bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards an automated data cleaning with deep learning in CRESST
Authors: Angloher G. , Banik S. , Bartolot D. , Benato G. , Bento A. , Bertolini A. , Breier R. , Bucci C. , Burkhart J. , Canonica L. , D’Addabbo A. , Di Lorenzo S. , Einfalt L. , Erb A. , Feilitzsch F. v. , Iachellini N. Ferreiro , Fichtinger S. , Fuchs D. , Fuss A. , Garai A. , Ghete V. M. , Gerster S. , Gorla P. , Guillaumon P. V. , Gupta S. , Hauff D. , Ješkovský M. , Jochum J. , Kaznacheeva M. , Kinast A. , Kluck H. , Kraus H. , Lackner M. , Langenkämper A. , Mancuso M. , Marini L. , Meyer L. , Mokina V. , Nilima A. , Olmi M. , Ortmann T. , Pagliarone C. , Pattavina L. , Petricca F. , Potzel W. , Povinec P. , Pröbst F. , Pucci F. , Reindl F. , Rizvanovic D. , Rothe J. , Schäffner K. , Schieck J. , Schmiedmayer D. , Schönert S. , Schwertner C. , Stahlberg M. , Stodolsky L. , Strandhagen C. , Strauss R. , Usherov I. , Wagner F. , Willers M. , Zema V. , Waltenberger W. ,   CRESST Collaboration
Published: January 2023

AbstractThe CRESST experiment employs cryogenic calorimeters for the sensitive measurement of nuclear recoils induced by dark matter particles. The recorded signals need to undergo a careful cleaning process to avoid wrongly reconstructed recoil energies caused by pile-up and read-out artefacts. We frame this process as a time series classification task and propose to automate it with neural networks. With a data set of over one million labeled records from 68 detectors, recorded between 2013 and 2019 by CRESST, we test the capability of four commonly used neural network architectures to learn the data cleaning task. Our best performing model achieves a balanced accuracy of 0.932 on our test set. We show on an exemplary detector that about half of the wrongly predicted events are in fact wrongly labeled events, and a large share of the remaining ones have a context-dependent ground truth. We furthermore evaluate the recall and selectivity of our classifiers with simulated data. The results confirm that the trained classifiers are well suited for the data cleaning task.
The contribution of archeometry in characterization of decorative materials from the site of Villa di Teodorico in Galeata (Italy)
Authors: Saviane Luciana , Aceto Maurizio , Fornasini Laura , Mantovani Luciana , Morigi Alessia , Villicich Riccardo , Bersani Danilo 
Published: January 2023

AbstractVilla di Teodorico in Galeata (Forlì-Cesena, Emilia Romagna) is an important archeological site in the north of Italy occupied from sixth century BC to twelfth century AD. The most interesting results concern the Roman age, when a large villa was built, and the late antiquity, when the Ostrogothic king Theodoric decided to build in this area his palatium (early sixth century AD). The archeometric investigation was performed on Roman wall paintings fragments and on late antique glass sectilia fragments belonging to Palazzo di Teodorico by using a multi-technique approach that included micro-Raman spectroscopy, scanning electron microscopy with energy-dispersive spectroscopy, X-ray powder diffraction, UV–visible–NIR diffuse reflectance spectrophotometry with optic fibers and optical stereo-microscopy.. This analytical approach allowed the identification of all components, collecting molecular, elemental, microscopic, morphological and chromatic data. The characterization of samples supplied essential archeological, historical and technological information. The production techniques and the rich materials employed suggest the importance of the site in different periods. The evolution of the manufacturing technologies and the possible trade routes mainly during late antique period are witnessed by the change in the raw materials.
Graphical abstract
Synthesis, aggregation, and photophysical properties of amphiphilic BODIPY-Pt(II) metallacycles
Authors: Rubio Pedro , Salazar Ainhoa , Durán-Sampedro Gonzalo , de la Torre Gema 
Published: January 2023

The construction of metallo-organic macrocycles using transition metals and optoelectronically active donor ligands is a very active area of research due to the potential applicability of these structures as sensors or as drugs for combined photodynamic/chemotherapy treatments. Herein, we report on the synthesis, photophysical properties, and aggregation behavior of a triangular Pt(II)-assembled metallo-supramolecular complex built by the coordination-driven assembly of a BODIPY functionalized with two pyridines at the 2,6 positions and an (R, R)-phenylalanine dipeptide moiety in the meso position. This hydrophilic group provides the metallacycle with water-solubility and self-assembly capabilities, which result in the formation of robust nanoparticles in aqueous solutions with a 50 nm average size.
How to Properly Use Quotations
Authors: Yaffe Philip 
Published: January 2023

Each "Communication Corner" essay is self-contained; however, they build on each other. For best results, before reading this essay and doing the exercise, go to the first essay "How an Ugly Duckling Became a Swan," then read each succeeding essay.
Using quotations from prominent people, or even clever quotations from not-so-prominent people, is always a useful addition to a text or speech. However, not all quotations are created equal. It is important to know how quotations differ in order to use them to their best effect.
LKB1-Dependent Regulation of TPI1 Creates a Divergent Metabolic Liability between Human and Mouse Lung Adenocarcinoma
Authors: Stein Benjamin D. , Ferrarone John R. , Gardner Eric E. , Chang Jae Won , Wu David , Hollstein Pablo E. , Liang Roger J. , Yuan Min , Chen Qiuying , Coukos John S. , Sindelar Miriam , Ngo Bryan , Gross Steven S. , Shaw Reuben J. , Zhang Chen , Asara John M. , Moellering Raymond E. , Varmus Harold , Cantley Lewis C. 
Published: January 2023

AbstractKRAS is the most frequently mutated oncogene in human lung adenocarcinomas (hLUAD), and activating mutations frequently co-occur with loss-of-function mutations in TP53 or STK11/LKB1. However, mutation of all three genes is rarely observed in hLUAD, even though engineered comutation is highly aggressive in mouse lung adenocarcinoma (mLUAD). Here, we provide a mechanistic explanation for this difference by uncovering an evolutionary divergence in the regulation of triosephosphate isomerase (TPI1). In hLUAD, TPI1 activity is regulated via phosphorylation at Ser21 by the salt inducible kinases (SIK) in an LKB1-dependent manner, modulating flux between the completion of glycolysis and production of glycerol lipids. In mice, Ser21 of TPI1 is a Cys residue that can be oxidized to alter TPI1 activity without a need for SIKs or LKB1. Our findings suggest this metabolic flexibility is critical in rapidly growing cells with KRAS and TP53 mutations, explaining why the loss of LKB1 creates a liability in these tumors.Significance:Utilizing phosphoproteomics and metabolomics in genetically engineered human cell lines and genetically engineered mouse models (GEMM), we uncover an evolutionary divergence in metabolic regulation within a clinically relevant genotype of human LUAD with therapeutic implications. Our data provide a cautionary example of the limits of GEMMs as tools to study human diseases such as cancers.This article is highlighted in the In This Issue feature, p. 799
CNP Promotes Antiarrhythmic Effects via Phosphodiesterase 2
Authors: Cachorro Eleder , Günscht Mario , Schubert Mario , Sadek Mirna S. , Siegert Johanna , Dutt Fabian , Bauermeister Carla , Quickert Susann , Berning Henrik , Nowakowski Felix , Lämmle Simon , Firneburg Rebecca , Luo Xiaojing , Künzel Stephan R. , Klapproth Erik , Mirtschink Peter , Mayr Manuel , Dewenter Matthias , Vettel Christiane , Heijman Jordi , Lorenz Kristina , Guan Kaomei , El-Armouche Ali , Wagner Michael , Kämmerer Susanne 
Published: January 2023

Background:
Ventricular arrhythmia and sudden cardiac death are the most common lethal complications after myocardial infarction. Antiarrhythmic pharmacotherapy remains a clinical challenge and novel concepts are highly desired. Here, we focus on the cardioprotective CNP (C-type natriuretic peptide) as a novel antiarrhythmic principle. We hypothesize that antiarrhythmic effects of CNP are mediated by PDE2 (phosphodiesterase 2), which has the unique property to be stimulated by cGMP to primarily hydrolyze cAMP. Thus, CNP might promote beneficial effects of PDE2-mediated negative crosstalk between cAMP and cGMP signaling pathways.

Methods:
To determine antiarrhythmic effects of cGMP-mediated PDE2 stimulation by CNP, we analyzed arrhythmic events and intracellular trigger mechanisms in mice in vivo, at organ level and in isolated cardiomyocytes as well as in human-induced pluripotent stem cell-derived cardiomyocytes.

Results:

In ex vivo perfused mouse hearts, CNP abrogated arrhythmia after ischemia/reperfusion injury. Upon high-dose catecholamine injections in mice, PDE2 inhibition prevented the antiarrhythmic effect of CNP. In mouse ventricular cardiomyocytes, CNP blunted the catecholamine-mediated increase in arrhythmogenic events as well as in I
CaL
, I
NaL
, and Ca
2+
spark frequency. Mechanistically, this was driven by reduced cellular cAMP levels and decreased phosphorylation of Ca
2+
handling proteins. Key experiments were confirmed in human iPSC-derived cardiomyocytes. Accordingly, the protective CNP effects were reversed by either specific pharmacological PDE2 inhibition or cardiomyocyte-specific PDE2 deletion.

Conclusions:
CNP shows strong PDE2-dependent antiarrhythmic effects. Consequently, the CNP-PDE2 axis represents a novel and attractive target for future antiarrhythmic strategies.
Sin and Bodily Illness in the Psalms
Authors: Zahl Simeon 
Published: January 2023

Abstract
Much recent Christian theology has sought to reconsider the significance of the body in theological reflection. At the same time, a number of areas of suffering traditionally associated with the experience of sin have come to be reinterpreted, for good reasons, as medical disorders without moral valence. The result is that the doctrine of sin has become increasingly dissociated from the body in contemporary theology. This article addresses this dissociation by exploring the difficulty posed to interpreters by the correlation in Psalms 32 and 38 between unforgiven sin and bodily suffering and dysfunction. After showing that this correlation has been a source of significant difficulties for modern interpreters, the essay concludes by examining the potential of an Augustinian reading of these Psalms in terms of the relationship between mortality and original sin.
Pitfalls of Climate Network Construction—A Statistical Perspective
Authors: Haas Moritz , Goswami Bedartha , von Luxburg Ulrike 
Published: January 2023

Abstract
Network-based analyses of dynamical systems have become increasingly popular in climate science. Here, we address network construction from a statistical perspective and highlight the often-ignored fact that the calculated correlation values are only empirical estimates. To measure spurious behavior as deviation from a ground truth network, we simulate time-dependent isotropic random fields on the sphere and apply common network-construction techniques. We find several ways in which the uncertainty stemming from the estimation procedure has a major impact on network characteristics. When the data have a locally coherent correlation structure, spurious link bundle teleconnections and spurious high-degree clusters have to be expected. Anisotropic estimation variance can also induce severe biases into empirical networks. We validate our findings with ERA5 data. Moreover, we explain why commonly applied resampling procedures are inappropriate for significance evaluation and propose a statistically more meaningful ensemble construction framework. By communicating which difficulties arise in estimation from scarce data and by presenting which design decisions increase robustness, we hope to contribute to more reliable climate network construction in the future.

Significance Statement
Network-based approaches have gained renewed attention regarding the prediction of climate phenomena such as El Niño events, extreme regional precipitation patterns, anomalous polar vortex dynamics, and regarding understanding the Earth system. Even though climate networks are constructed from a limited amount of noisy data, they typically are not studied from a statistical perspective. However, such an approach is crucial: due to sampling uncertainty, climate networks unavoidably contain false and missing edges. We analyze how sampling artifacts impact the conclusions drawn from the networks and present both pitfalls and statistically robust procedures of network construction and evaluation. We aim to contribute to understanding the limitations and fully leveraging the potentials of network methods in climate and Earth system science.
Multimodal imaging for the management of Lyme-associated uveitis: A case report from an Italian tertiary center
Authors: Ferro Desideri Lorenzo , Rosa Raffaella , Forte Paolo , Manocchio Riccardo , Vagge Aldo , Traverso Carlo Enrico , Nicolò Massimo 
Published: January 2023

Introduction Lyme borreliosis may present with different systemic manifestations and also the ocular involvement may be difficult to diagnose because of its multifaceted presentation. Considering the growing incidence of Lyme disease in European countries, ophthalmologist should be trained to distinguish ocular borreliosis. Case Report Several clinical presentations have been previously described, including uveitis, unilateral or bilateral chorioretinitis, keratitis, episcleritis, papillitis and ischemic optic neuropathy, retinal vasculitis and acute posterior multifocal placoid pigment epitheliopathy (APMPPE); however our case report showed a rare presentation with the presence of unilateral uveitis with vitreitis and multiple, patchy, yellowish lesions, in association with retinal vasculitis. This clinical picture was to be considered in differential diagnosis with ocular Toxoplasmosis. Conclusions The appropriate management of this patient was made possible by the combination of multimodal imaging and appropriate laboratory tests, representing the optimal process in the diagnostic and therapeutic pathway in high-risk patients for ocular Lyme disease.
Poly Lactic-Co-Glycolic Acid Nano-Carriers for Encapsulation and Controlled Release of Hydrophobic Drug to Enhance the Bioavailability and Antimicrobial Properties
Authors: Bukhari Attaullah , Fatima Zuha , Atta Madiha , Nazir Arif , Alshawwa Samar Z. , Alotaibi Hadil F. , Iqbal Munawar 
Published: January 2023

This study focusses on the fabrication of nano-carriers for delivery of ciprofloxacin through the nanoprecipitation process. This was done to examine the release of drug at the pH of stomach to find out the antibacterial action of ciprofloxacin loaded nanoparticles (NPs). Prepared NPs were characterized by Fourier Transform Infra-Red (FTIR) spectroscopy, Scanning Electron Microscopy (SEM), and particle size analyzer (PSA) techniques. Drug yield, loading, and sustained release was studied as function of time (up to 8 h). Antibacterial activity of ciprofloxacin loaded NPs were also determined against different gram-positive and gram-negative bacteria. Results revealed that nanoprecipitation is a suitable method for encapsulation of ciprofloxacin in poly(lactic-co-glycolic acid) PLGA NPs. The drug yield and drug loading were found to be 60%. The size range of NPs observed by PSA was in the range of 5.03–6.60 nm. It can be concluded that nanoformulation of ciprofloxacin loaded PLGA NPs can be used in stomach for longer period of time to enhance the bioavailability of the drug.
The genome of sheep ked (Melophagus ovinus) reveals potential mechanisms underlying reproduction and narrower ecological niches
Authors: Zhang Qingxun , Zhou Qingsong , Han Shuyi , Li Ying , Wang Ye , He Hongxuan 
Published: January 2023

Abstract
Background
Melophagus ovinus is considered to be of great veterinary health significance. However, little is known about the information on genetic mechanisms of the specific biological characteristics and novel methods for controlling M. ovinus.

Results
In total, the de novo genome assembly of M. ovinus was 188.421 Mb in size (330 scaffolds, N50 Length: 10.666 Mb), with a mean GC content of 27.74%. A total of 13,372 protein-coding genes were functionally annotated. Phylogenetic analysis indicated that the diversification of M. ovinus and Glossina fuscipes took place 72.76 Mya within the Late Cretaceous. Gene family expansion and contraction analysis revealed that M. ovinus has 65 rapidly-evolving families (26 expansion and 39 contractions) mainly involved DNA metabolic activity, transposases activity, odorant receptor 59a/67d-like, IMD domain-containing protein, and cuticle protein, etc. The universal and tightly conserved list of milk protein orthologues has been assembled from the genome of M. ovinus. Contractions and losses of sensory receptors and vision-associated Rhodopsin genes were significant in M. ovinus, which indicate that the M. ovinus has narrower ecological niches.

Conclusions
We sequenced, assembled, and annotated the whole genome sequence of M. ovinus, and launches into the preliminary genetic mechanisms analysis of the adaptive evolution characteristics of M. ovinus. These resources will provide insights to understand the biological underpinnings of this parasite and the disease control strategies.
No need for a gold-standard test: on the mining of diagnostic test performance indices merely based on the distribution of the test value
Authors: Habibzadeh Farrokh , Roozbehi Hooman 
Published: January 2023

Abstract
Background
Diagnostic tests are important in clinical medicine. To determine the test performance indices — test sensitivity, specificity, likelihood ratio, predictive values, etc. — the test results should be compared against a gold-standard test. Herein, a technique is presented through which the aforementioned indices can be computed merely based on the shape of the probability distribution of the test results, presuming an educated guess.

Methods
We present the application of the technique to the probability distribution of hepatitis B surface antigen measured in a group of people in Shiraz, southern Iran. We assumed that the distribution had two latent subpopulations — one for those without the disease, and another for those with the disease. We used a nonlinear curve fitting technique to figure out the parameters of these two latent populations based on which we calculated the performance indices.

Results
The model could explain > 99% of the variance observed. The results were in good agreement with those obtained from other studies.

Conclusion
We concluded that if we have an appropriate educated guess about the distributions of test results in the population with and without the disease, we may harvest the test performance indices merely based on the probability distribution of the test value without need for a gold standard. The method is particularly suitable for conditions where there is no gold standard or the gold standard is not readily available.
Clinical and genomic features in patients with second primary glioblastoma following first primary renal cell carcinoma
Authors: Zhang Guang-Tao , Liu Qi , Zuo Fu-Xing , Liu Hou-Jie , Wang Song-Quan , Yuan Qing , Liu Ang-Si , Hu Ke , Meng Xiao-Li , Wang Wei-Jia , Qian Hai-Peng , Wan Jing-Hai , Cai Hong-Qing 
Published: January 2023

Abstract
Purpose
To explore the potential pathogenesis and clinical features of second primary glioblastoma (spGBM) following first primary renal cell carcinoma (fpRCC).

Methods
Patients with spGBM after fpRCC were enrolled from our institution and the SEER dataset. Sanger sequencing, whole genome sequencing, and immunehistochemistry were used to detect molecular biomarkers.

Results
Four and 122 cases from our institution and the SEER dataset, respectively, were collected with an overall median age of 69 years at spGBM diagnosis following fpRCC. The median interval time between fpRCC and spGBM was 50.7 months and 4 years, for the four and 122 cases respectively. The median overall survival time was 11.2 and 6.0 months for the two datasets. In addition, spGBM patients of younger age (< 75 years) or shorter interval time (< 1 year) had favorable prognosis (p = 0.081 and 0.05, respectively). Moreover, the spGBM cases were molecularly classified as TERT only paired with TP53 mutation, PIK3CA mutation, EGFR alteration, low tumor mutation burden, and stable microsatellite status.

Conclusions
This is the first study to investigate the pathogenesis and clinical features of spGBM following spRCC. We found that spGBMs are old-age related, highly malignant, and have short survival time. Moreover, they might be misdiagnosed and treated as brain metastases from RCC. Thus, the incidence of spGBMs after fpRCC is underestimated. Further studies are needed to investigate the underlying molecular mechanisms and clinical biomarkers for the development of spGBM following fpRCC.
Prevalence of and factors associated with alexithymia among patients with chronic obstructive pulmonary disease in China: a cross-sectional study
Authors: Zhang Huaizhong , Wang Yixuan , Lou Heqing , Zhu Yanan , Dong Zongmei , Dong Dong , Chen Peipei , Zhu Xuan , Chen Bi , Zhang Pan 
Published: January 2023

Abstract
Background
Alexithymia is a common psychological disorder. However, few studies have investigated its prevalence and predictors in patients with chronic obstructive pulmonary disease (COPD). Therefore, we aimed to determine the prevalence and predictors of alexithymia in Chinese patients.

Methods
This cross-sectional study included 842 COPD patients to assess the prevalence and predictors of alexithymia using the 20-item Toronto Alexithymia Scale (TAS-20). We used the Hospital Anxiety and Depression Scale (HADS) to assess anxiety and depression, the modified British Medical Research Council dyspnea Rating Scale (mMRC) to assess dyspnea, St. George's Respiratory Questionnaire (SGRQ) to assess quality of life, and the age-adjusted Charlson comorbidity index (ACCI) to assess comorbidities. Alexithymia-related predictors were identified using univariate and multivariate logistic regression analyses.

Results
The prevalence of alexithymia in COPD patients was 23.6% (199/842). Multivariate analysis showed that age [odds ratio (OR) 0.886; 95% confidence interval (CI) 0.794–0.998], body mass index (OR 0.879; 95% CI 0.781–0.989), HADS-anxiety (OR 1.238; 95% CI 1.097–1.396), HADS-depression (OR 1.178; 95% CI 1.034–1.340), mMRC (OR 1.297; 95% CI 1.274–1.320), SGRQ (OR 1.627; 95% CI 1.401–1.890), ACCI (OR 1.165; 95% CI 1.051–1.280), and GOLD grade (OR 1.296; 95% CI 1.256–1.337) were independent predictors for alexithymia in patients with COPD.

Conclusions
The prevalence of alexithymia was high in Chinese COPD patients. Anxiety, depression, dyspnea, quality of life, comorbidities, and disease severity are independent risk factors, and age and BMI are predictive factors for alexithymia in COPD patients.