julilili42/papers huggingface dataset:
A broadband spectral analysis of 4U 1702-429 using XMM-Newton and BeppoSAX data
2018-12-07

Context. Most of the X-ray binary systems containing neutron stars classified as Atoll sources show two different spectral states, referred to as soft and hard. Moreover, a large number of these systems show a reflection component relativistically smeared in their spectra, which provides information on the innermost region of the system. Aims. Our aim is to investigate the poorly studied broadband spectrum of the low-mass X-ray binary system 4U 1702-429, which was recently analysed combining XMM-Newton and INTEGRAL data. The peculiar value of the reflection fraction brought us to analyse further broadband spectra of 4U 1702-429. Methods. We re-analysed the spectrum of the XMM-Newton /INTEGRAL observation of 4U 1702-429 in the 0.3–60 keV energy range and we extracted three 0.1–100 keV spectra of the source analysing three observations collected with the Beppo SAX satellite. Results. We find that the XMM-Newton /INTEGRAL spectrum is well fitted using a model composed of a disc blackbody plus a Comptonised component and a smeared reflection component. We used the same spectral model for the Beppo SAX spectra, finding that the addition of a smeared reflection component is statistically significant. The best-fit values of the parameters are compatible to each other for the Beppo SAX spectra. We find that the reflection fraction is 0.05 −0.01 +0.3 for the XMM-Newton /INTEGRAL spectrum and between 0.15 and 0.4 for the Beppo SAX ones. Conclusions. The relative reflection fraction and the ionisation parameter are incompatible between the XMM-Newton /INTEGRAL and the Beppo SAX observations and the characteristics of the Comptonising corona suggest that the source was in a soft state in the former observation and in a hard state in the latter.
Between-speaker rhythmic variability is not dependent on language rhythm, as evidence from Persia reveals
2018-12-07

Acoustic measures of speech rhythm based on the durational characteristics of consonantal and vocalic intervals (henceforth C- or V-intervals) as well as syllabic intensity reveal between-speaker variability. The evidence obtained so far is based on speakers of stressed-timed languages, which are assumed to have complex consonant clusters and a higher degree of vowel reduction. Speakers of stressed-timed languages might operate their articulatory organs in different ways due to the syllable complexity and vowel reduction. Complex consonant clusters are released differently, and vowel reduction tends to be produced more or less strongly depending on speakers. When a language lacks such features, it is possible that rhythmic variation between its speakers decreases. In the present study, we aimed at exploring between- and within-speaker rhythmic variability in Persian, an Indo-European language categorised as syllable-timed. Acoustic correlates of speech rhythm (%V, ?V[ln], ?C[ln], n-PVI-V) and articulation rate were obtained from two Persian corpora with different sources of within-speaker variability. In the first corpus, the source of within-speaker variability mainly comes from non-contemporaneous recording sessions, and in the second corpus, from different speech rates. Results revealed that there were significant differences between speakers in all investigated speech rhythm measures in Persian and %V best discriminated between speakers. This reveals that the lack of typical stress-time features does not affect between-speaker variability in speech rhythm.
Improving social functioning in depressed mothers: results from a randomised controlled trial
2018-12-07

Clinical social work (CSW) may play an important role in the treatment of persons with depressive disorders. The aim of this study was to investigate the effects of a resource-oriented CSW intervention on social functioning in a population of mothers diagnosed with depression. In a randomised controlled trial (RCT), 61 mothers were assigned to a clinical social work intervention group (CSW; N = 30) or a treatment-as-usual group (TAU; N = 31). Assessment points were before and after the 10-session intervention. Global psychosocial functioning assessed with the Global Assessment of Functioning Scale of the Diagnostic and Statistical Manual (DSM) was the primary outcome variable. Other relevant variables included depressed mood, psychopathological symptoms, satisfaction with life and self-efficacy. Overall, 55 of the 61 participants completed the study; intention-to-treat analyses included data from 59 participants. All outcome measures revealed significant main effects with high effect sizes for the time of measurement. In addition, the results showed significantly stronger improvements in psychosocial functioning, psychopathological symptoms, and self-efficacy in the CSW group compared to the TAU group. Additional clinical social work was associated with larger improvements in global level of functioning and other psychologically relevant variables than treatment-as-usual.
Glycolipid composition of the heterocyst envelope of Anabaena sp. PCC 7120 is crucial for diazotrophic growth and relies on the UDP-galactose 4-epimerase HgdA
2018-12-07

The nitrogenase complex in the heterocysts of the filamentous freshwater cyanobacterium Anabaena sp. PCC 7120 fixes atmospheric nitrogen to allow diazotrophic growth. The heterocyst cell envelope protects the nitrogenase from oxygen and consists of a polysaccharide and a glycolipid layer that are formed by a complex process involving the recruitment of different proteins. Here we studied the function of the putative nucleoside-diphosphate-sugar epimerase HgdA, which along with HgdB and HgdC is essential for deposition of the glycolipid layer and growth without a combined nitrogen source. Using site-directed mutagenesis and single homologous recombination approach, we performed a thoroughly functional characterization of HgdA and confirmed that the glycolipid layer of the hgdA mutant heterocyst is aberrant as shown by transmission electron microscopy and chemical analysis. The hgdA gene was expressed during late stages of the heterocyst differentiation. GFP-tagged HgdA protein localized inside the heterocysts. The purified HgdA protein had UDP-galactose 4-epimerase activity in vitro. This enzyme could be responsible for synthesis of heterocyst-specific glycolipid precursors, which could be transported over the cell wall by the ABC transporter components HgdB/HgdC.
Organ-on-a-chip technologies that can transform ophthalmic drug discovery and disease modeling
2018-12-08

Disorders of the eye that lead to visual impairment are affecting millions of people worldwide. Nevertheless, for many of these disorders, there are still no effective treatment options available due to the lack of in vitro model systems that emulate the physiological in vivo structure and function of human eyes. Microphysiological organ-on-a-chip (OoC) technology represents a novel and powerful approach to overcome the limitations of conventional model systems and lead to a paradigm shift in ophthalmic research. Areas covered: This review provides an overview of the various tissues of interest in ophthalmology and summarizes existing model systems, including their applications and limitations. Additionally, novel OoC systems with applications in ophthalmology are described and the advantages of these systems compared to conventional models are highlighted. Expert opinion: The physiological relevance of the first ophthalmic OoC systems that mimic human ocular compartments, such as the cornea and retina, has been successfully demonstrated in recent years. There is a great potential for the application of these platforms for future pharmacological target identification, safety, and efficacy testing, as well as personalized medicine. Further improvements and the development of new systems are of upmost importance, especially to model complex disorders affecting several tissues.
Comparison of speed versus complexity effects on the hemodynamic response of the trail making test in block designs
2018-12-08

The use of functional near-infrared spectroscopy (fNIRS) in block designs provides measures of cortical activity in ecologically valid environments. However, in some cases, the use of block designs may be problematic when data are not corrected for performance in a time-restricted block. We sought to investigate the effects of task complexity and processing speed on hemodynamic responses in an fNIRS block design. To differentiate the effects of task complexity and processing speed, 20 subjects completed the trail making test (TMT) in two versions (TMT-A versus TMT-B) and three different speed levels (slow versus moderate versus fast). During TMT-A, subjects are asked to connect encircled numbers in numerically ascending order (1-2-3...). In the more complex TMT-B, subjects are instructed to connect encircled numbers and letters in alternating ascending order (1-A-2-B...). To illustrate the obscuring effects of processing speed on task complexity, we perform two different analyses. First, we analyze the classical measures of oxygenated blood, and second, we analyze the measures corrected for the number of processed items. Our results show large effects for processing speed within the bilateral inferior frontal gyrus, left dorsolateral prefrontal cortex, and superior parietal lobule (SPL). The TMT contrast did not show significant effects with classical measures, although trends are observed for higher activation during TMT-B. When corrected for processed items, higher activity for TMT-B in comparison to TMT-A is found within the SPL. The results are discussed in light of recent research designs, and simple to use correction methods are suggested.
Asynchronous non-invasive high-speed BCI speller with robust non-control state detection
2018-12-08

Brain-Computer Interfaces (BCIs) enable users to control a computer by using pure brain activity. Recent BCIs based on visual evoked potentials (VEPs) have shown to be suitable for high-speed communication. However, all recent high-speed BCIs are synchronous, which means that the system works with fixed time slots so that the user is not able to select a command at his own convenience, which poses a problem in real-world applications. In this paper, we present the first asynchronous high-speed BCI with robust distinction between intentional control (IC) and non-control (NC), with a nearly perfect NC state detection of only 0.075 erroneous classifications per minute. The resulting asynchronous speller achieved an average information transfer rate (ITR) of 122.7 bit/min using a 32 target matrix-keyboard. Since the method is based on random stimulation patterns it allows to use an arbitrary number of targets for any application purpose, which was shown by using an 55 target German QWERTZ-keyboard layout which allowed the participants to write an average of 16.1 (up to 30.7) correct case-sensitive letters per minute. As the presented system is the first asynchronous high-speed BCI speller with a robust non-control state detection, it is an important step for moving BCI applications out of the lab and into real-life.
High Expression of Somatostatin Receptors 2A, 3, and 5 in Corticotroph Pituitary Adenoma
2018-12-09

The development of somatostatin analogs for the treatment of pituitary Cushing’s disease has been based on somatostatin receptor expression analyses of small cohorts of pituitary adenomas. Additionally, the classification of pituitary adenomas has recently changed. To enable progress with this treatment option, we assessed somatostatin receptors in a large cohort of corticotroph and other pituitary adenomas according to the new WHO classification of endocrine tumors. Paraffin-embedded tumor samples of 88 corticotroph pituitary adenomas and 30 nonadenomatous pituitary biopsies were analyzed after processing into tissue microarrays and immunohistochemical staining for SSTR 1, SSTR2A, SSTR3, SSTR4, and SSTR5. For comparison, 159 other noncorticotroph pituitary adenomas were analyzed. SSTR3 expression was higher in corticotroph adenomas compared to PIT-1-positive, gonadotroph, and nonfunctioning pituitary adenomas (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mi>p</mml:mi><mml:mo>&lt;</mml:mo><mml:mn>0.0001</mml:mn></mml:math>, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.0280</mml:mn></mml:math>, and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M3"><mml:mi>p</mml:mi><mml:mo>&lt;</mml:mo><mml:mn>0.0001</mml:mn></mml:math>, respectively). This was also the case for the expression of SSTR5 (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M4"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.0003</mml:mn></mml:math>, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M5"><mml:mi>p</mml:mi><mml:mo>&lt;</mml:mo><mml:mn>0.0001</mml:mn></mml:math>, and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M6"><mml:mi>p</mml:mi><mml:mo>&lt;</mml:mo><mml:mn>0.0001</mml:mn></mml:math>, respectively). SSTR2A expression was higher compared to gonadotroph and nonfunctioning pituitary adenomas (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M7"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.0217</mml:mn></mml:math> and 0.0126, respectively) while PIT-1-positive adenomas showed even higher SSTR2A expression (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M8"><mml:mi>p</mml:mi><mml:mo>&lt;</mml:mo><mml:mn>0.0001</mml:mn></mml:math>). SSTR2A and SSTR5 were both expressed higher in nonadenomatous pituitary biopsies than in pituitary adenomas (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M9"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.0126</mml:mn></mml:math> and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M10"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.0008</mml:mn></mml:math>, respectively). There are marked expression differences of SSTR1-5 as well as changes in expression in recurrent disease that need to be addressed when looking for other possible substances for the treatment of Cushing’s disease. SSTR2A, SSTR3, and SSTR5 seem to be most suitable biomarkers for a targeted therapy with somatostatin analogs.
Ethics codes and use of new and innovative drugs
2018-12-10

Treatment with new and/or innovative drugs with uncertain safety and efficacy profile is associated with substantial ethical concerns. The main objective of this paper is to present guidance on the use of such drugs contained in: (i) major international codes and guidelines pertaining to medical ethics and biomedical research; (ii) national codes of medical ethics and professional conduct of the USA, Canada, Australia, New Zealand, the UK, Ireland, France and Germany. Out of the four international codes and guidelines analysed, only the Declaration of Helsinki addresses the question of the use of unproven drugs. Among national codes, only two (USA and New Zealand) explicitly allow for use of new or innovative drugs. Moreover, treatment with unproven drugs seems to be permissible under the French code, though this is not stated explicitly. The remaining codes do not contain any articles on the use of new and innovative drugs. An update of existing articles, as well as the addition of new guidelines to the codes, should be considered in view of the rapid pace of development and introduction to clinical practice of new drugs. This work is relevant to innovative off‐label applications of approved drugs and expanded access to investigational drugs.
Timing of the advertisement call of the common tink frog (Diasporus diastema) shifts with the acoustic behaviour of local conspecifics
2018-12-10

We investigated the temporal dynamics of acoustically interacting common tink frogs (Diasporus diastema), a species in which advertising males maintain large inter-individual distances that may influence call timing behaviours among nearest neighbours. This species produces advertisement calls in temporally structured bouts, with decreasing inter-note intervals that culminate in a 'burst' sequence of rapidly emitted notes. We broadcast playbacks of unaltered and temporally manipulated conspecific advertisement calls to focal male individuals vocalizing within triads (comprised of closely neighbouring focal and non-focal males and a more distant, outsider male). Focal males demonstrated rhythmic entrainment and adjusted their calling behaviour to overlap their call sequences with those of their nearest vocalizing neighbour, including the unaltered conspecific playback. When presented with a playback of conspecific calls lacking the natural temporal sequence, focal males reduced the duration of the silent interval between call bouts and reduced the number of notes in the burst phase of their call bout, indicating the significance of the multi-element temporally complex call bout structure in mediating male–male vocal interactions.
Iron minerals inhibit the growth of bacteria via a free-radical mechanism: Implications for soil carbon storage
2018-12-10

Abstract. Natural minerals in soil can inhibit the growth of bacteria that protect organic carbon from decay. However, the mechanism inhibiting the bacterial growth remains poorly understood. Here, using a series of cultivation experiments and biological, chemical and synchrotron-based spectral analyses, we showed that kaolinite, hematite, goethite and ferrihydrite had a significant inhibitory effect on the growth of Pseudomonas J12, which was more prominent with a concentration of 25 mg mL−1 than it was with either 10 mg mL−1 or 5 mg mL−1. In contrast, montmorillonite promoted the growth of Pseudomonas J12. Compared to Al-containing minerals, Fe(III)-containing minerals produced more hydroxyl radical (HO•) that have high efficiency for the inhibition of bacteria. Moreover, a significant positive correlation between HO• radical and Fe(II) was found, suggesting that Fe(II) contributes to the generation of HO•. Furthermore, both micro X-ray fluorescence and X-ray photoelectron spectroscopies indicated that surface Fe(III) was reduced to Fe(II) which can produce HO• through the well-known Fenton reaction series. Together, these findings indicate that the reduced surface Fe(II) derived from Fe(III)-containing minerals inhibit bacteria via a free-radical mechanism, which may further contribute to soil carbon storage.
Report on 1810.12967v1
2018-12-10

We present the most recent solar neutrino results from the Borexino experiment at the Gran Sasso underground laboratory.In particular, refined measurements of all neutrinos produced in the pp fusion chain have been made.It is the first time that the same detector measures the entire range of solar neutrinos at once.These new data weakly favor a high-metallicity Sun.Prospects for measuring CNO solar neutrinos are also discussed.Contents 1 Introduction: solar neutrinos and Borexino 3 2 Brief summary of Borexino results 4 3 Latest results from Borexino 5 4 Outlook: measuring CNO neutrinos 7 5 Conclusion 8
Report on 1807.02697v3
2018-12-10

We present a functional renormalization group (fRG) study of the two dimensional Hubbard model, performed with an algorithmic implementation which lifts some of the common approximations made in fRG calculations.In particular, in our fRG flow; (i) we take explicitly into account the momentum and the frequency dependence of the vertex functions; (ii) we include the feedback effect of the self-energy; (iii) we implement the recently introduced multiloop extension which allows us to sum up all the diagrams of the parquet approximation with their exact weight.Due to its iterative structure based on successive one-loop computations, the loop convergence of the fRG results can be obtained with an affordable numerical effort.In particular, focusing on the analysis of the physical response functions, we show that the results become independent from the chosen cutoff scheme and from the way the fRG susceptibilities are computed, i.e., either through flowing couplings to external fields, or through a "post-processing" contraction of the interaction vertex at the end of the flow.The presented substantial refinement of fRG-based computation schemes paves a promising route towards future quantitative fRG analyses of more challenging systems and/or parameter regimes.
CCND2 and CCND3 hijack immunoglobulin light-chain enhancers in cyclin D1− mantle cell lymphoma
2018-12-11

Abstract Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) translocation resulting in overexpression of cyclin D1. However, a small subset of cyclin D1− MCL has been recognized, and approximately one-half of them harbor CCND2 translocations while the primary event in cyclin D1−/D2− MCL remains elusive. To identify other potential mechanisms driving MCL pathogenesis, we investigated 56 cyclin D1−/SOX11+ MCL by fluorescence in situ hybridization (FISH), whole-genome/exome sequencing, and gene-expression and copy-number arrays. FISH with break-apart probes identified CCND2 rearrangements in 39 cases (70%) but not CCND3 rearrangements. We analyzed 3 of these negative cases by whole-genome/exome sequencing and identified IGK (n = 2) and IGL (n = 1) enhancer hijackings near CCND3 that were associated with cyclin D3 overexpression. By specific FISH probes, including the IGK enhancer region, we detected 10 additional cryptic IGK juxtapositions to CCND3 (6 cases) and CCND2 (4 cases) in MCL that overexpressed, respectively, these cyclins. A minor subset of 4 cyclin D1− MCL cases lacked cyclin D rearrangements and showed upregulation of CCNE1 and CCNE2. These cases had blastoid morphology, high genomic complexity, and CDKN2A and RB1 deletions. Both genomic and gene-expression profiles of cyclin D1− MCL cases were indistinguishable from cyclin D1+ MCL. In conclusion, virtually all cyclin D1− MCLs carry CCND2/CCND3 rearrangements with immunoglobulin genes, including a novel IGK/L enhancer hijacking mechanism. A subset of cyclin D1−/D2−/D3− MCL with aggressive features has cyclin E dysregulation. Specific FISH probes may allow the molecular identification and diagnosis of cyclin D1− MCL.
The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy
2018-12-11

Abstract Antileukemia immunity plays an important role in disease control and maintenance of tyrosine kinase inhibitor (TKI)-free remission in chronic myeloid leukemia (CML). Thus, antigen-specific immunotherapy holds promise for strengthening immune control in CML but requires the identification of CML-associated targets. In this study, we used a mass spectrometry–based approach to identify naturally presented HLA class I– and class II–restricted peptides in primary CML samples. Comparative HLA ligandome profiling using a comprehensive dataset of different hematological benign specimens and samples from CML patients in deep molecular remission delineated a panel of novel frequently presented CML-exclusive peptides. These nonmutated target antigens are of particular relevance because our extensive data-mining approach suggests the absence of naturally presented BCR-ABL– and ABL-BCR–derived HLA-restricted peptides and the lack of frequent tumor-exclusive presentation of known cancer/testis and leukemia-associated antigens. Functional characterization revealed spontaneous T-cell responses against the newly identified CML-associated peptides in CML patient samples and their ability to induce multifunctional and cytotoxic antigen-specific T cells de novo in samples from healthy volunteers and CML patients. Thus, these antigens are prime candidates for T-cell–based immunotherapeutic approaches that may prolong TKI-free survival and even mediate cure of CML patients.