bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner
Authors: Cherlin Tess , Magee Rogan , Jing Yi , Pliatsika Venetia , Loher Phillipe , Rigoutsos Isidore 
Published: April 2020

Abstract
Background
The advent of next generation sequencing (NGS) has allowed the discovery of short and long non-coding RNAs (ncRNAs) in an unbiased manner using reverse genetics approaches, enabling the discovery of multiple categories of ncRNAs and characterization of the way their expression is regulated. We previously showed that the identities and abundances of microRNA isoforms (isomiRs) and transfer RNA-derived fragments (tRFs) are tightly regulated, and that they depend on a person’s sex and population origin, as well as on tissue type, tissue state, and disease type. Here, we characterize the regulation and distribution of fragments derived from ribosomal RNAs (rRNAs). rRNAs form a group that includes four (5S, 5.8S, 18S, 28S) rRNAs encoded by the human nuclear genome and two (12S, 16S) by the mitochondrial genome. rRNAs constitute the most abundant RNA type in eukaryotic cells.

Results
We analyzed rRNA-derived fragments (rRFs) across 434 transcriptomic datasets obtained from lymphoblastoid cell lines (LCLs) derived from healthy participants of the 1000 Genomes Project. The 434 datasets represent five human populations and both sexes. We examined each of the six rRNAs and their respective rRFs, and did so separately for each population and sex. Our analysis shows that all six rRNAs produce rRFs with unique identities, normalized abundances, and lengths. The rRFs arise from the 5′-end (5′-rRFs), the interior (i-rRFs), and the 3′-end (3′-rRFs) or straddle the 5′ or 3′ terminus of the parental rRNA (x-rRFs). Notably, a large number of rRFs are produced in a population-specific or sex-specific manner. Preliminary evidence suggests that rRF production is also tissue-dependent. Of note, we find that rRF production is not affected by the identity of the processing laboratory or the library preparation kit.

Conclusions
Our findings suggest that rRFs are produced in a regimented manner by currently unknown processes that are influenced by both ubiquitous as well as population-specific and sex-specific factors. The properties of rRFs mirror the previously reported properties of isomiRs and tRFs and have implications for the study of homeostasis and disease.
Ovarian mucinous tumors with mural nodules: immunohistochemical and molecular analysis of 3 cases
Authors: Shao Ying , Liu Qin , Shi Haiyan , Lu Bingjian 
Published: April 2020

Abstract
Background
Primary ovarian mucinous tumors with mural nodules are very rare. The histogenesis of the mural nodules remains unclear.

Methods
We investigated the clincopathological and molecular features in 3 cases with mural nodules.

Results
Patient 1 was diagnosed as mucinous carcinoma with mural nodules of anaplastic carcinoma that was composed of CK+ and CK7+ spindled cells and polygonal cells with marked pleomorphism. Aberrant p53 staining was found in the mural nodules rather than in the mucinous components. A concordant KRAS mutation (c.35G > A p.G12A) was identified in both mucinous tumors and mural nodules. She died of disease at 44 months. The mural nodule in patient 2 was interpreted as a sarcoma, no other specified. The uniform short spindle cells were separated by abundant myxoid matrix. They were CD10 + , CCND1-, SMA-, and negative for break-apart BCOR, PHF1, and JAZF1 FISH assay. The adenocarcinomatous component harbored LOH at D18S51 and FGA loci while the sarcomatous component had LOH at D19S433. She had lung metastasis at 18 months and was alive without evidence of disease for 40 months. Patient 3 harbored multiple mural nodules that were composed of vimentin+, focal CK+, atypical spindle cells. A diagnosis of sarcoma-like mural nodules was rendered. She was alive with no evidence of disease for 13 months. No hotspot mutant AKT1, KRAS, HRAS, and PI3KCA alleles were found in patients 2 and 3.

Conclusions
Mural nodules with anaplastic carcinoma or with true sarcomas may represent the dedifferentiation form of mucinous tumors or collision tumors, respectively. The worrisome histology in sarcoma-like mural nodules necessitates meticulous treatment for these patients.
High-intensity interval training accelerates oxygen uptake kinetics and improves exercise tolerance for individuals with cystic fibrosis
Authors: Reuveny Ronen , DiMenna Fred J. , Gunaratnam Cedric , Arad Avigdor D. , McElvaney Gerry N. , Susta Davide , Peled Michael , Moyna Niall M. 
Published: April 2020

AbstractBackgroundExercise training provides benefits for individuals with cystic fibrosis; however, the optimal program is unclear. High-intensity interval training is safe and effective for improving ‘functional capacity’ in these individuals with peak rate of O2uptake typically referenced. The ability to adjust submaximal rate of oxygen uptake (V̇O2kinetics) might be more important for everyday function because maximal efforts are usually not undertaken. Moreover, the ability of high-intensity training to accelerate V̇O2kinetics for individuals with cystic fibrosis could be enhanced with O2supplementation during training.MethodsNine individuals with cystic fibrosis completed incremental cycling to limit of tolerance followed by 8 weeks of high-intensity interval cycling (2 sessions per week x ~ 45 min per session) either with (n = 5; O2+) or without (AMB) oxygen supplementation (100%). Each session involved work intervals at 70% of peak work rate followed by 60 s of recovery at 35%. For progression, duration of work intervals was increased according to participant tolerance.ResultsBoth groups experienced a significant increase in work-interval duration over the course of the intervention (O2+, 1736 ± 141v. 700 ± 154 s; AMB, 1463 ± 598v. 953 ± 253 s;P = 0.000); however, the increase experienced by O2+ was greater (P = 0.027). During low-intensity constant-work-rate cycling, the V̇O2mean response time was shortened post compared to pre training (O2+, 34 ± 11v. 44 ± 9 s; AMB, 39 ± 14v. 45 ± 17 s;P = 0.000) while during high-intensity constant-work-rate cycling, time to exhaustion was increased (O2+, 1628 ± 163v. 705 ± 133 s; AMB, 1073 ± 633v. 690 ± 348 s;P = 0.002) and blood [lactate] response was decreased (O2+, 4.5 ± 0.9v. 6.3 ± 1.4 mmol.L− 1; AMB, 4.5 ± 0.6v. 5.2 ± 1.4 mmol.L− 1;P = 0.003). These positive adaptations were similar regardless of gas inspiration during training.ConclusionEight weeks of high-intensity interval training for patients with cystic fibrosis accelerated V̇O2kinetics and increased time to exhaustion. This provides some evidence that these patients may benefit from this type of exercise.Trial registrationThis study was retrospectively registered in the ISRTCN registry on 22/06/2019 (#ISRCTN13864650).
The Effect of Fly Ash and Recycled Aggregate on the Strength and Carbon Emission Impact of FRCCs
Authors: Lee Jong-Won , Jang Young-Il , Park Wan-Shin , Yun Hyun-Do , Kim Sun-Woo 
Published: April 2020

AbstractConcrete is the most widely used construction material in the world. In particular, cementitious composites that contain reinforced fibers have a relatively large amount of cement. Therefore, in this study, the target is to maintain at least 90% of the performance along with a reduction of CO2 emissions from the material stage during fiber-reinforced cementitious composites (FRCCs) production by applying fly ash (FA) and recycled sand (RS). To calculate the amount of CO2 emission at the stage of manufacturing the FRCCs, life cycle inventory database (LCI DB) were referenced from domestic and Japan. As the performance efficiency indicators, simple equations to evaluate the amount of CO2 emission of FRCCs were then formulated as a function of the replacement ratio of FA and RS. And binder and CO2 intensities were analyzed by FRCCs strength. Based on the results for the test, a mix of FA 25% and RS 25% of W/B 0.45, is considered most suitable in terms of performance of FRCCs and reduction of CO2 emissions.
Evaluating the effectiveness of traumatic brain injury state laws among high school athletes
Authors: Arakkal Alan T. , Barón Anna E. , Lamb Molly M. , Fields Sarah K. , Comstock R. Dawn 
Published: April 2020

Abstract
Background
Traumatic brain injury legislation varies across states. A comprehensive nationwide evaluation of state traumatic brain injury laws is vital given growing populations of high school athletes. This study evaluates the effectiveness of traumatic brain injury laws by examining longitudinal trends in incident and recurrent concussion rates and determines if state level variations in legislation’s language affected the observed trends.

Methods
In this retrospective ecological study of a large national sample of US high schools from 2005/06 through 2017/18, piecewise regression models along with a profile likelihood approach were utilized to examine longitudinal trends in incident and recurrent concussion rates.

Results
Overall incident concussion rates increased by an additional 1.85%/standardized month (STDM) (95% confidence interval (CI): 1.14, 2.56%) prior to law passage and decreased by an additional 1.08%/ STDM (95%CI: − 1.43, − 0.72%) after law passage. Similar trends were observed for overall recurrent concussion rates. Among states that specified the category of healthcare provider for return to play clearance, post-law recurrent concussion rates decreased on average by an additional 1.59%/STDM (95%CI: − 3.42, 0.22%) compared to states that did not specify the category of healthcare provider.

Conclusions
The passage of state level traumatic brain injury laws was associated with an increase in overall incident and recurrent concussion rates prior to law passage and a decrease in rates after law passage. Although not statistically significant, states with traumatic brain injury laws specifying the category of healthcare provider for return to play clearance had a greater rate of decline in post-law recurrent concussion rates compared to states not specifying the category of healthcare provider. The findings suggest that state traumatic brain injury laws may benefit from specifying the category of healthcare provider allowed to provide return to play clearance, if they do not already include such language.
Endovascular treatment of aortic stump blow-out after extra-anatomical repair of aortoduodenal fistula: a case report and review of literature
Authors: Beijer E. , Scholtes V. P. W. , Moerbeek P. , Coveliers H. M. E. , Lely R. J. , Hoksbergen A. W. J. 
Published: April 2020

Abstract
Background
An aortoduodenal fistula (ADF) is an unusual, but serious complication following surgical or endovascular aortic repair. The optimal treatment for ADF consists of removal of the infected graft with in situ or extra-anatomical repair and is associated with high mortality. Part of this mortality is caused by re-bleeding or aortic stump ruptures. Classical treatment of an aortic stump rupture involves immediate re-laparotomy, removal of infected tissue, aortic stump formation and reinforcement with soft tissue flaps.
However, this invasive treatment is often difficult to perform and the condition of the patient frequently requires a more rapid response. We describe a case in which an aortic stump rupture was treated endovascularly by using an Amplatzer® Vascular Plug, which successfully stopped the bleeding.

Case presentation
This report describes a 67-year-old man who was presented with persistent duodenal leakage (due to secondary duodenal perforation) after resection and open in-situ repair of an infected aorto-bi-femoral prosthetic graft. An extra-anatomical reconstruction was performed with an axillo-bi-femoral bypass, followed by excision of the prosthesis, aortic stump formation, partial duodenal resection and duodenojejunal reconstruction. Twelve weeks later, sudden severe hematemesis with severe hemodynamic instability occurred. Computed tomography angiography showed extravasation of blood from the aortic stump into the duodenal loop. Endovascular treatment of the aortic stump blow-out with an Amplatzer® Vascular Plug was performed, which successfully stopped the bleeding and stabilized the patient. The duodenal fistula was treated conservatively. Three months later, the patient was discharged to a rehabilitation clinic in a good clinical condition. The patient was still alive after a follow-up of 4 years.

Conclusions
Rapid treatment is requested in cases of aortic stump rupture. Re-laparotomy is practically never the most suitable solution and most of these aortic stump ruptures are fatal. Endovascular treatment could be a suitable alternative. Whether the endovascular treatment of aortic stump rupture is a definitive treatment or a bridge to surgery remains to be elucidated.
Outcome of late preterm newborns in Upper Egypt
Authors: Algameel Alkassem , Elhawary Manal , Amin Sayed , Abd Elmenem Marwa 
Published: April 2020

Abstract
Background
The incidence of preterm births is increasing and has become a global health concern. This study aimed to compare the outcome of late preterm (LPT) to full term (FT) neonates at two large hospitals in Upper Egypt.

Results
Out of 250 newborns included in the study, 180 (72%) were FT and 70 (28%) were LPT. More than half of the LPT newborns (52.9%) were admitted to the neonatal intensive care unit (NICU), compared with 26.7% of FT newborns. Delivery of LPT was associated with an increased risk of neonatal morbidity, including jaundice requiring phototherapy (34.3% vs. 7.8%), respiratory morbidities (32.9% vs. 13.9%), hypoglycemia (8.6% vs. 1.7 %), and convulsions (4.3% vs. 0.6%).

Conclusions
LPT neonates were more susceptible to suffer from jaundice and respiratory distress among other morbidities. They also had a higher rate of NICU admission, longer duration of NICU stay, as well as a higher mortality rate. The best treatment of late prematurity is to prevent it. Public and professional awareness of the problems associated with late prematurity should be highlighted. Follow-up programs for early detection and intervention for long term complications are recommended.
Post-treatment benign changes versus recurrence in non-lymphoid head and neck malignancies: can diffusion-weighted magnetic resonance imaging end up the diagnostic challenge?
Authors: Serour Dalia K. , Adel Khaled M. , Osman Ayman M. A. 
Published: April 2020

Abstract
Background
The aim of this prospective cohort study is to substantiate the added value of diffusion-weighted magnetic resonance imaging (DW-MRI) over conventional MRI assessment in the differentiation between locoregional recurrence/residual tumour and post-treatment benign changes in patients with non-lymphoid head and neck malignancies.
Thirty adult patients, each with a suspicious lesion on post-treatment imaging scans at the primary site of a previously treated non-lymphoid head and neck malignancy, were evaluated by MRI and diffusion-weighted imaging (DWI). The apparent diffusion coefficient (ADC) values of the lesions were calculated.

Results
Diffusion-weighted MRI yielded an accuracy of 90%, a sensitivity of 88.9%, a specificity of 91.7%, a positive predictive value of 94.1% and a negative predictive value of 84.6%. The mean ADC value of the lesions was lower in the “locoregional recurrence/residual tumour” group (1.08 × 10−3 mm2/s) compared to the “post-treatment benign changes” group (1.95 × 10−3 mm2/s); P < 0.001. An ADC cutoff value of 1.43 × 10−3 mm2/s achieved the same accuracy as the visual assessment by DW-MRI.

Conclusion
Incorporating the DWI sequence into the post-treatment imaging assessment protocol brings a substantial added value to conventional MRI assessment in patients with non-lymphoid head and neck malignancies. This valuable merit of DW-MRI can help avoid or, at least, largely minimize unnecessary or unfeasible tissue sampling. An ADC cutoff value of 1.43 × 10−3 mm2/s can also be utilized to aid in the assessment process.
An Automated Algorithm Incorporating Poincaré Analysis Can Quantify the Severity of Opioid-Induced Ataxic Breathing
Authors: Ermer Sean C. , Farney Robert J. , Johnson Ken B. , Orr Joseph A. , Egan Talmage D. , Brewer Lara M. 
Published: April 2020

BACKGROUND:
Opioid-induced respiratory depression (OIRD) is traditionally recognized by assessment of respiratory rate, arterial oxygen saturation, end-tidal CO2, and mental status. Although an irregular or ataxic breathing pattern is widely recognized as a manifestation of opioid effects, there is no standardized method for assessing ataxic breathing severity. The purpose of this study was to explore using a machine-learning algorithm for quantifying the severity of opioid-induced ataxic breathing. We hypothesized that domain experts would have high interrater agreement with each other and that a machine-learning algorithm would have high interrater agreement with the domain experts for ataxic breathing severity assessment.

METHODS:
We administered target-controlled infusions of propofol and remifentanil to 26 healthy volunteers to simulate light sleep and OIRD. Respiration data were collected from respiratory inductance plethysmography (RIP) bands and an intranasal pressure transducer. Three domain experts quantified the severity of ataxic breathing in accordance with a visual scoring template. The Krippendorff alpha, which reports the extent of interrater agreement among N raters, was used to assess agreement among the 3 domain experts. A multiclass support vector machine (SVM) was trained on a subset of the domain expert-labeled data and then used to quantify ataxic breathing severity on the remaining data. The Vanbelle kappa was used to assess the interrater agreement of the machine-learning algorithm with the grouped domain experts. The Vanbelle kappa expands on the Krippendorff alpha by isolating a single rater—in this case, the machine-learning algorithm—and comparing it to a group of raters. Acceptance criteria for both statistical measures were set at >0.8. The SVM was trained and tested using 2 sensor inputs for the breath marks: RIP and intranasal pressure.

RESULTS:
Krippendorff alpha was 0.93 (95% confidence interval [CI], 0.91–0.95) for the 3 domain experts. Vanbelle kappa was 0.98 (95% CI, 0.96–0.99) for the RIP SVM and 0.96 (0.92–0.98) for the intranasal pressure SVM compared to the domain experts.

CONCLUSIONS:
We concluded it may be feasible for a machine-learning algorithm to quantify ataxic breathing severity in a manner consistent with a panel of domain experts. This methodology may be helpful in conjunction with traditional measures to identify patients experiencing OIRD.
Parsimony of Hemodynamic Monitoring Data Sufficient for the Detection of Hemorrhage
Authors: Pinsky Michael R. , Wertz Anthony , Clermont Gilles , Dubrawski Artur 
Published: April 2020

BACKGROUND:
Individualized hemodynamic monitoring approaches are not well validated. Thus, we evaluated the discriminative performance improvement that might occur when moving from noninvasive monitoring (NIM) to invasive monitoring and with increasing levels of featurization associated with increasing sampling frequency and referencing to a stable baseline to identify bleeding during surgery in a porcine model.

METHODS:
We collected physiologic waveform (WF) data (250 Hz) from NIM, central venous (CVC), arterial (ART), and pulmonary arterial (PAC) catheters, plus mixed venous O2 saturation and cardiac output from 38 anesthetized Yorkshire pigs bled at 20 mL/min until a mean arterial pressure of 30 mm Hg following a 30-minute baseline period. Prebleed physiologic data defined a personal stable baseline for each subject independently. Nested models were evaluated using simple hemodynamic metrics (SM) averaged over 20-second windows and sampled every minute, beat to beat (B2B), and WF using Random Forest Classification models to identify bleeding with or without normalization to personal stable baseline, using a leave-one-pig-out cross-validation to minimize model overfitting. Model hyperparameters were tuned to detect stable or bleeding states. Bleeding models were compared use both each subject’s personal baseline and a grouped-average (universal) baseline. Timeliness of bleed onset detection was evaluated by comparing the tradeoff between a low false-positive rate (FPR) and shortest time to bleed detection. Predictive performance was evaluated using a variant of the receiver operating characteristic focusing on minimizing FPR and false-negative rates (FNR) for true-positive and true-negative rates, respectively.

RESULTS:
In general, referencing models to a personal baseline resulted in better bleed detection performance for all catheters than using universal baselined data. Increasing granularity from SM to B2B and WF progressively improved bleeding detection. All invasive monitoring outperformed NIM for both time to bleeding detection and low FPR and FNR. In that regard, when referenced to personal baseline with SM analysis, PAC and ART + PAC performed best; for B2B CVC, PAC and ART + PAC performed best; and for WF PAC, CVC, ART + CVC, and ART + PAC performed equally well and better than other monitoring approaches. Without personal baseline, NIM performed poorly at all levels, while all catheters performed similarly for SM, with B2B PAC and ART + PAC performing the best, and for WF PAC, ART, ART + CVC, and ART + PAC performed equally well and better than the other monitoring approaches.

CONCLUSIONS:
Increasing hemodynamic monitoring featurization by increasing sampling frequency and referencing to personal baseline markedly improves the ability of invasive monitoring to detect bleed.