bluuebunny/crossref_metadata_2025_split huggingface dataset:
Language-integrated privacy-aware distributed queries
Authors: Salvaneschi Guido , Köhler Mirko , Sokolowski Daniel , Haller Philipp , Erdweg Sebastian , Mezini Mira 
Published: October 2019

Distributed query processing is an effective means for processing large amounts of data. To abstract from the technicalities of distributed systems, algorithms for operator placement automatically distribute sequential data queries over the available processing units. However, current algorithms for operator placement focus on performance and ignore privacy concerns that arise when handling sensitive data.
We present a new methodology for privacy-aware operator placement that both prevents leakage of sensitive information and improves performance. Crucially, our approach is based on an information-flow type system for data queries to reason about the sensitivity of query subcomputations. Our solution unfolds in two phases. First, placement space reduction generates deployment candidates based on privacy constraints using a syntax-directed transformation driven by the information-flow type system. Second, constraint solving selects the best placement among the candidates based on a cost model that maximizes performance. We verify that our algorithm preserves the sequential behavior of queries and prevents leakage of sensitive data. We implemented the type system and placement algorithm for a new query language SecQL and demonstrate significant performance improvements in benchmarks.
PlanAlyzer: assessing threats to the validity of online experiments
Authors: Tosch Emma , Bakshy Eytan , Berger Emery D. , Jensen David D. , Moss J. Eliot B. 
Published: October 2019

Online experiments have become a ubiquitous aspect of design and engineering processes within Internet firms. As the scale of experiments has grown, so has the complexity of their design and implementation. In response, firms have developed software frameworks for designing and deploying online experiments. Ensuring that experiments in these frameworks are correctly designed and that their results are trustworthy---referred to as internal validity---can be difficult. Currently, verifying internal validity requires manual inspection by someone with substantial expertise in experimental design.
We present the first approach for statically checking the internal validity of online experiments. Our checks are based on well-known problems that arise in experimental design and causal inference. Our analyses target PlanOut, a widely deployed, open-source experimentation framework that uses a domain-specific language to specify and run complex experiments. We have built a tool called PlanAlyzer that checks PlanOut programs for a variety of threats to internal validity, including failures of randomization, treatment assignment, and causal sufficiency. PlanAlyzer uses its analyses to automatically generate contrasts, a key type of information required to perform valid statistical analyses over the results of these experiments. We demonstrate PlanAlyzer's utility on a corpus of PlanOut scripts deployed in production at Facebook, and we evaluate its ability to identify threats to validity on a mutated subset of this corpus. PlanAlyzer has both precision and recall of 92% on the mutated corpus, and 82% of the contrasts it generates match hand-specified data.
Investigating the Contribution of Collagen to the Tumor Biomechanical Phenotype with Noninvasive Magnetic Resonance Elastography
Authors: Li Jin , Zormpas-Petridis Konstantinos , Boult Jessica K.R. , Reeves Emma L. , Heindl Andreas , Vinci Maria , Lopes Filipa , Cummings Craig , Springer Caroline J. , Chesler Louis , Jones Chris , Bamber Jeffrey C. , Yuan Yinyin , Sinkus Ralph , Jamin Yann , Robinson Simon P. 
Published: October 2019

AbstractIncreased stiffness in the extracellular matrix (ECM) contributes to tumor progression and metastasis. Therefore, stromal modulating therapies and accompanying biomarkers are being developed to target ECM stiffness. Magnetic resonance (MR) elastography can noninvasively and quantitatively map the viscoelastic properties of tumors in vivo and thus has clear clinical applications. Herein, we used MR elastography, coupled with computational histopathology, to interrogate the contribution of collagen to the tumor biomechanical phenotype and to evaluate its sensitivity to collagenase-induced stromal modulation. Elasticity (Gd) and viscosity (Gl) were significantly greater for orthotopic BT-474 (Gd = 5.9 ± 0.2 kPa, Gl = 4.7 ± 0.2 kPa, n = 7) and luc-MDA-MB-231-LM2-4 (Gd = 7.9 ± 0.4 kPa, Gl = 6.0 ± 0.2 kPa, n = 6) breast cancer xenografts, and luc-PANC1 (Gd = 6.9 ± 0.3 kPa, Gl = 6.2 ± 0.2 kPa, n = 7) pancreatic cancer xenografts, compared with tumors associated with the nervous system, including GTML/Trp53KI/KI medulloblastoma (Gd = 3.5 ± 0.2 kPa, Gl = 2.3 ± 0.2 kPa, n = 7), orthotopic luc-D-212-MG (Gd = 3.5 ± 0.2 kPa, Gl = 2.3 ± 0.2 kPa, n = 7), luc-RG2 (Gd = 3.5 ± 0.2 kPa, Gl = 2.3 ± 0.2 kPa, n = 5), and luc-U-87-MG (Gd = 3.5 ± 0.2 kPa, Gl = 2.3 ± 0.2 kPa, n = 8) glioblastoma xenografts, intracranially propagated luc-MDA-MB-231-LM2-4 (Gd = 3.7 ± 0.2 kPa, Gl = 2.2 ± 0.1 kPa, n = 7) breast cancer xenografts, and Th-MYCN neuroblastomas (Gd = 3.5 ± 0.2 kPa, Gl = 2.3 ± 0.2 kPa, n = 5). Positive correlations between both elasticity (r = 0.72, P &lt; 0.0001) and viscosity (r = 0.78, P &lt; 0.0001) were determined with collagen fraction, but not with cellular or vascular density. Treatment with collagenase significantly reduced Gd (P = 0.002) and Gl (P = 0.0006) in orthotopic breast tumors. Texture analysis of extracted images of picrosirius red staining revealed significant negative correlations of entropy with Gd (r = −0.69, P &lt; 0.0001) and Gl (r = −0.76, P &lt; 0.0001), and positive correlations of fractal dimension with Gd (r = 0.75, P &lt; 0.0001) and Gl (r = 0.78, P &lt; 0.0001). MR elastography can thus provide sensitive imaging biomarkers of tumor collagen deposition and its therapeutic modulation.Significance:MR elastography enables noninvasive detection of tumor stiffness and will aid in the development of ECM-targeting therapies.
Centrosome Amplification in Cancer Disrupts Autophagy and Sensitizes to Autophagy Inhibition
Authors: Denu Ryan A. , Kaur Gulpreet , Sass Madilyn M. , Lakkaraju Aparna , Burkard Mark E. 
Published: October 2019

Abstract

Centrosome amplification (CA), or a numerical increase in centrosomes, is common in human cancers, particularly those with high-risk features. We have discovered that cells with CA have an increased burden of autophagy, a catabolic process whereby autophagosomes engulf damaged organelles and proteins and deliver these contents to the lysosome for degradation and subsequent recycling. Cells with CA demonstrate an accumulation of autophagosomes. We evaluated the alternative hypotheses that CA alters autophagy by modulating microtubule networks and impairing trafficking versus altering lysosome clustering and organization versus chromosome missegregation-induced proteotoxic stress. Using LC3 reporter assays and autophagosome tracking experiments, we demonstrate that CA causes an accumulation of autophagosomes by interfering with autophagosome trafficking. To establish whether this was a druggable weakness, we tested autophagy inhibitors in our cell models of CA. Cells with CA are sensitized to chemical and genetic autophagy inhibition. Taken together, our results suggest that autophagy is disrupted by CA and sensitizes cells to inhibition of autophagy. These findings suggest a novel precision medicine strategy, whereby CA increases reliance on autophagy and serves as a biomarker for autophagy inhibitors in high-risk cancers.

Implications:
Our study suggests that CA could be used as a predictive biomarker for treatment with autophagy inhibitors.
“Let’s Take the Text Seriously”
Authors: Young Stephen L. 
Published: October 2019

Abstract
Mainstream New Testament Studies is often a space of repeating, elaborating on, identifying with, or valorizing the voices of NT writings. These common features of NT Studies resemble what scholars in Religious Studies refer to as protectionism: the privileging of a source’s own claims to such an extent that interpreters let them dictate academic analysis. Through examining debates about NT sources and both Greco-Roman ethnic rhetorics and Hellenistic philosophy, this article argues that protectionism structures the doxa of mainstream NT Studies—the commonsense that shapes what is thinkable and what questions / categories feel the most obvious. The field’s protectionism often manifests itself in confused rhetoric about “taking the text seriously” and in the invalidating of scholarship that does something other than describe (i.e., “exegesis”) or elaborate upon NT writings. Protectionism thus helps explain the gendered hierarchies of knowledge in NT Studies: “exegesis” and supposedly “objective Historical-Criticism” are dominant norms that reproduce the field as a masculine dominated space. As a result, critical and redescriptive research—especially by or about women—gets passed over since it seems “niche” or “political / agenda” driven by comparison. Interrogating the protectionism of NT Studies thus permits rethinking the politics of what kinds of scholarship seem the most obvious.
Post-Socialist Sufi Revival in Albania
Authors: Bria Gianfranco 
Published: October 2019

Abstract
This work analyses the case of Sufi revival in post-socialist Albania, where the religious field has been fragmented by the competing actions of different actors (local, regional and foreign) and by the critical and individualised religiosity of the faithful. Sufi public life is substantially marginalised by the monopoly of the esoteric Baktashis and Sunni political strategies. Thus, many Sufi faithful prefer to live their religious experience and express their practice in inner, private and virtual spaces. This dynamics has transformed the Sufi path and the charismatic authority of the Shaykhs.
Genesis of Tibetan Plateau Vortex: Roles of Surface Diabatic and Atmospheric Condensational Latent Heating
Authors: Zhang Feimin , Wang Chenghai , Pu Zhaoxia 
Published: October 2019

AbstractNumerical simulations of a nighttime-generated Tibetan Plateau vortex (TPV) are conducted using the advanced Weather Research and Forecasting (WRF) Model. It is found that the nighttime TPV forms as a result of the merging of convections. Although the WRF Model can reproduce the genesis of the nighttime TPV well, colder and drier biases in the lower atmosphere and drier biases in the upper atmosphere are still presented, thus degrading the simulation performance. Intercomparisons among the experiments indicate that the simulations are more sensitive to land surface schemes than to cloud microphysics schemes. The development of convection is more favorable when daytime surface diabatic heating is vigorous. Surface diabatic heating during daytime plays a dominant role in the development of daytime convection and the genesis of nighttime TPV. Further diagnosis of the PV budget reveals that the obvious increase in PV in the lower atmosphere is associated with the evidently strengthened cyclonic vorticity during TPV genesis. This could be attributed to the increased vertical component of net cross-boundary PV fluxes during the merging of convections as well as the significant positive contribution of diabatic heating effects in the lower atmosphere. Therefore, strong daytime surface diabatic heating, which is essential to convection development, could provide a favorable condition for nighttime TPV genesis. Overall results illuminate the complicated process of TPV genesis.
Dynamics of the ENSO Teleconnection and NAO Variability in the North Atlantic–European Late Winter
Authors: Mezzina Bianca , García-Serrano Javier , Bladé Ileana , Kucharski Fred 
Published: October 2019

AbstractThe winter extratropical teleconnection of El Niño–Southern Oscillation (ENSO) in the North Atlantic–European (NAE) sector remains controversial, concerning both the amplitude of its impacts and the underlying dynamics. However, a well-established response is a late-winter (January–March) signal in sea level pressure (SLP) consisting of a dipolar pattern that resembles the North Atlantic Oscillation (NAO). Clarifying the relationship between this “NAO-like” ENSO signal and the actual NAO is the focus of this study. The ENSO–NAE teleconnection and NAO signature are diagnosed by means of linear regression onto the sea surface temperature (SST) Niño-3.4 index and an EOF-based NAO index, respectively, using long-term reanalysis data (NOAA-20CR, ERA-20CR). While the similarity in SLP is evident, the analysis of anomalous upper-tropospheric geopotential height, zonal wind, and transient-eddy momentum flux, as well as precipitation and meridional eddy heat flux, suggests that there is no dynamical link between the phenomena. The observational results are further confirmed by analyzing two 10-member ensembles of atmosphere-only simulations (using an intermediate-complexity and a state-of-the-art model) with prescribed SSTs over the twentieth century. The SST-forced variability in the Northern Hemisphere is dominated by the extratropical ENSO teleconnection, which provides modest but significant SLP skill in the NAE midlatitudes. The regional internally generated variability, estimated from residuals around the ensemble mean, corresponds to the NAO pattern. It is concluded that distinct dynamics are at play in the ENSO–NAE teleconnection and NAO variability, and caution is advised when interpreting the former in terms of the latter.
Regenerative effects of spring water-derived bacterial lysates on human skin fibroblast in in vitro culture: preliminary results
Authors: Nicoletti Giovanni , Saler Marco , Tresoldi Marco Mario , Faga Angela , Benedet Mattia , Cristofolini Mario 
Published: October 2019

Objective: Previous studies have shown regenerative power of the skin with Comano (Trento, Italy) spring water and resident non-pathogenic microflora. This study investigated the action of bacterial lysates that were isolated from Comano spring water on in vitro culture of human skin fibroblasts. Methods: For this study, we selected the following four bacterial lysates: L1 (closest relative: Rudaea cellulosilytica), L2 (closest relative: Mesorhizobium erdmanii), L3 (closest relative: Herbiconiux ginsengi), and L4 (closest relative: Fictibacillus phosphorivorans). Human fibroblasts were cultured under Dulbecco’s modified Eagle’s medium (DMEM) with bacterial lysates added or DMEM (controls). Cell proliferation was evaluated by spectrophotometric absorbance analysis after the XTT-Microculture Tetrazolium Assay. Results: At 24 hours, cultures with L2, L3, and L4 showed a higher absorbance compared with controls. At 48 hours, cultures with L1, L2, and L3 showed slightly lower absorbance compared with controls, and culture with L4 showed a higher absorbance than in the other experimental conditions. At 72 hours, absorbance was lower in cultures with L1, L2, and L3 than in controls, and absorbance was higher in culture with L4 than in the other experimental conditions. Conclusions: Our study indicates a favorable action of Comano spring water microbiota on proliferation of human skin fibroblasts.
Associations of cytosine deaminase gene polymorphisms with effectiveness of gemcitabine/cisplatin chemotherapy in patients of Xinjiang Uyghur and Han nationality with non-small cell lung cancer
Authors: Li Jing , Xu Dan , Huang Jian , Wang Yan-Na , Ma Xiao-Ping , Lin Zhi-Yi , Gong Ping 
Published: October 2019

Background: Cytidine deaminase (CDA) polymorphisms may affect the response to gemcitabine/cisplatin chemotherapy in patients with non-small cell lung cancer (NSCLC). This study is designed to investigate the associations of CDA-79A>C and 208G>A polymorphisms and gemcitabine/cisplatin chemotherapy effectiveness in Xinjiang Uyghur and Han patients. Methods: This prospective cohort study enrolled consecutive patients with stage IIIb/IV NSCLC administered gemcitabine/cisplatin chemotherapy at the First Affiliated Hospital, Medical College of Shihezi University and the First People’s Hospital, Kashgar Region. CDA-A79C and CDA-G208A polymorphisms were detected by direct sequencing. Progression-free survival was analyzed by the Kaplan-Meier method. Associations of A79C and G208A polymorphisms with treatment effectiveness and progression-free survival were analyzed using logistic regression and multivariate Cox regression analyses. Subgroup analyses based on ethnicity were performed. Results: The study enrolled 120 patients. A79C and G208A polymorphisms followed the Hardy-Weinberg equilibrium. The frequencies of the AA, AC, and CC genotypes and the A and C alleles of A79C were 52.2%, 29.9%, 17.9%, 67.2%, and 32.8%, respectively, in Han patients and 75.4%, 18.9%, 5.7%, 84.9%, and 5.1%, respectively, in Uyghur patients. Uyghur patients had lower frequencies of A79C-AC/CC genotypes, A79C-C allele, G208A-GA genotype, and G208A-A allele ( P<0.05). Compared with A79C-AA, the odds of ineffective chemotherapy were increased for A79C-AC (odds ratio [OR] 2.818; 95% confidence interval [95% CI] 1.031, 7.705; P=0.043) and A79C-CC (OR 9.864; 95% CI 1.232, 78.966; P=0.031). G208A polymorphisms did not influence chemotherapy effectiveness. Chemotherapy was more effective in Han patients than in Uyghur patients for A79C-AC and G208A-GG. Progression-free survival was longer for A79C-AA versus A79C-AC/CC (10 vs. 7 months, P=0.004) and G208A-GA/AA vs. G208A-AA (12 vs. 8 months, P=0.010). Polymorphisms of A79C (hazard ratio [HR] 1.617; 95% CI 1.009, 2.592; P=0.046) and G208A (HR 2.193; 95% CI 1.055, 4.557; P=0.035) were associated with progression-free survival. Conclusion: For Uyghur and Han ethnic groups, A79C and G208A polymorphisms can be used as a promising biomarker for the chemotherapy efficacy and prognosis of NSCLC.
Characterization of Sinus Disease in Patients with Yellow Nail Syndrome
Authors: Gutierrez Claudia N. , Low Christopher M. , Stokken Janalee K. , Choby Garret , O’Brien Erin K. 
Published: October 2019

Objective Yellow nail syndrome (YNS) is characterized by the triad of thickened yellow nails, primary lymphedema, and respiratory manifestations including bronchiectasis, chronic cough, pleural effusions, and sinusitis. The purpose of this study is to describe the manifestations of chronic rhinosinusitis (CRS) in patients with YNS and the comorbid manifestations. Methods A retrospective review of patients with YNS with CRS from January 1, 1998 to January 1, 2018 was conducted. Their symptoms, comorbidities, and labs were reviewed. The patient’s sinus computed tomography (CT) scans were then scored using the Lund–Mackay (LM) scoring system. Result Thirty-six patients met the inclusion criteria. The average LM score was 10.2 ± 0.5 (mean ± SD). Sinus involvement included “frothy” dependent sinus secretions in 32 of 36 subjects. The most common location of sinus involvement was the maxillary sinuses (85%), then posterior ethmoid (81%), anterior ethmoid (76%), sphenoid (74%), and frontal sinuses (54%). Comorbid chronic cough (86%), bronchiectasis (65%), lymphedema (39%), and pleural effusion (19%) were also identified. Three patients (8%) had immunodeficiencies. Conclusion This is the largest series describing the sinus manifestations of CRS in patients with YNS. Sinus CT scans showed frothy dependent secretions in the maxillary sinuses and posterior ethmoid sinuses most commonly. YNS patients with sinusitis more commonly presented with chronic cough or bronchiectasis than with pleural effusions or lymphedema. Otolaryngologists should consider the possibility of YNS in patients with CRS, chronic cough, yellow or thickened nail, and CT findings of frothy, dependent sinus secretions.
Evidence for a Single Step Mechanism in the Origin of Hyperdiploid Childhood Acute Lymphoblastic Leukemia.
Authors: Paulsson Kajsa , Morse Helena , Fioretos Thoas , Behrendtz Mikael , Strombeck Bodil , Mitelman Felix , Johansson Bertil 
Published: October 2019

Abstract
High hyperdiploidy (>50 chromosomes) in childhood acute lymphoblastic leukemia (ALL) is characterized by non-random multiple trisomies and tetrasomies, involving in particular chromosomes X, 4, 6, 8, 10, 14, 17, 18, and 21. It is the most common cytogenetic subgroup in pediatric ALL, but in spite of this, the mechanisms behind its formation remain elusive. Four different pathways are possible: (1) initial near-haploidy followed by doubling of the chromosomes, (2) prior polyploidization with subsequent losses of chromosomes, (3) sequential gains of chromosomes in consecutive cell divisions, and (4) a simultaneous gain of all additional chromosomes in a single abnormal mitosis. Although these alternatives are difficult to distinguish experimentally, investigations of possible uniparental disomies (UPDs) and of the allelic ratios of loci located on tetrasomic chromosomes may provide some clues. In a previous study of 10 cases of hyperdiploid childhood ALL, we could exclude the first pathway as a general mechanism. Furthermore, the results did not favor the second alternative. Finally, our findings of equal allele dosage for chromosome 21 loci in cases with tetrasomy 21 suggested that the hyperdiploidy arose by a simultaneous gain of chromosomes. However, because all disomies and tetrasomies were not investigated, formation via a polyploid state or by a sequential gain could not be definitely excluded. In the present study, we have addressed this issue further by investigating 15 new cases of hyperdiploid childhood ALL using a total of 57 polymorphic microsatellite markers mapped to 23 of the 24 human chromosomes. Ten of the cases were analyzed with multicolor fluorescence in situ hybridization (M-FISH) and the remaining five with interphase FISH using probes for X, 4, 6, 8, 10, 14, 17, 18, and 21. Markers localized to all disomic and all tetrasomic chromosomes were then applied. One case displayed multiple UPDs and a non-typical pattern with only tetrasomies; this ALL probably arose via a near-haploid pathway. Two other cases had UPDs for 4/9 and 2/14 disomic chromosomes, respectively, and may have originated via a polyploid state. However, in the vast majority of the cases (12/15) there was no evidence for any UPDs, excluding that the hyperdiploidy originated by the near-haploid or polyploid mechanisms. Investigating the tetrasomies, 25 of a total of 27 tetrasomies present among the 15 cases displayed equal allele dosages, indicating a simultaneous gain of chromosomes as opposed to sequential gains. The two tetrasomies with unequal allele dosages were present in the same case, suggesting that this ALL constituted an exception. In conclusion, the results of the present study strongly suggest that hyperdiploidy in childhood ALL generally arises by a simultaneous gain of all additional chromosomes in a single abnormal mitosis.