bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more
Authors: Gatter Thomas , Stadler Peter F 
Published: July 2021

Abstract

Motivation
Accurate assembly of RNA-seq is a crucial step in many analytic tasks such as gene annotation or expression studies. Despite ongoing research, progress on traditional single sample assembly has brought no major breakthrough. Multi-sample RNA-Seq experiments provide more information than single sample datasets and thus constitute a promising area of research. Yet, this advantage is challenging to utilize due to the large amount of accumulating errors.

Results
We present an extension to Ryūtō enabling the reconstruction of consensus transcriptomes from multiple RNA-seq datasets, incorporating consensus calling at low level features. We report stable improvements already at three replicates. Ryūtō outperforms competing approaches, providing a better and user-adjustable sensitivity-precision trade-off. Ryūtō’s unique ability to utilize a (incomplete) reference for multi sample assemblies greatly increases precision. We demonstrate benefits for differential expression analysis.
Ryūtō consistently improves assembly on replicates of the same tissue independent of filter settings, even when mixing conditions or time series. Consensus voting in Ryūtō is especially effective at high precision assembly, while Ryūtō’s conventional mode can reach higher recall.

Availability and implementation
Ryūtō is available at https://github.com/studla/RYUTO.

Supplementary information
Supplementary data are available at Bioinformatics online.
Effects of LPXRFamide peptides on chub mackerel gonadotropin secretion
Authors: Ohga Hirofumi , Matsuyama Michiya 
Published: July 2021

AbstractGonadotropin-inhibitory hormone (GnIH), a neuropeptide, suppresses gonadotropin (GTH) secretion in birds and mammals. In fish, the GnIH homolog LPXRFamide (LPXRFa) produces mature peptides with species-dependent effects on sexual reproduction. Here, we investigated the effects of LPXRFa on GTH secretion in the chub mackerel (cm; Scomber japonicus). We cloned cmlpxrfa (603 bp) and cmlpxrfa-r (1416 bp). Additionally, we isolated lpxrfa from the bluefin tuna (Thunnus orientalis) to confirm the conservation of the LPXRFa mature sequence. Phylogenetic analysis showed that the LPXRFa precursor protein produces three mature peptides, LPXRFa-1, -2, and -3, in both species. Reverse transcription-quantitative polymerase chain reaction revealed that cmlpxrfa is expressed in the hypothalamus and thalamus and midbrain (T.MB), and sexual differences were observed. Receptor expression was observed in the preoptic area, hypothalamus, T.MB, and pituitary. Female hypothalamic lpxrfa expression did not change during puberty. Reporter gene assay showed that LPXRFa induced receptor activation via the CRE and SRE signaling pathways. However, in the presence of forskolin, an intracellular cyclic AMP enhancer, none of the LPXRFa could suppress receptor activity. The in vitro bioassay results showed that gonadotropin-releasing hormone-1 (GnRH1) had no effect on follicle-stimulating hormone (FSH) secretion, whereas the three LPXRFa significantly increased FSH secretion in pituitary cells from male chub mackerel. Contrarily, GnRH1 and three LPXRFa significantly increased luteinizing hormone secretion. The in vivo administration of LPXRFa had no effect on fshb and lhb expression in prepubertal and mature male chub mackerel. Overall, cmLPXRFa lacks the ability to suppress GTH secretion but can promote GTH secretion.
A deep learning approach for monitoring parietal-dominant Alzheimer’s disease in World Trade Center responders at midlife
Authors: Chen Allen P F , Clouston Sean A P , Kritikos Minos , Richmond Lauren , Meliker Jaymie , Mann Frank , Santiago-Michels Stephanie , Pellecchia Alison C , Carr Melissa A , Kuan Pei-Fen , Bromet Evelyn J , Luft Benjamin J 
Published: July 2021

Abstract
Little is known about the characteristics and causes of early-onset cognitive impairment. Responders to the 2001 New York World Trade Center disaster represent an ageing population that was recently shown to have an excess prevalence of cognitive impairment. Neuroimaging and molecular data demonstrate that a subgroup of affected responders may have a unique form of parietal-dominant Alzheimer’s Disease. Recent neuropsychological testing and artificial intelligence approaches have emerged as methods that can be used to identify and monitor subtypes of cognitive impairment. We utilized data from World Trade Center responders participating in a health monitoring program and applied a deep learning approach to evaluate neuropsychological and neuroimaging data to generate a cortical atrophy risk score. We examined risk factors associated with the prevalence and incidence of high risk for brain atrophy in responders who are now at midlife. Training was conducted in a randomly selected two-thirds sample (N = 99) enrolled using of the results of a structural neuroimaging study. Testing accuracy was estimated for each training cycle in the remaining third subsample. After training was completed, the scoring methodology that was generated was applied to longitudinal data from 1441 World Trade Center responders. The artificial neural network provided accurate classifications of these responders in both the testing (Area Under the Receiver Operating Curve, 0.91) and validation samples (Area Under the Receiver Operating Curve, 0.87). At baseline and follow-up, responders identified as having a high risk of atrophy (n = 378) showed poorer cognitive functioning, most notably in domains that included memory, throughput, and variability as compared to their counterparts at low risk for atrophy (n = 1063). Factors associated with atrophy risk included older age [adjusted hazard ratio, 1.045 (95% confidence interval = 1.027–1.065)], increased duration of exposure at the WTC site [adjusted hazard ratio, 2.815 (1.781–4.449)], and a higher prevalence of post-traumatic stress disorder [aHR, 2.072 (1.408–3.050)]. High atrophy risk was associated with an increased risk of all-cause mortality [adjusted risk ratio, 3.19 (1.13–9.00)]. In sum, the high atrophy risk group displayed higher levels of previously identified risk factors and characteristics of cognitive impairment, including advanced age, symptoms of post-traumatic stress disorder, and prolonged duration of exposure to particulate matter. Thus, this study suggests that a high risk of brain atrophy may be accurately monitored using cognitive data.
Comparative analysis of experimental testing procedures for the elicitation of rescue actions in ants
Authors: Turza Filip , Miler Krzysztof 
Published: July 2021

Abstract
Rescue behavior is observed when 1 individual provides help to another individual in danger. Most reports of rescue behavior concern ants (Formicidae), in which workers rescue each other from various types of entrapment. Many of these entrapment situations can be simulated in the laboratory using an entrapment bioassay, in which ants confront a single endangered nest mate entrapped on a sandy arena by means of an artificial snare. Here, we compared numerous characteristics of rescue actions (contact between individuals, digging around the entrapped individual, pulling at its body parts, transport of the sand covering it, and biting the snare entrapping it) in Formica cinerea ants. We performed entrapment tests in the field and in the laboratory, with the latter under varying conditions in terms of the number of ants potentially engaged in rescue actions and the arena substrate (marked or unmarked by ants’ pheromones). Rescue actions were more probable and pronounced in the field than in the laboratory, regardless of the type of test. Moreover, different test types in the laboratory yielded inconsistent results and showed noteworthy variability depending on the tested characteristic of rescue. Our results illustrate the specifics of ant rescue actions elicited in the natural setting, which is especially important considering the scarcity of field data. Furthermore, our results underline the challenges related to the comparison of results from different types of entrapment tests reported in the available literature. Additionally, our study shows how animal behavior differs in differing experimental setups used to answer the same questions.
Nutrient, Fibre, and FODMAP Intakes and Food-related Quality of Life in Patients with Inflammatory Bowel Disease, and Their Relationship with Gastrointestinal Symptoms of Differing Aetiologies
Authors: Cox Selina R , Clarke Hazel , O’Keeffe Majella , Dubois Patrick , Irving Peter M , Lindsay James O , Whelan Kevin 
Published: July 2021

Abstract

Background and Aims
Certain foods are reported as gut symptom triggers in inflammatory bowel disease [IBD], and fructans are shown to worsen non-inflammatory symptoms in inactive IBD, which may result in self-imposed dietary restrictions. The aim of this study was to investigate nutrient and FODMAP intakes, and the relationship between gut symptoms and dietary intake, in IBD.

Methods
Nutrient, fibre, and FODMAP intakes were estimated using 7-day food records in patients with active IBD [Active IBD], inactive IBD with non-inflammatory gut symptoms [Inactive IBD-GI], inactive IBD without gut symptoms [Inactive IBD], and healthy controls. Nutrient intakes, numbers of participants achieving national recommendations, and food-related quality of life [FR-QoL] were compared across study groups.

Results
Food diaries were obtained from 232 patients with IBD [65 Active IBD, 86 Inactive IBD-GI, 81 Inactive IBD] and 84 healthy controls. Patients with Active IBD had significantly lower intakes of numerous micronutrients, including iron, folate, and vitamin C, compared with controls. All IBD groups consumed less total fibre [4.5 to 5.8 g/day] than controls [p = 0.001], and total FODMAP and fructan intakes were lower in Active IBD compared with controls. Strikingly, FR-QoL was significantly lower in all IBD groups compared with controls [all p = 0.001].

Conclusions
This study revealed lower intakes of fibre, FODMAPs, and micronutrients, in addition to poorer FR-QoL, in Active IBD and Inactive IBD-GI with gut symptoms compared with healthy controls. Future research should address dietary restrictions responsible for these differences.
A case report showing unusual atrial communication with severe regurgitation of multiple valves and pulmonary aneurysm: double atrial septum with persistent interatrial space
Authors: Ortiz de Murua José Antonio , de la Fuente Blanco Laura , Trigo-Bautista Alberto , Ruiz-Olgado María José 
Published: July 2021

Abstract

Background
We discuss an unusual association: double atrial septum, pulmonary artery aneurysm, and severe regurgitation of multiple valves.

Case summary
A 70-year-old man was admitted into the hospital because of progressive dyspnoea. Physical examination showed a blood pressure of 132/70 mmHg, a systolic murmur on the right upper sternal border, another systolic murmur at the apex, and a diastolic murmur at the lower left sternal border. Electrocardiogram revealed atrial fibrillation and complete left bundle branch block. Transthoracic echocardiography showed mitral prolapse, severe mitral, aortic, and pulmonary regurgitation, a 60 mm diameter pulmonary artery aneurysm, mild to moderate tricuspid regurgitation, and moderate pulmonary hypertension. Transoesophageal echocardiography also showed an unusual atrial communication consisting of a double atrial septum with a mid-line chamber between both atria. A cardiac magnetic resonance scan was performed and confirmed echocardiography findings and QP:QS ratio = 1.3.

Discussion
In our knowledge, this is the first case report with this association. We present the main clinical features of the double atrial septum with persistent interatrial space, its echocardiography anatomy, differential diagnosis, and embryology.
A case report of successful stent implantation through a fractured stent-strut in a superficial femoral artery based on bench testing simulation
Authors: Yamane Haruya , Kosugi Shumpei , Date Motoo , Ueda Yasunori 
Published: July 2021

Abstract

Background
Stent implantation through the stent-strut of a previously implanted self-expandable stent in the superficial femoral artery (SFA) is not usually performed because the additional stent cannot dilate sufficiently. The key point to achieve sufficient expansion of an additional stent is to break the stent-strut of the previously implanted stent. However, there is no report of how to break the stent-strut.

Case summary
A 72-year-old man was admitted to our hospital with acute rest pain and coldness of his left leg; he was diagnosed with acute limb ischaemia. The angiogram demonstrated a fractured stent as well as stent occlusion in the left distal SFA. The guidewire could pass only through the stent-strut because of stent fracture. Fortunately, balloon angioplasty through the stent-strut and thrombolysis achieved successful revascularization. Thereafter, an additional stent was implanted in an attempt to manage the fractured and deformed stent. To obtain sufficient expansion of the additional stent, an experimental study to examine the balloon diameter and pressure to break the stent-strut was performed. Based on the results of the experiment, the stent-strut was successfully broken, and the additional stent was expanded through the stent-strut on the second intervention.

Discussion
If an additional self-expandable stent is deployed through the stent-strut directly, it would not be sufficiently dilated. The key point in such a case is to break the stent-strut of the previously implanted stent by balloon inflation before deployment of the additional stent. The experimental study examined the balloon diameter and pressure that can break the stent-strut. This information would be useful when we implant an additional stent through a stent-strut.
Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare
Authors: Mogro Ezequiel G , Ambrosis Nicolás M , Lozano Mauricio J 
Published: July 2021

AbstractBacterial genomes are composed of core and accessory genomes. The first is composed of housekeeping and essential genes, while the second is highly enriched in mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLISs) on assembled genomes. Here, we introduce ISCompare, a new program to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyze multiple ISs at the same time and outputs a list of candidate DLISs. ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.
De-politicization and Corporate Transformation: Evidence from China
Authors: Berkowitz Daniel , Lin Chen , Liu Sibo 
Published: July 2021

Abstract
It is well understood that when firms receive favorable treatment from the government because of their political connections and not necessarily their economic merits, they may operate inefficiently while enjoying market advantages over their unconnected peers. However, just how firms respond to the sustained removal of their political connections has not been carefully studied. This article evaluates an unanticipated reform in China that removed government-related personnel from independent directorships of publicly listed companies. Our evidence indicates that treated firms experienced a temporary increase in their cost of debt, but invested more in R&D, imported more machinery, and became more productive and transparent. These adjustments counterbalanced the negative value effect from the financial markets when the regulation was first announced (JEL G38, P26, K20).
Ultra-short-period massive black hole binary candidates in LSST as LISA ‘verification binaries’
Authors: Xin Chengcheng , Haiman Zoltán 
Published: July 2021

ABSTRACT
The Legacy Survey of Space and Time (LSST) by the Vera C. Rubin Observatory is expected to discover tens of millions of quasars. A significant fraction of these could be powered by coalescing massive black hole (MBH) binaries, since many quasars are believed to be triggered by mergers. We show that under plausible assumptions about the luminosity functions, lifetimes, and binary fractions of quasars, we expect the full LSST quasar catalogue to contain between 20 and 100 million compact MBH binaries with masses M = 105–9M⊙, redshifts z = 0–6, and orbital periods P = 1–70 d. Their light-curves are expected to be distinctly periodic, which can be confidently distinguished from stochastic red-noise variability, because LSST will cover dozens, or even hundreds of cycles. A very small subset of 10–150 ultracompact (P ≲ 1 d) binary quasars among these will, over ∼5–15 yr, evolve into the mHz gravitational-wave frequency band and can be detected by LISA. They can therefore be regarded as ‘LISA verification binaries’, analogous to short-period Galactic compact-object binaries. The practical question is how to find these handful of ‘needles in the haystack’ among the large number of quasars: this will likely require a tailored co-adding analysis optimized for this purpose.
High-contrast observations of brown dwarf companion HR 2562 B with the vector Apodizing Phase Plate coronagraph
Authors: Sutlieff Ben J , Bohn Alexander J , Birkby Jayne L , Kenworthy Matthew A , Morzinski Katie M , Doelman David S , Males Jared R , Snik Frans , Close Laird M , Hinz Philip M , Charbonneau David 
Published: July 2021

ABSTRACT
The vector Apodizing Phase Plate (vAPP) is a class of pupil plane coronagraph that enables high-contrast imaging by modifying the Point Spread Function (PSF) to create a dark hole of deep flux suppression adjacent to the PSF core. Here, we recover the known brown dwarf HR 2562 B using a vAPP coronagraph, in conjunction with the Magellan Adaptive Optics (MagAO) system, at a signal-to-noise of S/N = 3.04 in the lesser studied L-band regime. The data contained a mix of field and pupil-stabilized observations, hence we explored three different processing techniques to extract the companion, including Flipped Differential Imaging (FDI), a newly devised Principal Component Analysis (PCA)-based method for vAPP data. Despite the partial field-stabilization, the companion is recovered sufficiently to measure a 3.94 $\mu\mathrm{ m}$ narrow-band contrast of (3.05 ± 1.00) × 10−4 ($\Delta \, {\rm m}_{3.94 \mu {\rm m}}$ = 8.79 ± 0.36 mag). Combined with archival GPI and SPHERE observations, our atmospheric modelling indicates a spectral type at the L/T transition with mass M = 29 ± 15 MJup, consistent with literature results. However, effective temperature and surface gravity vary significantly depending on the wavebands considered (1200 ≤ Teff(K) ≤ 1700 and 4.0 ≤ log(g)(dex) ≤ 5.0), reflecting the challenges of modelling objects at the L/T transition. Observations between 2.4 and 3.2 $\mu\mathrm{ m}$ will be more effective in distinguishing cooler brown dwarfs due to the onset of absorption bands in this region. We explain that instrumental scattered light and wind-driven halo can be detrimental to FDI+PCA and thus must be sufficiently mitigated to use this processing technique. We thus demonstrate the potential of vAPP coronagraphs in the characterization of high-contrast substellar companions, even in sub-optimal conditions, and provide new complementary photometry of HR 2562 B.
Classification of true progression after radiotherapy of brain metastasis on MRI using artificial intelligence: a systematic review and meta-analysis
Authors: Kim Hae Young , Cho Se Jin , Sunwoo Leonard , Baik Sung Hyun , Bae Yun Jung , Choi Byung Se , Jung Cheolkyu , Kim Jae Hyoung 
Published: July 2021

Abstract

Background
Classification of true progression from nonprogression (eg, radiation-necrosis) after stereotactic radiotherapy/radiosurgery of brain metastasis is known to be a challenging diagnostic task on conventional magnetic resonance imaging (MRI). The scope and status of research using artificial intelligence (AI) on classifying true progression are yet unknown.

Methods
We performed a systematic literature search of MEDLINE and EMBASE databases to identify studies that investigated the performance of AI-assisted MRI in classifying true progression after stereotactic radiotherapy/radiosurgery of brain metastasis, published before November 11, 2020. Pooled sensitivity and specificity were calculated using bivariate random-effects modeling. Meta-regression was performed for the identification of factors contributing to the heterogeneity among the studies. We assessed the quality of the studies using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) criteria and a modified version of the radiomics quality score (RQS).

Results
Seven studies were included, with a total of 485 patients and 907 tumors. The pooled sensitivity and specificity were 77% (95% CI, 70–83%) and 74% (64–82%), respectively. All 7 studies used radiomics, and none used deep learning. Several covariates including the proportion of lung cancer as the primary site, MR field strength, and radiomics segmentation slice showed a statistically significant association with the heterogeneity. Study quality was overall favorable in terms of the QUADAS-2 criteria, but not in terms of the RQS.

Conclusion
The diagnostic performance of AI-assisted MRI seems yet inadequate to be used reliably in clinical practice. Future studies with improved methodologies and a larger training set are needed.
Extended Retrosigmoid Approach for Resection of a Lateral Pontine Arteriovenous Malformation: 2-Dimensional Operative Video
Authors: Catapano Joshua S , Singh Rohin , Srinivasan Visish M , Lawton Michael T 
Published: July 2021

Abstract
Pontine arteriovenous malformations (AVMs) are uncommon lesions, with few reports in the literature. The best treatment option is debated, with options including surgical resection, endovascular embolization, and radiosurgery. Patient consent for the procedure was obtained. Herein, we report the successful resection of a ruptured lateral pontine AVM with an associated aneurysm in a woman in her early 70s. Surgical resection can be considered an effective treatment option for brainstem AVMs and should be considered alone or in conjunction with other treatment modalities. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.