researchers and students, as a step toward creating a community of photographer-programmers who develop algorithms, applications, and hardware for computational cameras.
Metabolomics approach for predicting response to neoadjuvant chemotherapy for breast cancer
2012-10-25

Breast cancer is a clinically heterogeneous disease, which necessitates a variety of treatments and leads to different outcomes. As an example, only some women will benefit from chemotherapy. Identifying patients who will respond to chemotherapy and thereby improve their long‐term survival has important implications to treatment protocols and outcomes, while identifying non responders may enable these patients to avail themselves of other investigational approaches or other potentially effective treatments. In this study, serum metabolite profiling was performed to identify potential biomarker candidates that can predict response to neoadjuvant chemotherapy for breast cancer. Metabolic profiles of serum from patients with complete (n = 8), partial (n = 14) and no response (n = 6) to chemotherapy were studied using a combination of nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography–mass spectrometry (LC–MS) and statistical analysis methods. The concentrations of four metabolites, three (threonine, isoleucine, glutamine) from NMR and one (linolenic acid) from LC–MS were significantly different when comparing response to chemotherapy. A prediction model developed by combining NMR and MS derived metabolites correctly identified 80% of the patients whose tumors did not show complete response to chemotherapy. These results show promise for larger studies that could result in more personalized treatment protocols for breast cancer patients.
Discovery of Depsides and Depsidones from Lichen as Potent Inhibitors of Microsomal Prostaglandin E2 Synthase‐1 Using Pharmacophore Models
2012-10-25

Nature in silico: Virtual screening using validated pharmacophore models identified lichen depsides and depsidones as potential inhibitors of mPGES-1, an emerging target for NSAIDs. Evaluation of the virtual hits in a cell-free assay revealed physodic acid and perlatolic acid as potent inhibitors of mPGES-1 (IC(50) = 0.4 and 0.43 μM, respectively), indicating that these natural products have potential as novel anti-inflammatory agents.
Serum and Cerebrospinal Fluid Levels of Transthyretin in Lewy Body Disorders with and without Dementia
2012-10-25

Parkinson’s disease (PD) without (non-demented, PDND) and with dementia (PDD), and dementia with Lewy bodies (DLB)&#13;\\nare subsumed under the umbrella term Lewy body disorders (LBD). The main component of the underlying pathologic&#13;\\nsubstrate, i.e. Lewy bodies and Lewy neurites, is misfolded alpha-synuclein (Asyn), and - in particular in demented LBD&#13;\\npatients - co-occurring misfolded amyloid-beta (Abeta). Lowered blood and cerebrospinal fluid (CSF) levels of transthyretin&#13;\\n(TTR) - a clearance protein mainly produced in the liver and, autonomously, in the choroid plexus - are associated with&#13;\\nAbeta accumulation in Alzheimer’s disease. In addition, a recent study suggests that TTR is involved in Asyn clearance. We&#13;\\nmeasured TTR protein levels in serum and cerebrospinal fluid of 131 LBD patients (77 PDND, 26 PDD, and 28 DLB) and 72&#13;\\ncontrols, and compared TTR levels with demographic and clinical data as well as neurodegenerative markers in the CSF. Five&#13;\\nsingle nucleotide polymorphisms of the TTR gene which are considered to influence the ability of the protein to carry its&#13;\\nligands were also analyzed. CSF TTR levels were significantly higher in LBD patients compared to controls. Post-hoc analysis&#13;\\ndemonstrated that this effect was driven by PDND patients. In addition, CSF TTR levels correlated negatively with CSF&#13;\\nAbeta1–42, total tau and phospho-tau levels. Serum TTR levels did not significantly differ among the studied groups. There&#13;\\nwere no relevant associations between TTR levels and genetic, demographic and clinical data, respectively. These results&#13;\\nsuggest an involvement of the clearance protein TTR in LBD pathophysiology, and should motivate to elucidate TTR-related&#13;\\nmechanisms in LBD in more detail.
Imaging of myocardial infarction using ultrasmall superparamagnetic iron oxide nanoparticles: a human study using a multi-parametric cardiovascular magnetic resonance imaging approach
2012-10-26

We could demonstrate in humans that USPIO-based contrast agents enable a more detailed characterization of myocardial infarct pathology mainly by detecting infiltrating macrophages. Considering the multi-functionality of USPIO-based particles and their superior safety profile compared with gadolinium-based compounds, these observations open up new vistas for the clinical application of USPIO.
Identification of two‐component system AfsQ1/Q2 regulon and its cross‐regulation with GlnR in Streptomyces coelicolor
2012-10-26

Summary The two‐component system AfsQ1/Q2 of S treptomyces coelicolor was identified in our previous work as a pleiotropic regulator for antibiotic biosynthesis and morphological differentiation under the condition of a minimal medium supplemented with 75 m M glutamate. In this work, we report the dissection of the mechanism underlying the function of AfsQ1/Q2 on antibiotic production and also the identification of the AfsQ1/Q2 regulon. The results showed that AfsQ1/Q2 stimulated antibiotic ACT , RED and CDA production directly through the pathway‐specific activator genes actII‐ORF4 , redZ and cdaR respectively. In addition, expression of sigQ that encodes a sigma factor and is divergently transcribed from afsQ1 was also subject to direct regulation by AfsQ1/Q2 . The precise AfsQ1 binding sites in the upstream regions of these target genes were determined by DN ase I footprinting assays coupled with site‐directed DNA mutagenesis. By computational prediction and functional analysis, at least 17 new AfsQ1 targets were identified, including pstS gene encoding a high‐affinity phosphate‐binding protein and two developmental genes whiD , bldM . For the AfsQ1/Q2 regulon, an AfsQ1 binding motif comprising the sequence GTnAC‐n 6 ‐GTnAC has been defined. Interestingly, we found from electrophoretic mobility shift assays and transcriptional analysis that AfsQ1/Q2 can also function as a repressor for nitrogen assimilation, and AfsQ1 can compete with GlnR for the promoter regions of glnA and nirB , suggesting the cross‐regulation between AfsQ1/Q2 and GlnR in nitrogen metabolism. These findings suggested that AfsQ1/Q2 is important not only for antibiotic biosynthesis but also in maintaining the metabolic homeostasis of nutrient utilization under the stress of high concentration of glutamate in S . coelicolor .
Generalized universality of higher transverse moments of quark transverse momentum dependent correlators
2012-10-26

The color gauge-invariant transverse momentum dependent (TMD) quark correlators contain process dependent gauge links in the bilocal matrix elements. In this paper, we split these process dependent correlators into universal TMD correlators, which in turn can be parametrized in universal TMD distribution functions. The process dependence is contained in gluonic pole factors, of which the value is determined by the gauge link. The operator structures of the universal TMD correlators are identified using transverse moments. In this paper, specific results for double transverse weighting of quark TMDs are given. In particular, we show that for a spin 1/2 target one has three universal time-reversal even leading "pretzelocity distributions," two of which involve double gluonic pole matrix elements and come with process dependent gluonic pole factors. We generalize the results for single and double weighting to TMD correlators of any specific rank, illustrating it for unpolarized, spin 1/2 and spin 1 targets.
Bilateral Theta-Burst TMS to Influence Global Gestalt Perception
2012-10-26

While early and higher visual areas along the ventral visual pathway in the inferotemporal cortex are critical for the recognition of individual objects, the neural representation of human perception of complex global visual scenes remains under debate. Stroke patients with a selective deficit in the perception of a complex global Gestalt with intact recognition of individual objects - a deficit termed simultanagnosia - greatly helped to study this question. Interestingly, simultanagnosia typically results from bilateral lesions of the temporo-parietal junction (TPJ). The present study aimed to verify the relevance of this area for human global Gestalt perception. We applied continuous theta-burst TMS either unilaterally (left or right) or bilateral simultaneously over TPJ. Healthy subjects were presented with hierarchically organized visual stimuli that allowed parametrical degrading of the object at the global level. Identification of the global Gestalt was significantly modulated only for the bilateral TPJ stimulation condition. Our results strengthen the view that global Gestalt perception in the human brain involves TPJ and is co-dependent on both hemispheres.
Codex Hermopolis
2012-10-26

Abstract Designation of a demotic manuscript (third century BCE ) written on the recto of apapyrus found at Hermupolis Magna (Ashmunein) in Upper Egypt in 1938, now in the Egyptian Museum at Cairo ( P.Cairo JE 89127–89130+ 89137–89143); on the verso is a mathematical text.
Pantelleria
2012-10-26

Abstract Pantelleria (Cossura) is a semiarid volcanic island in the “Street of Sicily” with the size of 82 km, 110 km west from Sicily and 70 km from Cape Bon, Tunisia. Due to its position in the narrowest space between Africa and Europe in the middle of the Mediterranean, Pantelleria became an ideal bridgehead and important military point of control. Intensive trade in obsidian from Pantelleria is attested since the third millennium BCE . The earliest settlement, located on a promontory in the west (Mursia), has an excellent preserved fortification wall and a large necropolis with massive, stone‐built tumuli for clan‐burials (sesi). It is documented for the seventeenth to the fourteenth centuries BCE .
Maeander
2012-10-26

Abstract The Maeander (Maiandros, from Hittite *Mai‐anda‐/du‐?; cf. Tischler 1977: 94) is the main river in southwest Asia Minor/Turkey, today's Büyük Menderes, and was first mentioned by Homer (II . 2.869).