bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new analytic framework for prediction of migration patterns and locations of historical manuscripts based on their script types
Authors: Prebor Gila , Zhitomirsky-Geffet Maayan , Miller Yitzchak 
Published: May 2019

Abstract
In this article, we utilized large-scale statistical analysis and data visualization techniques of the greatest collection in the world of Hebrew manuscript metadata records to develop a new methodology for quantitative investigation of the palaeographic, geographic, and temporal characteristics of historical manuscripts. The study aims to explore whether and to what extent the script type of the manuscript and its changes over time can be used to automatically predict and complete missing geospatial data of the manuscripts. To this end, various ontological entities were used as features to train supervised machine-learning algorithms to predict the places of writing of manuscripts which were often absent in the catalogue records. The obtained results show that while the script type as an only feature might not be sufficient for prediction of the location of the manuscript’s writing, its combination with temporal data of the manuscript yielded about 80% accuracy. Eventually, our system was able to complete the missing places of writing for over 60% of the manuscripts in the corpus. Moreover, we found that through typical and marginal script types in different regions and their changes over time, it is possible to draw the migration map of the Jewish communities over the centuries. This reinforces the findings of historical research on Jewish migration patterns and communal formation. For example, the waves of immigration from Western Europe can be seen clearly from the second half of the 13th century, which continued until the 17th century and greatly increased the Eastern European Jewish community.
Usefulness of ICU criteria for diagnosis of invasive pulmonary aspergillosis in nonhematologic critically ill patients
Authors: Lee Song-I , Sung Heungsup , Hong Sang-Bum , Lim Chae-Man , Koh Younsuck , Huh Jin-Won 
Published: May 2019

Abstract
Invasive pulmonary aspergillosis (IPA) is a life-threatening disease in the intensive care unit (ICU). The ICU criteria were proposed to diagnose IPA in critically ill patients. This study aims to evaluate the usefulness of ICU criteria for diagnosis and treatment of IPA in nonhematologic patients in the ICU. We retrospectively reviewed 103 ICU patients with positive galactomannan test in blood and respiratory tract from January 1, 2016, to May 31, 2017. We excluded patients with hematologic malignancy. We divided the treatment and non-treatment groups according to the IPA treatment. We compared the baseline characteristics and outcomes between two groups and the agreement with ICU criteria. There were 49 patients in treatment groups and 54 patients in non-treatment groups. There were more cases of solid organ transplantation (P = .003), immunosuppressive therapy (P &lt; .001) and bacterial viral coinfection (P = .048) in the treatment group compared to nontreatment group. There was no statistically significant difference in mortality, the use of ventilator, and septic shock between the two groups. The agreement rate between the putative group and treatment was low (59.2%). There was no statistically significant difference in outcome between the putative and colonization groups according to the ICU criteria in each group. The treatment of IPA based on the symptom, radiologic finding and galactomannan test did not showed the better outcome. Also, the treatment based on the ICU criteria didn’t show the difference of outcome. The new criteria for diagnosis of IPA in critically ill patients are needed.
A near-infrared study of the multiphase outflow in the type-2 quasar J1509+0434
Authors: Ramos Almeida C , Acosta-Pulido J A , Tadhunter C N , González-Fernández C , Cicone C , Fernández-Torreiro M 
Published: May 2019

ABSTRACT
Based on new near-infrared spectroscopic data from the instrument Espectrógrafo Multiobjeto Infra-Rojo (EMIR) on the 10.4 m Gran Telescopio Canarias, we report the presence of an ionized and warm molecular outflow in the luminous type-2 quasar J150904.22+043441.8 (z = 0.1118). The ionized outflow is faster than its molecular counterpart, although the outflow sizes that we derive for them are consistent within the errors (1.34 ± 0.18 and 1.46 ± 0.20 kpc, respectively). We use these radii, the broad emission-line luminosities and in the case of the ionized outflow, the density calculated from the trans-auroral [O ii] and [S ii] lines, to derive mass outflow rates and kinetic coupling efficiencies. While the ionized and warm molecular outflows represent a small fraction of the AGN power (≤0.033 and 0.0001 per cent of Lbol, respectively), the total molecular outflow, whose mass is estimated from an assumed warm-to-cold gas mass ratio of 6 × 10−5, has a kinetic coupling efficiency of ∼1.7 per cent Lbol. Despite the large uncertainty, this molecular outflow represents a significant fraction ofLbol and it could potentially have a significant impact on the host galaxy. In addition, the quasar spectrum reveals bright and patchy narrow Paα emission extending out to 4 arcsec (8 kpc) south-east and north-west from the active nucleus.
Prophage Hunter: an integrative hunting tool for active prophages
Authors: Song Wenchen , Sun Hai-Xi , Zhang Carolyn , Cheng Li , Peng Ye , Deng Ziqing , Wang Dan , Wang Yun , Hu Ming , Liu Wenen , Yang Huanming , Shen Yue , Li Junhua , You Lingchong , Xiao Minfeng 
Published: May 2019

Abstract
Identifying active prophages is critical for studying coevolution of phage and bacteria, investigating phage physiology and biochemistry, and engineering designer phages for diverse applications. We present Prophage Hunter, a tool aimed at hunting for active prophages from whole genome assembly of bacteria. Combining sequence similarity-based matching and genetic features-based machine learning classification, we developed a novel scoring system that exhibits higher accuracy than current tools in predicting active prophages on the validation datasets. The option of skipping similarity matching is also available so that there's higher chance for novel phages to be discovered. Prophage Hunter provides a one-stop web service to extract prophage genomes from bacterial genomes, evaluate the activity of the prophages, identify phylogenetically related phages, and annotate the function of phage proteins. Prophage Hunter is freely available at https://pro-hunter.bgi.com/.
Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome
Authors: Hwang Soonkyu , Lee Namil , Jeong Yujin , Lee Yongjae , Kim Woori , Cho Suhyung , Palsson Bernhard O , Cho Byung-Kwan 
Published: May 2019

AbstractDetermining transcriptional and translational regulatory elements in GC-rich Streptomyces genomes is essential to elucidating the complex regulatory networks that govern secondary metabolite biosynthetic gene cluster (BGC) expression. However, information about such regulatory elements has been limited for Streptomyces genomes. To address this limitation, a high-quality genome sequence of β-lactam antibiotic-producing Streptomyces clavuligerus ATCC 27 064 is completed, which contains 7163 newly annotated genes. This provides a fundamental reference genome sequence to integrate multiple genome-scale data types, including dRNA-Seq, RNA-Seq and ribosome profiling. Data integration results in the precise determination of 2659 transcription start sites which reveal transcriptional and translational regulatory elements, including −10 and −35 promoter components specific to sigma (σ) factors, and 5′-untranslated region as a determinant for translation efficiency regulation. Particularly, sequence analysis of a wide diversity of the −35 components enables us to predict potential σ-factor regulons, along with various spacer lengths between the −10 and −35 elements. At last, the primary transcriptome landscape of the β-lactam biosynthetic pathway is analyzed, suggesting temporal changes in metabolism for the synthesis of secondary metabolites driven by transcriptional regulation. This comprehensive genetic information provides a versatile genetic resource for rational engineering of secondary metabolite BGCs in Streptomyces.
Understanding mitochondrial DNA maintenance disorders at the single muscle fibre level
Authors: Lehmann Diana , Tuppen Helen A L , Campbell Georgia E , Alston Charlotte L , Lawless Conor , Rosa Hannah S , Rocha Mariana C , Reeve Amy K , Nicholls Thomas J , Deschauer Marcus , Zierz Stephan , Taylor Robert W , Turnbull Doug M , Vincent Amy E 
Published: May 2019

Abstract
Clonal expansion of mitochondrial DNA (mtDNA) deletions is an important pathological mechanism in adults with mtDNA maintenance disorders, leading to a mosaic mitochondrial respiratory chain deficiency in skeletal muscle. This study had two aims: (i) to determine if different Mendelian mtDNA maintenance disorders showed similar pattern of mtDNA deletions and respiratory chain deficiency and (ii) to investigate the correlation between the mitochondrial genetic defect and corresponding respiratory chain deficiency. We performed a quantitative analysis of respiratory chain deficiency, at a single cell level, in a cohort of patients with mutations in mtDNA maintenance genes. Using the same tissue section, we performed laser microdissection and single cell genetic analysis to investigate the relationship between mtDNA deletion characteristics and the respiratory chain deficiency. The pattern of respiratory chain deficiency is similar with different genetic defects. We demonstrate a clear correlation between the level of mtDNA deletion and extent of respiratory chain deficiency within a single cell. Long-range and single molecule PCR shows the presence of multiple mtDNA deletions in approximately one-third of all muscle fibres. We did not detect evidence of a replicative advantage for smaller mtDNA molecules in the majority of fibres, but further analysis is needed to provide conclusive evidence.
A kinetochore-based ATM/ATR-independent DNA damage checkpoint maintains genomic integrity in trypanosomes
Authors: Zhou Qing , Pham Kieu T M , Hu Huiqing , Kurasawa Yasuhiro , Li Ziyin 
Published: May 2019

AbstractDNA damage-induced cell cycle checkpoints serve as surveillance mechanisms to maintain genomic stability, and are regulated by ATM/ATR-mediated signaling pathways that are conserved from yeast to humans. Trypanosoma brucei, an early divergent microbial eukaryote, lacks key components of the conventional DNA damage-induced G2/M cell cycle checkpoint and the spindle assembly checkpoint, and nothing is known about how T. brucei controls its cell cycle checkpoints. Here we discover a kinetochore-based, DNA damage-induced metaphase checkpoint in T. brucei. MMS-induced DNA damage triggers a metaphase arrest by modulating the abundance of the outer kinetochore protein KKIP5 in an Aurora B kinase- and kinetochore-dependent, but ATM/ATR-independent manner. Overexpression of KKIP5 arrests cells at metaphase through stabilizing the mitotic cyclin CYC6 and the cohesin subunit SCC1, mimicking DNA damage-induced metaphase arrest, whereas depletion of KKIP5 alleviates the DNA damage-induced metaphase arrest and causes chromosome mis-segregation and aneuploidy. These findings suggest that trypanosomes employ a novel DNA damage-induced metaphase checkpoint to maintain genomic integrity.
Understanding the role of the cytoprotective transcription factor nuclear factor erythroid 2-related factor 2—lessons from evolution, the animal kingdom and rare progeroid syndromes
Authors: Stenvinkel Peter , Meyer Colin J , Block Geoffrey A , Chertow Glenn M , Shiels Paul G 
Published: May 2019

Abstract
The cytoprotective transcriptor factor nuclear factor erythroid 2– related factor 2 (NRF2) is part of a complex regulatory network that responds to environmental cues. To better understand its role in a cluster of inflammatory and pro-oxidative burden of lifestyle diseases that accumulate with age, lessons can be learned from evolution, the animal kingdom and progeroid syndromes. When levels of oxygen increased in the atmosphere, mammals required ways to protect themselves from the metabolic toxicity that arose from the production of reactive oxygen species. The evolutionary origin of the NRF2–Kelch-like ECH-associated protein 1 (KEAP1) signalling pathway from primitive origins has been a prerequisite for a successful life on earth, with checkpoints in antioxidant gene expression, inflammation, detoxification and protein homoeostasis. Examples from the animal kingdom suggest that superior antioxidant defense mechanisms with enhanced NRF2 expression have been developed during evolution to protect animals during extreme environmental conditions, such as deep sea diving, hibernation and habitual hypoxia. The NRF2–KEAP1 signalling pathway is repressed in progeroid (accelerated ageing) syndromes and a cluster of burden of lifestyle disorders that accumulate with age. Compelling links exist between tissue hypoxia, senescence and a repressed NRF2 system. Effects of interventions that activate NRF2, including nutrients, and more potent (semi)synthetic NRF2 agonists on clinical outcomes are of major interest. Given the broad-ranging actions of NRF2, we need to better understand the mechanisms of activation, biological function and regulation of NRF2 and its inhibitor, KEAP1, in different clinical conditions to ensure that modulation of this thiol-based system will not result in major adverse effects. Lessons from evolution, the animal kingdom and conditions of accelerated ageing clarify a major role of a controlled NRF2–KEAP1 system in healthy ageing and well-being.
The Safety and Efficacy of Continuous Tirofiban as a Monoantiplatelet Therapy in the Management of Ruptured Aneurysms Treated Using Stent-Assisted Coiling or Flow Diversion and Requiring Ventricular Drainage
Authors: Limaye Kaustubh , Zanaty Mario , Hudson Joseph , Nakagawa Daichi , Al Kasab Sami , Alvarez Carlos , Dandapat Sudeepta , Kung David K , Ortega-Gutierrez Santiago , Jabbour Pascal , Samaniego Edgar A , Hasan David 
Published: May 2019

Abstract

BACKGROUND
Hemorrhagic complications are a major concern for aneurysmal subarachnoid hemorrhage patients treated with stenting or stent-assisted coiling and undergoing additional procedures such as shunting, ventriculostomy placement, and craniotomies/craniectomies.

OBJECTIVE
To assess the safety and efficacy of using a continuous infusion of tirofiban as a monoantiplatelet therapy in the management of ruptured aneurysms in the setting of either stent-assisted coiling (SAC) or flow diversion devices (FDD) in patients requiring either an external ventricular drain (EVD) or ventriculoperitoneal shunt (VPS).

METHODS
Aneurysmal subarachnoid hemorrhage (aSAH) patients between July 2017 and September 2018 who were treated with SAC or FDD were started on a continuous tirofiban infusion protocol (0.10 μg/kg/min) with no preceding loading dose as a monoantiplatelet therapy. Safety analysis was performed retrospectively to assess the complication rate, hemorrhagic rate, and rate of ischemic events. There were no hemorrhages related to the VPS surgery.

RESULTS
Nineteen subjects were included in the series. The patients received a total of 25 procedures that included 19 EVDs and 6 VPSs. Two patients (8.3%) developed small asymptomatic track hemorrhages after EVD placement. One patient developed a large retroperitoneal hemorrhage due to renal artery branch injury during procedure, and another patient developed an idiosyncratic transient thrombocytopenia which resolved after stopping the medication. One patient (4%) developed a transient ischemic attack, which resolved after a bolus of tirofiban.

CONCLUSION
Our study suggests that long-term use of intravenous tirofiban monotherapy in aSAH subjects for endovascular SAC or FDD is safe in the perioperative setting.
Does Neck Disability Index Correlate With 12-Month Satisfaction After Elective Surgery for Cervical Radiculopathy? Results From a National Spine Registry
Authors: Khan Inamullah , Sivaganesan Ahilan , Archer Kristin R , Bydon Mohamad , McGirt Matthew J , Nian Hui , Harrell Frank E , Foley Kevin T , Mummaneni Praveen V , Bisson Erica F , Shaffrey Christopher , Harbaugh Robert , Asher Anthony L , Devin Clinton J ,   QOD Vanguard Sites, Asher Anthony L , McGirt Matthew J , Devin Clinton J , Foley Kevin T , Sorenson Jeffrey M , Briggs Thomas B , Kremer Adam , Griffitt Wesley E , Bisson Erica F , Shaffrey Mark E , Shaffrey Christopher , Fassett Daniel , Oetting Gregory , Elowitz Eric H , Rumana Christopher 
Published: May 2019

Abstract

BACKGROUND
Modern healthcare reforms focus on identifying and measuring the quality and value of care. Patient satisfaction is particularly important in the management of degenerative cervical radiculopathy (DCR) since it leads to significant neck pain and disability primarily affecting the patients’ quality of life.

OBJECTIVE
To determine the association of baseline and 12-mo Neck Disability Index (NDI) with patient satisfaction after elective surgery for DCR.

METHODS
The Quality Outcomes Database cervical module was queried for patients who underwent elective surgery for DCR. A multivariable proportional odds regression model was fitted with 12-mo satisfaction as the outcome. The covariates for this model included patients’ demographics, surgical characteristics, and baseline and 12-mo patient reported outcomes (PROs). Wald-statistics were calculated to determine the relative importance of each independent variable for 12-mo patient satisfaction.

RESULTS
The analysis included 2206 patients who underwent elective surgery for DCR. In multivariable analysis, after adjusting for baseline and surgery specific variables, the 12-mo NDI score showed the highest association with 12-mo satisfaction (Waldχ2-df = 99.17, 58.1% of total χ2). The level of satisfaction increases with decrease in 12-mo NDI score regardless of the baseline NDI score.

CONCLUSION
Our study identifies 12-mo NDI score as a very influential driver of 12-mo patient satisfaction after surgery for DCR. In addition, there are lesser contributions from other 12-mo PROs, baseline Numeric Rating Scale for arm pain and American Society of Anesthesiologists (ASA) grade. The baseline level of disability was found to be irrelevant to patients. They seemed to only value their current level of disability, compared to baseline, in rating satisfaction with surgical outcome.
Relationship between arginine intake in parenteral nutrition and preterm neonatal population plasma arginine concentrations: a systematic review
Authors: Premakumar Chandini M , Turner Mark A , Morgan Colin 
Published: May 2019

AbstractContextVery preterm neonates (VPNs) are unable to digest breast milk and therefore rely on parenteral nutrition (PN) formulations. This systematic review was prepared following PRISMA-P 2015 guidelines. For the purpose of this review, desirable mean plasma arginine concentration is defined as ≥80 micromoles/L.ObjectiveThe review was performed to answer the following research question: “In VPNs, are high amounts of arginine in PN, compared with low amounts of arginine, associated with appropriate circulating concentrations of arginine?” Therefore, the aims were to 1) quantify the relationship between parenteral arginine intakes and plasma arginine concentrations in PN-dependent VPNs; 2) identify any features of study design that affect this relationship; and 3) estimate the target parenteral arginine dose to achieve desirable preterm plasma arginine concentrations.Data SourcesThe PubMed, Scopus, Web of Science, and Cochrane databases were searched regardless of study design; review articles were not included.Data ExtractionOnly articles that discussed amino acid (AA) intake and measured plasma AA profile post PN in VPNs were included. Data were obtained using a data extraction checklist that was devised for the purpose of this review.Data AnalysisTwelve articles met the inclusion criteria. The dose–concentration relationship of arginine content (%) and absolute arginine intake (mg/(kg × d)) with plasma arginine concentrations showed a significant positive correlation (P < 0.001).ConclusionFuture studies using AA solutions with arginine content of 17%–20% and protein intakes of 3.5–4.0 g/kg per day may be needed to achieve higher plasma arginine concentrations.
Speaking for the People in Early Modern England*
Authors: Coast David 
Published: May 2019

Abstract
The voice of the people is assumed to have carried little authority in early modern England. Elites often caricatured the common people as an ignorant multitude and demanded their obedience, deference and silence. Hostility to the popular voice was an important element of contemporary political thought. However, evidence for a very different set of views can be found in numerous polemical tracts written between the Reformation and the English Civil War. These tracts claimed to speak for the people, and sought to represent their alleged grievances to the monarch or parliament. They subverted the rules of petitioning by speaking for ‘the people’ as a whole and appealing to a wide audience, making demands for the redress of grievances that left little room for the royal prerogative. In doing so, they contradicted stereotypes about the multitude, arguing that the people were rational, patriotic and potentially better informed about the threats to the kingdom than the monarch themselves. ‘Public opinion’ was used to confer legitimacy on political and religious demands long before the mass subscription petitioning campaigns of the 1640s.
Factors associated with undiagnosed type II diabetes mellitus, undiagnosed impaired fasting glucose and these patients’ quality of life in Lebanon
Authors: Hallit Souheil , Saade Sylvia , Zeidan Rouba Karen , Iskandar Katia , Kheir Nelly , Youssef Lara , Costantine Rachelle , Hallit Rabih , Salameh Pascale 
Published: May 2019

AbstractObjectiveTo assess the association between undiagnosed impaired fasting glucose (UIFG) and diabetes (UD), their risk factors and the patients’ knowledge about diabetes and their quality of life (QOL).MethodsA cross-sectional study was conducted between May and September 2017 in four laboratories enrolling 495 patients. We used the Diabetes Knowledge and SF-12 questionnaires to assess the patients’ knowledge about diabetes and QOL. This study meets the Wilson and Jungner criteria for disease screening.ResultsA higher knowledge score (ORa = 0.85) was significantly associated with the absence of diabetes compared to UPD, whereas an increased age (ORa = 1.2) and a positive family history of diabetes (ORa = 1.81) were significantly associated with higher odds of UPD. An increased knowledge score (ORa = 0.55) was significantly associated with an absence of diabetes compared to UD, whereas an increased BMI (ORa = 1.40) and an increased age (ORa = 1.07) were associated with increased odds of having UD.UD (Beta = −5.799) was significantly associated with decreased total physical component QOL score, whereas increased diabetes knowledge score (Beta = 0.415) was significantly associated with increased physical QOL. A higher diabetes knowledge score (Beta = 0.459) were associated with increased mental QOL.ConclusionSeeing the relatively high percentage of UD and UIFG, we propose that screening should be considered and subject to proper assessment in the light of the findings of this study.