julilili42/papers huggingface dataset:
Two cases of cyclic neutropenia with acquired CSF3R mutations, with 1 developing AML
2016-03-31

2][3] Due to overlaps in their genetic profiles, CyN can be distinguished from CN by cycling neutrophil counts, usually at 21-day intervals, in the former.In contrast to CN, CyN is also characterized by cycling of platelets, monocytes, and reticulocytes. 4,5Infectious episodes are usually less severe in patients with CyN vs CN.[8][9][10][11] This report describes a 17-year-old female with CyN who developed AML (French-American-British classification M2).She was first diagnosed with severe neutropenia at age 4 weeks while experiencing Pseudomonas septicemia; at that time, serial blood counts were not collected.Treatment with granulocyte colony-stimulating factor (G-CSF), at a dose of 5.7 mg/kg per day, was initiated at age 2 years.The amount of G-CSF administered was not adjusted for increasing body weight, resulting in a dose of 1.7 mg/kg per day at age 13 years.After a liver abscess at age 14 years, she was referred to our center.She presented with large variations in absolute neutrophil count (ANC), suggesting a cyclic pattern of ANC.Because her median ANC was deemed insufficient, her G-CSF dose was increased to 7.5 mg/kg per day.This relatively high dosage is still in the range of G-CSF dosages required for CyN patients (0.5-10.5 mg/kg per day); however, it is higher than the median dose (2.6 mg/kg per day) in CyN patients within our European branch of the Severe Chronic Neutropenia International Registry (SCNIR) and might be associated with the risk of malignant development.Sequential neutrophil counts, determined at least 3 times per week for 6 weeks, over 2 time periods 4 months apart, confirmed a diagnosis of CyN (Figure 1A-B).Cycling platelet counts have been reported previously in patients with CyN, but not CN. 4,5No cytogenetic aberrations were detected prior to a diagnosis of AML.BM at the time of AML showed 33% blasts, monosomy 7, and trisomy 21.The patient recently received a BM transplant from an HLA-matched unrelated donor and was released from the hospital after successful engraftment.Interestingly, this CyN-AML patient was found to harbor 2 ELANE mutations, p.Ala233Pro and p.Val235TrpfsX (NP_001963.1),both located on 1 allele (Figure 1C).The ELANE fragment spanning c.697G,C and c.703delG was cloned from genomic DNA isolated from this patient's peripheral blood MNCs.Sequencing of 20 individual bacterial clones showed that all clones carried both ELANE mutations (Figure 1C).Sequencing of DNA isolated from peripheral blood MNCs of both parents revealed no ELANE mutations (Figure 1C).Moreover, neither parent has shown signs of neutropenia
Can Nanofluidic Chemical Release Enable Fast, High Resolution Neurotransmitter-Based Neurostimulation?
2016-03-31

Artificial chemical stimulation could provide improvements over electrical neurostimulation. Physiological neurotransmission between neurons relies on the nanoscale release and propagation of specific chemical signals to spatially-localized receptors. Current knowledge of nanoscale fluid dynamics and nanofluidic technology allows us to envision artificial mechanisms to achieve fast, high resolution neurotransmitter release. Substantial technological development is required to reach this goal. Nanofluidic technology-rather than microfluidic-will be necessary; this should come as no surprise given the nanofluidic nature of neurotransmission. This perspective reviews the state of the art of high resolution electrical neuroprostheses and their anticipated limitations. Chemical release rates from nanopores are compared to rates achieved at synapses and with iontophoresis. A review of microfluidic technology justifies the analysis that microfluidic control of chemical release would be insufficient. Novel nanofluidic mechanisms are discussed, and we propose that hydrophobic gating may allow control of chemical release suitable for mimicking neurotransmission. The limited understanding of hydrophobic gating in artificial nanopores and the challenges of fabrication and large-scale integration of nanofluidic components are emphasized. Development of suitable nanofluidic technology will require dedicated, long-term efforts over many years.
Side Effects of Motivational Interventions? Effects of an Intervention in Math Classrooms on Motivation in Verbal Domains
2016-04-01

One way to address the leaking pipeline toward STEM-related careers (i.e., science, technology, engineering, and mathematics) is to intervene on students’ STEM motivation in school. However, a neglected question in intervention research is how such interventions affect motivation in subjects not targeted by the intervention. This question was addressed through data from a cluster-randomized study in which a value intervention was successfully implemented in 82 ninth-grade math classrooms. Side effects on value, self-concept, and effort in German as students’ native language and English as a foreign language were assessed 6 weeks and 5 months after the intervention. Negative effects on value for German, but not for English, were found 5 months after the intervention. The theoretical and educational implications of such effects are discussed.
Stream solute tracer timescales changing with discharge and reach length confound process interpretation
2016-04-01

Abstract Improved understanding of stream solute transport requires meaningful comparison of processes across a wide range of discharge conditions and spatial scales. At reach scales where solute tracer tests are commonly used to assess transport behavior, such comparison is still confounded due to the challenge of separating dispersive and transient storage processes from the influence of the advective timescale that varies with discharge and reach length. To better resolve interpretation of these processes from field‐based tracer observations, we conducted recurrent conservative solute tracer tests along a 1 km study reach during a storm discharge period and further discretized the study reach into six segments of similar length but different channel morphologies. The resulting suite of data, spanning an order of magnitude in advective timescales, enabled us to (1) characterize relationships between tracer response and discharge in individual segments and (2) determine how combining the segments into longer reaches influences interpretation of dispersion and transient storage from tracer tests. We found that the advective timescale was the primary control on the shape of the observed tracer response. Most segments responded similarly to discharge, implying that the influence of morphologic heterogeneity was muted relative to advection. Comparison of tracer data across combined segments demonstrated that increased advective timescales could be misinterpreted as a change in dispersion or transient storage. Taken together, our results stress the importance of characterizing the influence of changing advective timescales on solute tracer responses before such reach‐scale observations can be used to infer solute transport at larger network scales.
Antimicrobial efficiency of mouthrinses versus and in combination with different photodynamic therapies on periodontal pathogens in an experimental study
2016-04-01

Background and Objective In the therapy of destructive periodontal disease, chemical antimicrobial agents and increasingly photodynamic therapy ( PDT ) play an important adjunctive role to standard mechanical anti‐infective treatment procedures. However, both antiseptic methods have their shortcomings in terms of eliminating periodontal pathogens. The aim of the study was to compare the antibacterial efficacy of different antiseptic mouthrinses, of a conventional and a new, modified PDT plus as well as of the different antiseptic mouthrinses combined with either the conventional or the modified PDT plus against periopathogens. Material and Methods Six representative periodontitis‐associated bacterial strains were grown for 24 h under anaerobic conditions. After mixing the individual cell pellets they were exposed to 10 different antiseptic mouthrinse formulations: chlorhexidine (0.2%, 0.06%, CHX ); CHX + cetylpyridinium chloride (each 0.05%); sodium hypochlorite (0.05%); polyhexanide (0.04%, PHMB 1; 0.1%, PHMB 2); octenidine dihydrochloride (0.1%); fluoride (250 ppm); essential oils; povidone iodine (10%); and saline (0.9%, NaCl) as control. Furthermore, the bacteria were treated with conventional PDT based on light‐emitting diodes and a new modified photodisinfection combining photosensitizer with hydrogen peroxide to PDT plus also based on light‐emitting diodes. In addition to the single treatments, a combined application of antiseptic exposure followed by use of PDT or PDT plus was performed. The microbial viability was characterized by analyzing colony growth and fluorescence‐based vitality proportions. Results Nearly all mouthrinses caused a statistically significant growth inhibition. The most effective antiseptics, CHX (0.2%), CHX /cetylpyridinium chloride and octenidine dihydrochloride, inhibited bacterial growth completely. Conventional PDT resulted in moderate reduction of colony growth. The modified PDT plus achieved maximum antimicrobial effect. The combination of antiseptic exposure and PDT against periopathogens predominantly increased antibacterial efficacy compared to the single applications. The mouthrinse containing essential oil seemed to interfere with PDT . Conclusion A combination therapy of preceding chemotherapeutical exposure and subsequent photodisinfection may be a more effective and promising antibacterial treatment than single applications of the antiseptic methods. The modified PDT plus using oxygen‐enriched toluidine showed a superior antibacterial effect on periodontal pathogens to conventional PDT and to the majority of the investigated mouthrinses.
Weekend versus weekday transplant surgery and outcomes after kidney transplantation in the USA: a retrospective national database analysis
2016-04-01

Objective To determine whether kidney transplants performed during a weekend had worse outcomes than those performed during weekdays. Design Retrospective national database study. Setting United Network for Organ Sharing database of the USA. Participants 136 715 adult recipients of deceased donor single organ kidney transplants in the USA between 4/1994 and 9/2010. Main outcome measures The primary outcomes were patient survival and death-censored and overall allograft survival. Secondary outcomes included initial length of hospital stay after transplantation, delayed allograft function, acute rejection within the first year of transplant, and patient and allograft survival at 1 month and at 1 year after transplantation. Cox proportional hazards models were used to evaluate the impact of weekend kidney transplant surgery on primary and secondary outcomes, adjusting for multiple covariates. Results Among the 136 715 kidney recipients, 72.5% underwent transplantation during a regular weekday (Monday–Friday) and 27.5% during a weekend (Saturday–Sunday). No significant association was noted between weekend transplant status and patient survival, death-censored allograft survival or overall allograft survival in the adjusted analyses (HR 1.01 (95% CI 0.92 to 1.04), 1.012 (95% CI 0.99 to 1.034), 1.012 (95% CI 0.984 to 1.04), respectively). In addition, no significant association was noted between weekend transplant status and the secondary outcomes of patient and graft survival at 1 month and 1 year, delayed allograft function or acute rejection within the first year. Results remained consistent across all definitions of weekend status. Conclusions The outcomes for deceased donor kidney transplantation in the USA are not affected by the day of surgery. The operationalisation of deceased donor kidney transplantation may provide a model for other surgeries or emergency procedures that occur over the weekend, and may help reduce length of hospital stay and improve outcomes.
Degassing of hydrous trachytic Campi Flegrei and phonolitic Vesuvius melts: Experimental limitations and chances to study homogeneous bubble nucleation
2016-04-01

Melt degassing by bubble nucleation and growth is a driving mechanism of magma ascent. Therefore, decompression experiments with hydrous silicate melts were used to investigate the onset and the dynamics of H2O degassing. Nominally H2O undersaturated trachytic Campi Flegrei and phonolitic Vesuvius melts representative for the magma compositions of the Campi Flegrei volcanic system were decompressed at a super-liquidus temperature of 1050 °C from 200 MPa to final pressures (Pfinal) of 100, 75, and 60 MPa using continuous decompression rates of 0.024 and 0.17 MPa/s. Experiments started from either massive glass cylinders or glass powder to demonstrate the infl of the starting material on melt degassing. Glass powder can be used to shorten the equilibration time (teq) prior to decompression for dissolution of H2O in the melt. The decompressed samples were quenched and compared in terms of bubble number density (NV), porosity, and residual H2O content in the melt.
Extensive Mobilome-Driven Genome Diversification in Mouse Gut-AssociatedBacteroides vulgatusmpk
2016-04-01

Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota.
Multi-scale analysis of porosity in diagenetically altered reservoir sandstone from the Permian Rotliegend (Germany)
2016-04-01

Abstract We present a multi-scale 3D analysis of the pore network in a Rotliegend reservoir sandstone, both at the scale of the sand grains and the scale of the diagenetic clay cements that grow in the intragranular volume (IGV). For this we combine optical microscopy, micro-CT, Broad Ion Beam polishing, Scanning Electron Microscopy, Woods Metal Porosimetry and Focussed Ion Beam–SEM tomography. In cm-scale layers the samples show differences in IGV and sand fabric. In the layers where IGV is higher, there is less diagenetic cement and the IGV forms a connected network; in the layers where the sand fabric is more compacted, larger pores are connected via the pore network in the diagenetic clay cements with pore throat size down to 20 nm in diameter. We show that the pore network in all types of diagenetic clay is connected and conclude that the total gas volume that can be produced from such a reservoir sandstone includes the pore volume in the diagenetic clay cements. We predict a major change in transport properties when the diagenetic clay fill renders the IGV disconnected.
High Plasma Levels of Gremlin‐1 and Macrophage Migration Inhibitory Factor, but Not Their Ratio, Indicate an Increased Risk for Acute Coronary Syndrome in Patients With Type 2 Diabetes Mellitus
2016-04-01

Abstract Background Chronic inflammation promotes atherosclerosis and is a prognostic factor in coronary artery disease ( CAD ). Patients with type 2 diabetes mellitus ( DM2 ) are at risk for progressive atherosclerosis. Macrophage migration inhibitory factor ( MIF ) is a key player in atherosclerosis, mediating pro‐inflammatory responses. Its endogenous antagonist Gremlin‐1 inhibits foam‐cell formation and atheroprogression by binding MIF , neutralizing its proatherosclerotic functions. Hypothesis Plasma levels of MIF and Gremlin‐1 correlate with the stability of CAD in patients with DM2 . Method We assessed plasma levels of Gremlin‐1 and MIF in 198 nondiabetic and 88 diabetic patients with symptomatic CAD using enzyme‐linked immunosorbent assays. Results Plasma levels of Gremlin‐1 were higher DM2 patients (278.8 ± 16.6 vs 224.7 ± 6.7 ng/ mL ; P = 0.001). MIF levels were elevated but not significantly increased in DM2 ( P = 0.098). Interestingly, we found that Gremlin‐1 plasma levels were significantly higher in diabetic patients with stable angina pectoris ( SAP ; n = 53) or acute coronary syndrome ( ACS ; n = 35) compared with nondiabetic patients with SAP ( P = 0.008 and P = 0.011, respectively). MIF levels were significantly higher in diabetic patients with ACS compared with SAP ( P &lt; 0.001). Although the single plasma parameters showed an association with DM2 and CAD status, we could not confirm that the Gremlin‐1/ MIF ratio is significantly different in patients stratified by DM2 and CAD ( P = 0.072). Hence, Gremlin‐1/ MIF ratio was significantly lower in patients with ACS compared with SAP (1.1 ± 0.1 vs 4.4 ± 1.1; P = 0.003). Conclusions Diabetic patients with ACS show increased levels of Gremlin‐1 and MIF , leading to unfavorable Gremlin‐1/ MIF ratios. However, DM2 alone is not associated with low Gremlin‐1/ MIF ratios.
INHIBITION OF FATTY ACID DESATURASES IN Drosophila melanogaster LARVAE BLOCKS FEEDING AND DEVELOPMENTAL PROGRESSION
2016-04-01

Fatty acid desaturases are metabolic setscrews. To study their systemic impact on growth in Drosophila melanogaster , we inhibited fatty acid desaturases using the inhibitor CAY10566. As expected, the amount of desaturated lipids is reduced in larvae fed with CAY10566. These animals cease feeding soon after hatching, and their growth is strongly attenuated. A starvation program is not launched, but the expression of distinct metabolic genes is activated, possibly to mobilize storage material. Without attaining the normal size, inhibitor‐fed larvae molt to the next stage indicating that the steroid hormone ecdysone triggers molting correctly. Nevertheless, after molting, expression of ecdysone‐dependent regulators is not induced. While control larvae molt a second time, these larvae fail to do so and die after few days of straying. These effects are similar to those observed in experiments using larvae deficient for the fatty acid desaturase1 gene. Based on these data, we propose that the ratio of saturated to unsaturated fatty acids adjusts a sensor system that directs feeding behavior. We also hypothesize that loss of fatty acid desaturase activity leads to a block of the genetic program of development progression indirectly by switching on a metabolic compensation program.
3D motion flow estimation using local all-pass filters
2016-04-01

Fast and accurate motion estimation is an important tool in biomedical imaging applications such as motion compensation and image registration. In this paper, we present a novel algorithm to estimate motion in volumetric images based on the recently developed Local All-Pass (LAP) optical flow framework. The framework is built upon the idea that any motion can be regarded as a local rigid displacement and is hence equivalent to all-pass filtering. Accordingly, our algorithm aims to relate two images, on a local level, using a 3D all-pass filter and then extract the local motion flow from the filter. As this process is based on filtering, it can be efficiently repeated over the whole image volume allowing fast estimation of a dense 3D motion. We demonstrate the effectiveness of this algorithm on both synthetic motion flows and in-vivo MRI data involving respiratory motion. In particular, the algorithm obtains greater accuracy for significantly reduced computation time when compared to competing approaches.
Annotated type catalogue of the continental fossil gastropods in the Staatliches Museum für Naturkunde Stuttgart, Germany
2016-04-01

The type specimens of fossil land and freshwater gastropods deposited in the Staatliches Museum für Naturkunde Stuttgart (SMNS), Germany, are listed and illustrated herein, comprising circa 180 nominal species-group taxa from Cenozoic fossil sites, mainly in the Baden-Württemberg and Bayern states in southern Germany. The list is arranged in alphabetical order of the specific epithets, with information on the original description, taxonomical status, type locality, record number in the collection and comments. A systematically arranged list of the taxa is also given, as well as a list arranged by authorship of the species-group names. At least one type specimen (holotype, lectotype, syntype or neotype) of each nominal species/subspecies is figured here, and further specimens were figured when they added information. In some cases lectotypes are designated herein.
Advanced communication modes for the publish/subscribe C-DAX middleware
2016-04-01

C-DAX is a cyber-secure publish/subscribe middleware tailored to the needs of smart grids, offering end-to-end security, and scalable and resilient communication among participants in a smart grid. While C-DAX' broker-based publish/subscribe mechanisms are well-suited for scalable information dissemination with regard to high numbers of publishers and subscribers, (1) additional transmission delays are inherent to the design because of multi-hop application layer forwarding, and (2) interactive (probably legacy) applications are prohibited due to the one-way publish/subscribe paradigm and potential dependencies on IP communication. This work presents two advanced communication modes for the C-DAX architecture, addressing those issues: (1) broker-less publish/subscribe for delay-sensitive applications, and (2) transparent IP-tunneling over publish/subscribe for legacy applications. Those modes further improve C-DAX' suitability for smart grid applications, including enhanced real-time application support, and transparent support for legacy smart grid communication protocols.
MuCCRA4-BB: A fine-grained body biasing capable DRP
2016-04-01

The partitioning, implementation and in-silicon leakage evaluation of MuCCRA4-BB proved the feasibility and validity of fine-grained BB. Furthermore, it demonstrated the superiority over coarse- and chip-grained BB, minimizing FBB leakage penalty and allowing far more RBB usage in all applications and scenarios. As leakage exacerbates in smaller geometries, fine-grained BB might be an answer with sensible overhead.
Zeta functions of ${\\mathbb F}_1$-buildings
2016-04-01

The analogue of the Bruhat–Tits building of a -adic group in F1-geometry is a single apartment. In this setting, the trace formula gives rise to a several variable zeta function analogously to the -adic case. The analogy carries on to the fact that the restriction to certain lines yield zeta functions which are defined in geometrical terms. Also, the classical formula of Ihara has an analogue in this setting.