bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Harmonization and Standardization of Expanded Newborn Screening Results by Optimization of the Legacy Flow Injection Analysis Tandem Mass Spectrometry Methods and Application of a Standardized Calibration Approach
Authors: Carling Rachel S , Whyte Emily , John Catharine , Garstone Rachelle , Goddard Philippa , Greenfield Toby , Hogg Sarah L , Le Masurier Clare , Cowen Simon , Moat Stuart J , Hopley Christopher 
Published: April 2022

Abstract

Background
Newborn screening (NBS) laboratories in the United Kingdom adhere to common protocols based on single analyte cutoff values (COVs); therefore, interlaboratory harmonization is of paramount importance. Interlaboratory variation for screening analytes in UK NBS laboratories ranges from 17% to 59%. While using common stable isotope internal standards has been shown to significantly reduce interlaboratory variation, instrument set-up, sample extraction, and calibration approach are also key factors.

Methods
Dried blood spot (DBS) extraction processes, instrument set-up, mobile-phase composition, sample introduction technique, and calibration approach of flow injection analysis–tandem mass spectrometry (FIA-MS/MS) methods were optimized. Inter- and intralaboratory variation of methionine, leucine, phenylalanine, tyrosine, isovaleryl-carnitine, glutaryl-carnitine, octanoyl-carnitine, and decanoyl-carnitine were determined pre- and postoptimization, using 3 different calibration approaches.

Results
Optimal recovery of analytes from DBS was achieved with a 35-min extraction time and 80% methanol (150 μL). Optimized methodology decreased the mean intralaboratory percentage relative SD (%RSD) for the 8 analytes from 20.7% (range 4.1–46.0) to 5.4% (range 3.0–8.5). The alternative calibration approach reduced the mean interlaboratory %RSD for all analytes from 16.8% (range 4.1–25.0) to 7.1% (range 4.1–11.0). Nuclear magnetic resonance analysis of the calibration material highlighted the need for standardization. The purities of isovaleryl-carnitine and glutaryl-carnitine were 85.13% and 69.94% respectively, below the manufacturer’s stated values of ≥98%.

Conclusions
For NBS programs provided by multiple laboratories using single analyte COVs, harmonization and standardization of results can be achieved by optimizing legacy FIA-MS/MS methods, adopting a common analytical protocol, and using standardized calibration material rather than internal calibration.
Tactics And Techniques Classification In Cyber Threat Intelligence
Authors: Yu Zhongkun , Wang JunFeng , Tang BinHui , Lu Li 
Published: April 2022

Abstract
Completing the classification of tactics and techniques in cyber threat intelligence (CTI) is an important way to obtain tactics, techniques and procedures (TTPs) and portray the behavior of cyber attacks. However, the high level of abstraction of tactics and techniques information and their presence in CTI, usually in the form of natural language text, make it difficult for traditional manual analysis methods and feature engineering-based machine learning methods to complete the classification of tactics and techniques effectively. Meanwhile, flat deep learning methods do not perform well in classifying more fine-grained techniques due to their inability to exploit the hierarchical relationship between tactics and techniques. Therefore, this paper regards the tactics and techniques of TTPs defined in Adversarial Tactics, Techniques and Common Knowledge knowledge base as labels and proposes a Convolutional Neural Network (CNN) model based on hierarchical knowledge migration and attention mechanism for classifying tactics and techniques in CTI, named HM-ACNN (CNN based on hierarchical knowledge migration and attention mechanism). HM-ACNN classifies tactics and techniques into two phases, and the underlying network model for both phases is the Attention-based CNN network. The first step in HM-ACNN is converting the CTI text into a two-dimensional image based on the word embedding model, and then start training the classification of tactics through the CNN structure based on the attention mechanism before the classification of techniques. Secondly, after the tactics classification training is completed, the tactic-to-technique knowledge migration is then completed by transforming the parameters of the CNN layer and the attention layer in the tactics classification process based on the special hierarchical relationship between tactics and techniques. Then, the classification of techniques is finished by fine-tuning. The experimental results show that HM-ACNN performs well in the tactics and techniques classification tasks, and the metric F1 values reach 93.66% and 86.29%, which are better than other models such as CNN, Recurrent Neural Network and CRNN (Recurrent Convolutional Neural Networks).
Survival estimates across five life stages of redfin (Perca fluviatilis) exposed to simulated pumped-storage hydropower stressors
Authors: Doyle Katherine E , Ning Nathan , Silva Luiz G M , Brambilla Eduardo M , Deng Z Daniel , Fu Tao , Boys Craig , Robinson Wayne , du Preez Jan A , Baumgartner Lee J 
Published: April 2022

Abstract
The global prevalence of pumped-storage hydropower (PSH) is expected to grow exponentially as countries transition to renewable energy sources. Compared to conventional hydropower, little is currently known regarding PSH impacts on aquatic biota. This study estimated the survival of five life stages (egg, two larval stages, juvenile and adult) of redfin (European) perch (Perca fluviatilis) following passage through a PSH facility during the pumping phase. This was achieved by simulating the individual stressors expected to occur during passage through a 2000-MW PSH facility using laboratory-simulated (shear strain and extreme compression) and modelling (blade strike, BS) approaches. Our results indicate that redfin could survive the shear, pressure and BS stressors expected within the PSH facility, but impacts varied among life stages. Juvenile survival was &gt;70% across all shear strain rates, while the survival of eggs and larvae declined markedly as strain rate increased. All life stages had high survival when exposed to rapid compression and BS. The high survival of redfin to the stressors tested suggests the PSH facility could facilitate the passage of redfin during the pumping phase from the lower to the higher elevation reservoir. This outcome would be welcomed in situations where the species is native, but could have adverse implications for the conservation of native biota where the species is considered a pest.
Induced bacterial sickness causes inflammation but not blood oxidative stress in Egyptian fruit bats (Rousettus aegyptiacus)
Authors: Costantini David , Weinberg Maya , Jordán Lilla , Moreno Kelsey R , Yovel Yossi , Czirják Gábor Á 
Published: April 2022

Abstract
Bats are particularly interesting vertebrates in their response to pathogens owing to extremes in terms of tolerance and resistance. Oxidation is often a by-product of processes involved in the acute phase response, which may result in antimicrobial or self-damaging effects. We measured the immunological and oxidative status responses of Egyptian fruit bats (Rousettus aegyptiacus) to a simulated bacterial infection using lipopolysaccharide injection. As expected, experimental bats exhibited increases in two humoral immunological markers. However, they surprisingly did not show any effects across two markers of oxidative damage and four antioxidant markers. We propose that this lack of effects on oxidative status may be due to a reduction in cell metabolism through sickness behaviours or given life history traits, such as a long lifespan and a frugivorous diet. Finally, the consistency in the pattern of elevation in haptoglobin and lysozyme between current and previous findings highlights their utility as diagnostic markers for extracellular infections in bats.
Development of an amphibian sperm biobanking protocol for genetic management and population sustainability
Authors: Burger Isabella J , Lampert Shaina S , Kouba Carrie K , Morin Dana J , Kouba Andrew J 
Published: April 2022

AbstractSperm cryopreservation is a vital tool in amphibian assisted reproductive technologies that aids in genetic and population management, specifically for at-risk species. Significant advancements have been made in the cryopreservation of amphibian sperm, yet there is little information on how the cryopreservation process influences fertilization and embryonic development. In this study, we tested several cryoprotective agents (CPAs) and freezing rates on sperm recovery, fertilization potential and embryo development using Fowler’s toads (Anaxyrus fowleri) as a model amphibian species for application to at-risk anurans. Three cryoprotectant treatments were tested, which included 10% trehalose + 0.25% bovine serum albumin with (1) 5% N,N-dimethylformamide (DMFA); (2) 10% DMFA; or (3) 10% dimethyl sulfoxide (DMSO). Additionally, sperm in each cryoprotectant was frozen at two different rates, −32 to −45°C/min and −20 to −29°C/min. Post-thaw sperm analysis included motility, morphology, viability, fertilization success and embryo development. Results show that 10% DMFA produced significantly higher (P = 0.005) post-thaw sperm motility than 5% DMFA and was similar to 10% DMSO. Furthermore, sperm frozen at −32 to −45°C/min had significantly higher post-thaw motility (P &lt; 0.001) compared to sperm frozen at −20 to −29°C/min. We also found that embryos fertilized with sperm frozen with 5% DMFA resulted in significantly higher (P = 0.02) cleavage than 10% DMSO, yet there was no other effect of CPA on fertilization or embryo development. Furthermore, embryos fertilized with sperm frozen at −32 to −45°C/min resulted in significantly higher cleavage (P = 0.001), neurulation (P = 0.001) and hatching (P = 0.002) numbers than sperm frozen at a rate of −20 to −29°C/min. Overall, eggs fertilized with frozen–thawed sperm produced 1327 tadpoles. These results provide insight towards a biobanking strategy that can be applied to imperilled species to preserve genetic lineages and bolster offspring genetic diversity for reintroduction.
On the idea of failure in Vergilian translation
Authors: Belle Marie-Alice 
Published: April 2022

AbstractThis article examines the idea of failure (and its corollary, success) in the critical discourse surrounding translations of Vergil’s works in the English-speaking world. Focusing mainly on (early) modern English translations of the Aeneid, with a few inroads into other Vergilian translation traditions, it identifies the main criteria for failure or success and situates them in their historical context. It also discusses the relationship between such judgements of value and the evolving — or, at times, conflicting — linguistic, aesthetic, social, and political norms surrounding the translation of Vergil’s poetry. The essay is an invitation to re-examine our own criteria for failure and success, through an increased awareness of their historical and cultural underpinnings.
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants
Authors: Desai Sanket , Mishra Rohit , Ahmad Suhail , Hait Supriya , Joshi Asim , Dutt Amit 
Published: April 2022

AbstractCancer is a somatic disease. The lack of Indian-specific reference germline variation resources limits the ability to identify true cancer-associated somatic variants among Indian cancer patients. We integrate two recent studies, the GenomeAsia 100K and the Genomics for Public Health in India (IndiGen) program, describing genome sequence variations across 598 and 1029 healthy individuals of Indian origin, respectively, along with the unique variants generated from our in-house 173 normal germline samples derived from cancer patients to generate the Tata Memorial Centre-SNP database (TMC-SNPdb) 2.0. To show its utility, GATK/Mutect2-based somatic variant calling was performed on 224 in-house tumor samples to demonstrate a reduction in false-positive somatic variants. In addition to the ethnic-specific variants from GenomeAsia 100K and IndiGenomes databases, 305 132 unique variants generated from 173 in-house normal germline samples derived from cancer patients of Indian origin constitute the Indian specific, TMC-SNPdb 2.0. Of 305 132 unique variants, 11.13% were found in the coding region with missense variants (31.3%) as the most predominant category. Among the non-coding variations, intronic variants (49%) were the highest contributors. The non-synonymous to synonymous SNP ratio was observed to be 1.9, consistent with the previous version of TMC-SNPdb and literature. Using TMC SNPdb 2.0, we analyzed a whole-exome sequence from 224 in-house tumor samples (180 paired and 44 orphans). We show an average depletion of 3.44% variants per paired tumor and significantly higher depletion (P-value &lt; 0.001) for orphan tumors (4.21%), demonstrating the utility of the rare, unique variants found in the ethnic-specific variant datasets in reducing the false-positive somatic mutations. TMC-SNPdb 2.0 is the most exhaustive open-source reference database of germline variants occurring across 1800 Indian individuals to analyze cancer genomes and other genetic disorders. The database and toolkit package is available for download at the following:Database URL http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNPdb2/TMCSNPdb2.html
Working Memory-Based Cognitive Rehabilitation: Spoken Language of Deaf and Hard-of-Hearing Children
Authors: Ashori Mohammad 
Published: April 2022

AbstractThis research examined the effect of the Working Memory-based Cognitive Rehabilitation (WMCR) intervention on the spoken language development of deaf and hard-of-hearing (DHH) children. In this clinical trial study, 28 DHH children aged between 5 and 6 years were selected by random sampling method. The participants were randomly assigned to experimental and control groups. The experimental group participated in the WMCR intervention involving 11 sessions. All participants were assessed pre-and postintervention. Data were collected by the Newsha Development Scale and analyzed through MANCOVA. The results revealed a significant difference between the scores of the receptive and expressive language of the experimental group that were exposed to the WMCR intervention compared with the control group. The receptive and expressive language skills of the experimental group indicated a significant improvement after the intervention. Therefore, the WMCR intervention is an effective method that affects the spoken language skills of DHH children. These findings have critical implications for teachers, parents, and therapists in supporting DHH young children to develop their language skills.
Chromosomal-level genome assembly of the orchid tree Bauhinia variegata (Leguminosae; Cercidoideae) supports the allotetraploid origin hypothesis of Bauhinia
Authors: Zhong Yan , Chen Yong , Zheng Danjing , Pang Jingyi , Liu Ying , Luo Shukai , Meng Shiyuan , Qian Lei , Wei Dan , Dai Seping , Zhou Renchao 
Published: April 2022

Abstract
Cercidoideae, one of the six subfamilies of Leguminosae, contains one genus Cercis with its chromosome number 2n = 14 and all other genera with 2n = 28. An allotetraploid origin hypothesis for the common ancestor of non-Cercis genera in this subfamily has been proposed; however, no chromosome-level genomes from Cercidoideae have been available to test this hypothesis. Here, we conducted a chromosome-level genome assembly of Bauhinia variegata to test this hypothesis. The assembled genome is 326.4 Mb with the scaffold N50 of 22.1 Mb and contains 37,996 protein-coding genes. The Ks distribution between gene pairs in the syntenic regions indicates two whole-genome duplications (WGDs): one is B. variegata-specific, and the other is shared among core eudicots. Although Ks between gene pairs generated by the recent WGD in Bauhinia is greater than that between Bauhinia and Cercis, the WGD was not detected in Cercis, which can be explained by an accelerated evolutionary rate in Bauhinia after divergence from Cercis. Ks distribution and phylogenetic analysis for gene pairs generated by the recent WGD in Bauhinia and their corresponding orthologs in Cercis support the allopolyploidy origin hypothesis of Bauhinia. The genome of B. variegata also provides a genomic resource for dissecting genetic basis of its ornamental traits.
Long-term outcome of minimally invasive thymectomy versus open thymectomy for locally advanced cases
Authors: Hwang Su Kyung , Lee Gun Dong , Kang Chang Hyun , Cho Jong Ho , Choi Yong Soo , Lee Jin Gu , Kim Dong Kwan 
Published: April 2022

Abstract

OBJECTIVES
Our goal was to compare the oncological outcomes and efficacy between minimally invasive thymectomy (MIT) and open thymectomy (OT) in patients with early or locally advanced thymoma using a multicentre study database.

METHODS
We retrospectively collected data from 1,239 patients who underwent thymectomy between January 2000 and December 2013, as recorded in the database of the Korean Association for Research on Thymus. We compared the postoperative outcomes of the MIT and OT groups using unmatched and propensity score (PS) matched data.

RESULTS
We excised the thymoma using MIT and OT in 455 and 784 patients, respectively. We matched 378 patients with Masaoka-Koga stage I or II thymoma by their PS. The operative time, duration of hospital stay and complications were significantly shorter in the MIT group than in the OT group (all P &lt; 0.005). In the PS matched data, the groups did not show significant differences in the 10-year survival rate (87.7% in OT vs 85.5% in MIT, stage II, mean follow-up duration: 12.9 years in OT vs 11.1 years in MIT), recurrence-free survival (94.0% in OT vs 86.4% in MIT) and R0 resection (97.35% in OT and MIT, P = 0.59).

CONCLUSIONS
Compared with OT, MIT was associated with shorter operative times, shorter durations of hospital stay and fewer complications. Long-term survival, recurrence-free survival and complete resection were not significantly different between the OT and MIT groups. Our findings may help physicians track the progress of patients with early or locally advanced thymomas and design treatment plans for them.
Patient risk factors for conversion during video-assisted thoracic surgery—the Epithor conversion score
Authors: Fourdrain Alex , Georges Olivier , Gossot Dominique , Falcoz Pierre-Emmanuel , Jougon Jacques , Baste Jean-Marc , Marty-Ane Charles-Henri , Berna Pascal 
Published: April 2022

Abstract

OBJECTIVES
Intraoperative conversion from video-assisted thoracic surgery (VATS) to thoracotomy may occur during anatomical lung resection. The objectives of the present study were to identify risk factors for intraoperative conversion and to develop a predictive score.

METHODS
We performed a multicentre retrospective analysis of French thoracic surgery departments that contributed data on anatomical lung resections to the Epithor database over a 10-year period (from January-2010 to December-2019). Using univariate and multivariate logistic regression analyses, we determined risk factors for intraoperative conversion and elaborated the Epithor conversion score (ECS). The ECS was then validated in a cohort of patients operated on between January- and June-2020.

RESULTS
From January-2010 to December-2019, 210,037 patients had been registered in the Epithor database. Of these, 55,030 had undergone anatomical lung resection. We excluded patients who had upfront a thoracotomy or robotic-assisted thoracoscopic surgery (n = 40,293) and those with missing data (6,794). Hence, 7943 patients with intent-to-treat VATS were assessed: 7100 with a full VATS procedure and 843 patients with intraoperative conversion to thoracotomy (conversion rate: 10.6%). Thirteen potential risk factors were identified among patients’ preoperative characteristics and planned surgical procedures and were weighted accordingly to give the ECS. The score showed acceptable discriminatory power (area under the curve: 0.62 in the development cohort and 0.64 in the validation cohort) and good calibration (P = 0.23 in the development cohort and 0.30 in the validation cohort).

CONCLUSIONS
Thirteen potential preoperative risk factors were identified, enabling us to develop and validate the ECS—an easy-to-use, reproducible tool for estimating the risk of intraoperative conversion during VATS.
At Which Age is Education the Great Equalizer? A Causal Mediation Analysis of the (In-)Direct Effects of Social Origin over the Life Course
Authors: Kratz Fabian , Pettinger Bettina , Grätz Michael 
Published: April 2022

Abstract
The mechanisms linking parental resources to their children’s opportunities are of fundamental interest to sociologists. This study is the first to provide a dynamic life course assessment of the origin–education–destination triangle using causal mediation analysis. While the age-as-equalizer hypothesis suggests that for the highly educated, direct effects of social origin are high at young ages and decrease over the life course, the age-as-stratifier hypothesis suggests that for individuals with low educational attainment, direct effects of social origin are low at young ages and increase over the life course. Findings using panel data from the German Socio-Economic Panel Study are largely consistent with these hypotheses for various measures of social origin and social destination. Overall, this study demonstrates how causal mediation analysis provides precise effect definitions that allow scholars to assess mechanisms when status transmission processes depend on educational attainment.
Lung function impairment and risk of incident heart failure: the NHLBI Pooled Cohorts Study
Authors: Eckhardt Christina M , Balte Pallavi P , Barr Robert Graham , Bertoni Alain G , Bhatt Surya P , Cuttica Michael , Cassano Patricia A , Chaves Paolo , Couper David , Jacobs David R , Kalhan Ravi , Kronmal Richard , Lange Leslie , Loehr Laura , London Stephanie J , O’Connor George T , Rosamond Wayne , Sanders Jason , Schwartz Joseph E , Shah Amil , Shah Sanjiv J , Smith Lewis , White Wendy , Yende Sachin , Oelsner Elizabeth C 
Published: April 2022

Abstract

Aims
The aim is to evaluate associations of lung function impairment with risk of incident heart failure (HF).

Methods and results
Data were pooled across eight US population-based cohorts that enrolled participants from 1987 to 2004. Participants with self-reported baseline cardiovascular disease were excluded. Spirometry was used to define obstructive [forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) &lt;0.70] or restrictive (FEV1/FVC ≥0.70, FVC &lt;80%) lung physiology. The incident HF was defined as hospitalization or death caused by HF. In a sub-set, HF events were sub-classified as HF with reduced ejection fraction (HFrEF; EF &lt;50%) or preserved EF (HFpEF; EF ≥50%). The Fine–Gray proportional sub-distribution hazards models were adjusted for sociodemographic factors, smoking, and cardiovascular risk factors. In models of incident HF sub-types, HFrEF, HFpEF, and non-HF mortality were treated as competing risks. Among 31 677 adults, there were 3344 incident HF events over a median follow-up of 21.0 years. Of 2066 classifiable HF events, 1030 were classified as HFrEF and 1036 as HFpEF. Obstructive [adjusted hazard ratio (HR) 1.17, 95% confidence interval (CI) 1.07–1.27] and restrictive physiology (adjusted HR 1.43, 95% CI 1.27–1.62) were associated with incident HF. Obstructive and restrictive ventilatory defects were associated with HFpEF but not HFrEF. The magnitude of the association between restrictive physiology and HFpEF was similar to associations with hypertension, diabetes, and smoking.

Conclusion
Lung function impairment was associated with increased risk of incident HF, and particularly incident HFpEF, independent of and to a similar extent as major known cardiovascular risk factors.