julilili42/papers huggingface dataset:
Dissipative Frustration in a One Dimensional Josephson Junction Chain
2019-11-19

We study the influence of dissipative frustration on the one dimensional Josephson junction chain. In particular we analyze the dissipative quantum phase transition between the chain being superconducting or insulating, the purity as a measure of quantum—environment correlation and the logarithmic negativity as an entanglement measure. The dissipative frustration is provided by coupling two non-commuting operators to the environment. A possible realization of these environmental couplings are shunt resistances between the superconducting islands and resistances to the ground. Using a self-consistent harmonic approximation we determine the critical line separating superconducting and insulating phases and find a nonmonotonic behavior as a function of the dissipative strength. The interplay between both environmental couplings is also reflected in the purity and the logarithmic negativity. We find a change in their behavior depending whether a second bath is present or not.
Titelbild: Luminescence and Light‐Driven Energy and Electron Transfer from an Exceptionally Long‐Lived Excited State of a Non‐Innocent Chromium(III) Complex (Angew. Chem. 50/2019)
2019-11-19

Durch Inversionssymmetrie erhöht sich die Lebensdauer des angeregten Zustands eines molekularen Rubins bei Raumtemperatur in flüssiger Lösung auf 4.5 ms, während die Photolumineszenzquantenausbeute bis zu 8.2 % beträgt. In ihrem Forschungsartikel auf S. 18243 zeigen K. Heinze et al., dass der Chrom(III)-Komplex [Cr(tpe)2]3+ sich zudem für lichtinduzierte Energie- und Elektronenübertragungsprozesse eignet und insofern klassischen Edelmetallkomplexen ähnelt. Durch Inversionssymmetrie erhöht sich die Lebensdauer des angeregten Zustands eines molekularen Rubins bei Raumtemperatur in flüssiger Lösung auf 4.5 ms, während die Photolumineszenzquantenausbeute bis zu 8.2 % beträgt. In ihrem Forschungsartikel auf S. 18243 zeigen K. Heinze et al., dass der Chrom(III)-Komplex [Cr(tpe)2]3+ sich zudem für lichtinduzierte Energie- und Elektronenübertragungsprozesse eignet und insofern klassischen Edelmetallkomplexen ähnelt. Photopolymerisation Nanofibrillen Homogene Katalyse
Cover Picture: Luminescence and Light‐Driven Energy and Electron Transfer from an Exceptionally Long‐Lived Excited State of a Non‐Innocent Chromium(III) Complex (Angew. Chem. Int. Ed. 50/2019)
2019-11-19

Inversion symmetry increases the excited-state lifetime of a molecular ruby at room temperature in fluid solution to 4.5 ms while the photoluminescence quantum yield remains as high as 8.2 %, as shown by K. Heinze and co-workers in their Research Article on page 18075. The chromium(III) complex [Cr(tpe)2]3+ is furthermore competent in light-induced electron and energy transfer processes, and thus resembles classical noble metal complexes.
On the ethics of algorithmic decision-making in healthcare
2019-11-20

In recent years, a plethora of high-profile scientific publications has been reporting about machine learning algorithms outperforming clinicians in medical diagnosis or treatment recommendations. This has spiked interest in deploying relevant algorithms with the aim of enhancing decision-making in healthcare. In this paper, we argue that instead of straightforwardly enhancing the decision-making capabilities of clinicians and healthcare institutions, deploying machines learning algorithms entails trade-offs at the epistemic and the normative level. Whereas involving machine learning might improve the accuracy of medical diagnosis, it comes at the expense of opacity when trying to assess the reliability of given diagnosis. Drawing on literature in social epistemology and moral responsibility, we argue that the uncertainty in question potentially undermines the epistemic authority of clinicians. Furthermore, we elucidate potential pitfalls of involving machine learning in healthcare with respect to paternalism, moral responsibility and fairness. At last, we discuss how the deployment of machine learning algorithms might shift the evidentiary norms of medical diagnosis. In this regard, we hope to lay the grounds for further ethical reflection of the opportunities and pitfalls of machine learning for enhancing decision-making in healthcare.
Distinct molecular profile of IRF4-rearranged large B-cell lymphoma
2019-11-20

Abstract Pediatric large B-cell lymphomas (LBCLs) share morphological and phenotypic features with adult types but have better prognosis. The higher frequency of some subtypes such as LBCL with IRF4 rearrangement (LBCL-IRF4) in children suggests that some age-related biological differences may exist. To characterize the genetic and molecular heterogeneity of these tumors, we studied 31 diffuse LBCLs (DLBCLs), not otherwise specified (NOS); 20 LBCL-IRF4 cases; and 12 cases of high-grade B-cell lymphoma (HGBCL), NOS in patients ≤25 years using an integrated approach, including targeted gene sequencing, copy-number arrays, and gene expression profiling. Each subgroup displayed different molecular profiles. LBCL-IRF4 had frequent mutations in IRF4 and NF-κB pathway genes (CARD11, CD79B, and MYD88), losses of 17p13 and gains of chromosome 7, 11q12.3-q25, whereas DLBCL, NOS was predominantly of germinal center B-cell (GCB) subtype and carried gene mutations similar to the adult counterpart (eg, SOCS1 and KMT2D), gains of 2p16/REL, and losses of 19p13/CD70. A subset of HGBCL, NOS displayed recurrent alterations of Burkitt lymphoma–related genes such as MYC, ID3, and DDX3X and homozygous deletions of 9p21/CDKN2A, whereas other cases were genetically closer to GCB DLBCL. Factors related to unfavorable outcome were age &amp;gt;18 years; activated B-cell (ABC) DLBCL profile, HGBCL, NOS, high genetic complexity, 1q21-q44 gains, 2p16/REL gains/amplifications, 19p13/CD70 homozygous deletions, and TP53 and MYC mutations. In conclusion, these findings further unravel the molecular heterogeneity of pediatric and young adult LBCL, improve the classification of this group of tumors, and provide new parameters for risk stratification.
Efficacy of Temozolomide Therapy in Patients With Aggressive Pituitary Adenomas and Carcinomas—A German Survey
2019-11-20

Abstract Context Despite growing evidence that temozolomide (TMZ) therapy is effective for the treatment of aggressive pituitary tumors (APTs) or carcinomas (PCs), individual therapy decisions remain challenging. Objective We therefore aimed to report on clinical characteristics leading to initiation of TMZ therapy and to add evidence on TMZ long-term effectiveness. Design and subjects Retrospective survey on TMZ treatment in patients with APTs or PCs. TMZ therapy was initiated in 47 patients (22 females) with APTs (n = 34) or PCs (n = 13). Mean age at diagnosis was 45 ± 15 years. The immunohistochemical subtypes were corticotroph (n = 20), lactotroph (n = 18), and nonfunctioning (n = 9) tumors. TMZ therapy started 8 years after initial diagnosis using a standard regimen (median 6 cycles) for the majority of patients. Results Long-term radiological response to TMZ after a median follow-up of 32 months with 4 patients still on TMZ therapy was tumor regression for 9 (20%), stable disease for 8 (17%), and tumor progression for 29 patients (63%) (outcome data available for 46 patients). Progression occurred 16 months after initiation of TMZ. Median estimated progression-free survival was 23 months. Disease stabilization and median progression-free survival did not differ between patients with APTs or PCs. Predictors of tumor response were not identified. Overall, TMZ was well tolerated. Conclusion We performed a nationwide survey on TMZ therapy in patients with APTs and PCs. While early response rates to TMZ are promising, long-term outcome is less favorable. Prolonged TMZ administration should be considered. We were not able to confirm previously reported predictors of tumor response to TMZ.
Translational Insights into Extremely Low Frequency Pulsed Electromagnetic Fields (ELF-PEMFs) for Bone Regeneration after Trauma and Orthopedic Surgery
2019-11-20

The finding that alterations in electrical potential play an important role in the mechanical stimulation of the bone provoked hype that noninvasive extremely low frequency pulsed electromagnetic fields (ELF-PEMF) can be used to support healing of bone and osteochondral defects. This resulted in the development of many ELF-PEMF devices for clinical use. Due to the resulting diversity of the ELF-PEMF characteristics regarding treatment regimen, and reported results, exposure to ELF-PEMFs is generally not among the guidelines to treat bone and osteochondral defects. Notwithstanding, here we show that there is strong evidence for ELF-PEMF treatment. We give a short, confined overview of in vitro studies investigating effects of ELF-PEMF treatment on bone cells, highlighting likely mechanisms. Subsequently, we summarize prospective and blinded studies, investigating the effect of ELF-PEMF treatment on acute bone fractures and bone fracture non-unions, osteotomies, spinal fusion, osteoporosis, and osteoarthritis. Although these studies favor the use of ELF-PEMF treatment, they likewise demonstrate the need for more defined and better controlled/monitored treatment modalities. However, to establish indication-oriented treatment regimen, profound knowledge of the underlying mechanisms in the sense of cellular pathways/events triggered is required, highlighting the need for more systematic studies to unravel optimal treatment conditions.
Discovery of the Streptoketides by Direct Cloning and Rapid Heterologous Expression of a Cryptic PKS II Gene Cluster from Streptomyces sp. Tü 6314
2019-11-20

Genome sequencing and bioinformatic analysis have identified numerous cryptic gene clusters that have the potential to produce novel natural products. Within this work, we identified a cryptic type II PKS gene cluster (<i>skt</i>) from <i>Streptomyces</i> sp. Tü 6314. Facilitated by linear plus linear homologous recombination-mediated recombineering (LLHR), we directly cloned the <i>skt</i> gene cluster using the <i>Streptomyces</i> site-specific integration vector pSET152. Direct cloning allowed for rapid heterologous expression in <i>Streptomyces coelicolor,</i> leading to the identification and structural characterization of six polyketides (three known compounds and new streptoketides), four of which exhibit anti-HIV activities. Our study shows that the pSET152 vector can be directly used for LLHR, expanding the Rec/ET direct cloning toolbox and providing the possibility for rapid heterologous expression of gene clusters from <i>Streptomyces</i>.
Supported Solid Lipid Bilayers as a Platform for Single-Molecule Force Measurements
2019-11-20

Biocompatible surfaces are important for basic and applied research in life science with experiments ranging from the organismal to the single-molecule level. For the latter, examples include the translocation of kinesin motor proteins along microtubule cytoskeletal filaments or the study of DNA-protein interactions. Such experiments often employ single-molecule fluorescence or force microscopy. In particular for force measurements, a key requirement is to prevent nonspecific interactions of biomolecules and force probes with the surface, while providing specific attachments that can sustain loads. Common approaches to reduce nonspecific interactions include supported lipid bilayers or PEGylated surfaces. However, fluid lipid bilayers do not support loads and PEGylation may require harsh chemical surface treatments and have limited reproducibility. Here, we developed and applied a supported <i>solid</i> lipid bilayer (SSLB) as a platform for specific, load bearing attachments with minimal nonspecific interactions. Apart from single-molecule fluorescence measurements, anchoring molecules to lipids in the solid phase enabled us to perform force measurements of molecular motors and overstretch DNA. Furthermore, using a heating laser, we could switch the SSLB to its fluid state allowing for manipulation of anchoring points. The assay had little nonspecific interactions, was robust, reproducible, and time-efficient, and required less hazardous and toxic chemicals for preparation. In the long term, we expect that SSLBs can be widely employed for single-molecule fluorescence microscopy, force spectroscopy, and cellular assays in mechanobiology.
NUMERACY OF RELIGIOUS MINORITIES IN SPAIN AND PORTUGAL DURING THE INQUISITION ERA
2019-11-20

ABSTRACT We assess the numeracy (age heaping) of religious minorities, particularly Jews, and other defendants of the Spanish and Portuguese Inquisitions, and compare it with the general Iberian population. Our database includes 13,000 individuals who took part in Inquisition trials, and 17,000 individuals recorded in censuses and parish registers who serve as a control group. We thoroughly discuss the representativeness of our samples for the populations we aim to capture. Our results point at a substantial numeracy advantage of the Judaism-accused over the Catholic majority. Furthermore, Catholic priests and other groups of the religious elite who were occasional targets of the Inquisition had a similarly high level of numeracy.
From the Inside Out: Teacher Responses to the AP Curriculum Redesign
2019-11-20

From 2012–2015, Advanced Placement (AP) science courses underwent a large-scale curricular reform to include more scientific inquiry and reasoning, reduce emphasis on broad content coverage, and focus on depth of understanding, with corresponding changes in high-stakes AP examinations. In this study, we explored how teachers prepared for and adapted to this reform over a three-year period. Data included four waves of individual interviews with 22 AP Biology and Chemistry teachers across the United States. Data were qualitatively analyzed using emic and etic coding. Four themes were developed from these data: (1) initial perceptions about the reform including uncertainty, anxiety, and excitement, (2) preparation for reform, (3) impact of time, and (4) intersection of affinity toward the reform with time and uncertainty. Although teachers faced a variety of implementation challenges, these did not always influence their professional development (PD) choices. Rather, choices were more often driven by the price and proximity of those activities, resulting in a jumbled mélange rather than a coherent, extended series of learning experiences. Despite a variety of attitudes, beliefs and instructional skills, teacher beliefs about the purpose and value of the reform—over and above their learning experiences—influenced the time needed to transition and to become comfortable with the redesigned course. This study has implications for how teachers may respond to large-scale, top-down, curriculum reforms (e.g., NGSS, Common Core) and how education leaders, policy makers, and PD providers might support teachers in their efforts to adapt efficiently and effectively.
Cross-category phonological effects on ERP amplitude demonstrate context-specific processing during reading aloud
2019-11-20

The phonetic realisation of speech sounds depends on their context: e.g., /t/ is aspirated in 'top', but unaspirated in 'stop'.Similarly, Beijing Mandarin Tone 3 (T3) usually has a low contour, but preceding another T3 syllablehas a rising contour (sandhiT3).Importantly, Tone 2 (T2) also has a similar rising contour.Yet how such phonetic variation is processed online during reading and speech production is not well understood.ERP amplitude was measured as native Mandarin speakers read aloud words preceded by a 48ms masked prime.Prime and target always differed in tone category.Critical targets were T2-initial words.Primes were either sandhi T3 (contourmatch) or low T3 (mismatch).Generalised additive mixed models (GAMs) revealed a complex interaction between prime type, prime frequency and target frequency emerging around 100ms and 300-400ms following target presentation.In the contourmatch condition, when prime and target frequency were both high or both low, there was increased negativity, suggesting competition between prime and target.In the mismatch condition, there was relatively little effect of item frequencies.This difference in the pattern of effects between the contour-match and mismatch primes provides evidence for top-down effects of context on phonological processing of masked primes during reading aloud.
Interaction of arsenic trioxide and etoposide in Ewing sarcoma cell lines
2019-11-20

Ewing sarcomas (ES) are highly malignant mesenchymal tumors, which most often occur in children and adolescents. The current treatment of choice comprises wide resection in combination with multimodal chemotherapy including etoposide (Eto). Due to the serious side effects associated with common chemotherapeutics and prevalent multidrug resistance in recurrent and metastatic ES, there is a growing demand for alternative strategies and add‐on drugs. Previous research has demonstrated efficient cell death induction by Eto in combination with arsenic trioxide (ATO) in ES cell lines. The aim of the present study was to investigate the effect of different temporal sequences of ATO and Eto administration on apoptosis induction and to explore the effect of both drugs on inhibitory glycogen synthase kinase‐3β (GSK3‐β) phosphorylation as well as multidrug transporter gene expression. The intensity of caspase activation was mainly determined by the Eto doses in A673 and TC‐71 cells, whereas in RD‐ES cells ATO application actively suppressed Eto‐induced apoptosis. This coincided with an increase in inhibitory GSK‐3β phosphorylation in ATO‐treated RD‐ES cells. Inherent mRNA expression of multidrug resistance‐associated protein 1 (MRP1) was low in the ES cell lines compared to that observed in the mesenchymal stem cells (MSC), whereas multidrug resistance protein 1 (MDR1) gene expression was considerably increased in the ES cell lines. ATO treatment reduced MRP1 mRNA expression in the A673 and TC‐71 cells, while expression was induced in the MSC and RD‐ES cells. In contrast, MDR1 mRNA expression was specifically induced by ATO in the A673 and TC‐71 cells, reinforcing the expression differences between MSC and the ES cell lines. Although a reliable cell death induction by the combination of ATO and Eto has been previously shown in ES cell lines, the present study showed marked heterogeneity of the ES cell response to ATO and Eto treatment, illustrating the difficulty of prediction of individual treatment outcome in ES.
Explicit and Implicit Timing of Short Time Intervals: Using the Same Method
2019-11-20

Up until now, there has been no study conducted in the field of time perception using very short intervals for a direct comparison between implicit and explicit timing tasks in order to uncover plausibly different underlying mechanisms. Therefore, the aim of this study was to compare human time estimation during implicit and explicit timing tasks with short intervals and the same method. A total of 81 adults were divided into three groups and completed two tasks with one of three different intervals: 500, 1,000, and 2,000 ms. The results revealed an overestimation for all three intervals of the implicit timing task, while participants overestimated 500 ms but underestimated 1,000 and 2,000 ms intervals of the explicit timing task. Moreover, explicit time estimation was more precise than implicit time estimation. We observed the opposite pattern as compared to a few previous studies with long intervals: Short intervals were perceived longer in the implicit timing task as compared to the explicit timing task. We concluded that nontemporal contents represent passing time during the implicit timing task but unlike temporal dimension during the explicit timing task. Therefore, even the same method of measurement led to a different performance in implicit and explicit timing tasks.
openPrimeR for multiplex amplification of highly diverse templates
2019-11-20

Abstract To study the diversity of immune receptors and pathogens, multiplex PCR has become a central approach in research and diagnostics. However, insufficient primer design against highly diverse templates often prevents amplification and therefore limits the correct understanding of biological processes. Here, we present openPrimeR, an R-based tool for evaluating and designing multiplex PCR primers. openPrimeR provides a functional and intuitive interface and uses either a greedy algorithm or an integer linear program to compute the minimal set of primers that performs full target coverage. As proof of concept, we used openPrimeR to find optimal primer sets for the amplification of highly mutated immunoglobulins. Comprehensive analyses on specifically generated immunoglobulin variable gene segment libraries resulted in the composition of highly effective primer sets (oPR-IGHV, oPR-IGKV and oPR-IGLV) that demonstrated to be particularly suitable for the isolation of novel human antibodies.
Eye movements reflect acoustic cue informativity and statistical noise
2019-11-20

Listeners rely on highly variable, non-discrete acoustic information to understand spoken messages.The present 'visual world' eye tracking study investigated whether the amount of acoustic cue variation affected Cantonese listeners' perception of speech contrasts.Participants saw pictures of word pairs which were identical except for initial consonants (unaspirated versus aspirated).Auditory stimuli were continua of increasing VOT presented in bimodal distributions.The amount of acoustic variation varied between conditions: high-variance versus low-variance.Generalised Additive Modelling analyses showed, in the low-variance condition, eye movements reflected cue values: there was differential fixation behaviour for category means, boundaries and peripheries.In contrast, in the high-variance condition, the acoustic cue had little effect: fixation behaviour was similar across the different acoustic cue values.This demonstrates listeners' high sensitivity to the discriminative value of acoustic cues.How much cue dimensions are utilised depends on their variance.
Clinical use, efficacy, and durability of maraviroc for antiretroviral therapy in routine care: A European survey
2019-11-21

This study reports on the largest observation cohort of patients who started maraviroc across 8 European countries. In this overall highly treatment-experienced population, with a small but appreciable subset that received maraviroc outside of standard treatment guidelines, maraviroc was safe and reasonably effective, with relatively low rates of discontinuation over 48 weeks and only 2 cases of serum transaminase elevations reported as reasons for discontinuation.
Denitrifier Method for Nitrite Removal in Electrochemical Analysis of the Electron Accepting Capacity of Humic Substances
2019-11-21

Humic substances (HSs) are important electron acceptors and donors in soils and aquifers. The coupling of anoxic nitrogen (N) cycling to the function of HSs as a redox battery, however, remains poorly understood. Mediated electrochemical analysis is an emerging tool to determine the redox properties (i.e., electron donating capacity (EDC), electron accepting capacity (EAC), and redox state) of HS. However, the presence of nitrite (NO<sub>2</sub><sup>-</sup>), a central intermediate of the N-cycle, interferes with the electrochemical determination of the EAC. To eliminate this interference, we developed a bioassay to remove nitrite in HS samples using the denitrifying bacterium <i>Pseudomonas nitroreducens</i>. Cell suspensions of <i>P. nitroreducens</i> completely removed NO<sub>2</sub><sup>-</sup> at various concentrations (1, 2, and 5 mM) from humic acid samples (1 g HA/L) of different redox states. As <i>P. nitroreducens</i> is not able to exchange electrons with dissolved humic acids, the procedure allows an accurate and reliable determination of the EAC of humic acid samples. The proposed method thus opens new perspectives in biogeochemistry to study interactions between HSs and N cycling.