bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies
Authors: Jia Yangyang , Zhao Shengguo , Guo Wenjie , Peng Ling , Zhao Fang , Wang Lushan , Fan Guangyi , Zhu Yuanfang , Xu Dayou , Liu Guilin , Wang Ruoqing , Fang Xiaodong , Zhang He , Kristiansen Karsten , Zhang Wenwei , Chen Jianwei 
Published: August 2022

Abstract
Background
Increasing studies have demonstrated potential disproportionate functional and ecological contributions of rare taxa in a microbial community. However, the study of the microbial rare biosphere is hampered by their inherent scarcity and the deficiency of currently available techniques. Sample-wise cross contaminations might be introduced by sample index misassignment in the most widely used metabarcoding amplicon sequencing approach. Although downstream bioinformatic quality control and clustering or denoising algorithms could remove sequencing errors and non-biological artifact reads, no algorithm could eliminate high quality reads from sample-wise cross contaminations introduced by index misassignment, making it difficult to distinguish between bona fide rare taxa and potential false positives in metabarcoding studies.

Results
We thoroughly evaluated the rate of index misassignment of the widely used NovaSeq 6000 and DNBSEQ-G400 sequencing platforms using both commercial and customized mock communities, and observed significant lower (0.08% vs. 5.68%) fraction of potential false positive reads for DNBSEQ-G400 as compared to NovaSeq 6000. Significant batch effects could be caused by stochastically introduced false positive or false negative rare taxa. These false detections could also lead to inflated alpha diversity of relatively simple microbial communities and underestimated that of complex ones. Further test using a set of cow rumen samples reported differential rare taxa by different sequencing platforms. Correlation analysis of the rare taxa detected by each sequencing platform demonstrated that the rare taxa identified by DNBSEQ-G400 platform had a much higher possibility to be correlated with the physiochemical properties of rumen fluid as compared to NovaSeq 6000 platform. Community assembly mechanism and microbial network correlation analysis indicated that false positive or negative rare taxa detection could lead to biased community assembly mechanism and identification of fake keystone species of the community.

Conclusions
We highly suggest proper positive/negative/blank controls, technical replicate settings, and proper sequencing platform selection in future amplicon studies, especially when the microbial rare biosphere would be focused.
Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments
Authors: Chiciudean Iulia , Russo Giancarlo , Bogdan Diana Felicia , Levei Erika Andrea , Faur Luchiana , Hillebrand-Voiculescu Alexandra , Moldovan Oana Teodora , Banciu Horia Leonard 
Published: August 2022

AbstractBackgroundMovile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave’s microbiome thriving beyond the sulfidic-rich water.ResultsA customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies’ taxonomy spanned 19 bacterial and three archaeal phyla withAcidobacteriota,Chloroflexota,Proteobacteria,Planctomycetota,Ca.Patescibacteria,Thermoproteota,Methylomirabilota,andCa.Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO43−, H+, Fe2+, Cu2+) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities.ConclusionsThese findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.
Melphalan intra-arterial chemotherapy for choroidal melanoma chemoreduction
Authors: Jorge Rodrigo , Coelho Igor , Viani Gustavo , Vieira Amanda Alexia R. , Chahud Fernando , Abud Daniel G. , Correa Zelia M. 
Published: August 2022

Abstract
Background
Intra-arterial chemotherapy (IAC) has been used to treat multiple cancers including liver metastasis from uveal and cutaneous melanoma but not as primary tumor treatment. We report the compassionate use of chemoreduction with intra-arterial melphalan before ruthenium brachytherapy to salvage an eye with choroidal melanoma.

Case presentation
A 61-year-old female patient complained of decreased vision and central-temporal scotoma in OS (left eye) for 1 month. Visual acuity was 20/20 in right eye (OD) and 20/125 OS. Anterior segment examination and intraocular pressure were unremarkable in both eyes, as was fundus examination of the OD. Fundus examination of OS revealed a brown, solid tumor partially obscuring the temporal optic disc margin and extending to the equatorial fundus midzone. Serous retinal detachment was present over the lesion and around it. Ultrasonography revealed a solid choroidal tumor with a largest basal diameter (LBD) of 13.0 mm and thickness of 10.4 mm. The tumor presented acoustic hollowness and a superimposing retinal detachment. After metastatic screening was negative, the patient underwent intra-arterial chemotherapy with melphalan. Three weeks later, her visual acuity was 20/200 and there was noticeable tumor regression to 11.9 mm (LBD) by 7.9 mm (thickness) allowing brachytherapy to be performed. Ten weeks after brachytherapy (13 weeks after IAC), visual acuity was HM due to biopsy-related vitreous hemorrhage (VH). Tumor dimensions were 9.9 (LBD) mm and 6.5 mm (thickness) and PPV was performed to remove VH. Six weeks after PPV (20 weeks after IAC), her visual acuity was 20/200 and further reduction of tumor dimensions was observed: largest basal diameter was 8.9 mm and thickness was 4.9 mm.

Conclusion
This case illustrates the feasibility of combining induction IAC prior to ruthenium brachytherapy for large choroidal melanoma. More studies are warranted to confirm these early preliminary findings.
Validity of foetal Doppler indices in predicting postnatal respiratory distress syndrome: a prospective study
Authors: Keshuraj Veena , Prakash Arjun , Boruah Deb K. , Ramanna H. C. , Sowmyashree A. R. , Mithun S. K. 
Published: August 2022

Abstract
Background
Respiratory distress syndrome (RDS) is a potentially fatal condition of neonate occurring due to alveolar surfactant deficiency causing inefficient gaseous exchange and leading to hampered respiratory function. Purpose of our study is to investigate the role of Doppler indices in antenatal prediction of clinical Respiratory Distress Syndrome (RDS) in late preterm and early term foetuses using Main pulmonary artery (MPA) Doppler indices. The current study was conducted on 342 pregnant women between 34 and 39 weeks of gestational age, who came for routine third trimester ultrasound examination. The standard foetal biometric parameters, gestational age and estimated foetal weight were first obtained. The MPA Doppler indices like pulsatility index (PI), resistivity index (RI), peak systolic velocity (PSV), systolic/diastolic ratio and acceleration time/ejection time (At/Et) were recorded and correlated with the postnatal development of RDS.

Results
Of the 342 foetuses, neonatal RDS was diagnosed in 47 foetuses. Foetuses diagnosed with RDS had statistically higher PI and RI values, whereas At/Et ratio and PSV were lower. At/Et ratio, PI and RI, PSV showed significant correlation with gestational age and the most statistically significant correlation was found with At/Et ratio. A cut-off value of 0.2865 (sensitivity 89.45%, specificity 94.79%) and 0.3155 (sensitivity 93.22%, specificity 96.78%) correlated strongly with development of RDS in late preterm foetuses and early term infants.

Conclusion
Foetal MPA indices like PSV, RI, PI and especially Foetal At/Et ratio is a promising non-invasive tool which helps in identifying foetuses at risk and may be very useful to plan delivery in complicated pregnancies and also for better post-natal care of the neonate.
Retroperitoneal approach in a child with ganglioneuroma: points of technique and literature review
Authors: Impellizzeri Pietro , Peri Flora M. , Arena Salvatore , Trimarchi Renato , Romeo Carmelo , Dionigi Gianlorenzo 
Published: August 2022

Abstract
Background data
Ganglioneuroma is rare in children and often incidentally discovered. The transperitoneal laparoscopic approach is the surgical choice for most of the surgeons because of the familiar anatomy and the wider working spaces. However, a posterior retroperitoneal approach started to be used in pediatric population demonstrating to be safe and effective.

Case presentation
We present a case of a child with radiological finding of a right adrenal mass. Due to the increased risk of having a malignant transformation, a surgical resection was decided using a retroperitoneal approach. The adrenal mass was recognized and completely enucleated. The histopathological examination revealed a GN. Clinical course was uneventful with hospital discharge after 3 days. The outcome was evaluated by ultrasound examination performed 3–6 to 12–24 months and then annually. After 24 months, the patient is completely asymptomatic, and no adrenal masses in both sides have been detected.

Conclusions
The posterior retroperitoneoscopy permits a more direct exposure of the adrenal gland, without violating the peritoneum, and a close vision to the main vessels. We believe that this technique is a valid option for pediatric patients with small adrenal lesions.
Ramadan fasting in hemodialysis population: single-center study
Authors: Emara Ahmed Abdelmoniem , Ghareeb Ahmed Hamed , Fayez Mahmoud , Elsharabasy Reem Mohsen 
Published: August 2022

Abstract
Background
Fasting Ramadan is one of the fundamental pillars of Islam. Although sick people are excluded from this duty, some of the hemodialysis patients insist to fast to enjoy the spiritual nature of the holy month.

Objectives
To monitor the tolerability of fasting Ramadan among the hemodialysis population.

Methodology
One hundred ninety-nine prevalent hemodialysis (HD) patients participated in the study and were allocated to 3 groups according to their fasting decision (complete, partial, and non- fasting). Basic demographic and laboratory data were collected before the start of the holy month; monitoring any inter or intradialytic complications or events during the holy month was done in addition to dry weight monitoring before and at the end of the month.

Results
One hundred ninety-nine HD patients were included (97 males, mean age 45 ± 15 SD). Patients were divided based on their fasting state into 3 groups: compete fasting 28 (14%), partial fasting 88 (44%), and non-fasting 83 (42%). Out of 116 total fasting patients, only 4 patients (3.4%) developed complications (intradialytic hypotension (IDH) and muscle cramps) during dialysis. On the other hand, 3 patients experienced improvement of IDH; also, one patient reported improvement in dyspepsia. We noted a significant reduction in dry weight in the complete and partial fasting groups (P < 0.001 for both), unlike the non-fasting group (P = 0.75).

Conclusion
We may conclude that fasting Ramadan in hemodialysis patients whether complete or partial fasting may be tolerated by most of patients and was associated with a significant reduction in dry weight.
Response of Aswan cable-stayed bridge to spatial non-synchronous seismic excitations
Authors: Seleemah Maryam A. , Helam Mohamed S. , Abu-alenein Mohamed A. , Hammad Eslam B. , Goda Mohamed S. , Seleemah Ayman A. , Elkady Amr Z. 
Published: August 2022

AbstractCable-stayed bridges are important infrastructure facilities serving the world today. Therefore, their safety against earthquake ground motions is crucial. However, due to their long spans, the affecting seismic excitations might be spatially non-synchronous. This paper presents a study of the effect of non-synchronous seismic excitations on Aswan cable-stayed bridge located at southern Egypt. Nonlinear time history analysis was conducted on a three-dimensional finite element model of the bridge. The spatial variability was represented in terms of the wave passage effect which was simulated via different delay times between the arrivals of the ground motion to bridge supports. Results indicated that spatial variability of earthquake ground motion has, in general, a favorable effect on most bridge response parameters. This is attributed to the flexibility of the overall bridge provided by the flexibility of the bridge structural system and/or by existence of seismic isolation.
Abaloparatide Increases Lumbar Spine and Hip BMD in Japanese Patients With Osteoporosis: The Phase 3 ACTIVE-J Study
Authors: Matsumoto Toshio , Sone Teruki , Soen Satoshi , Tanaka Sakae , Yamashita Akiko , Inoue Tetsuo 
Published: August 2022

AbstractContextAbaloparatide reduced fracture risk in postmenopausal women with osteoporosis in the Abaloparatide Comparator Trial In Vertebral Endpoints (ACTIVE). Its effect in Japanese patients remains unexamined.ObjectiveThis work aimed to determine the efficacy and safety of abaloparatide in increasing bone mineral density (BMD) in Japanese patients with osteoporosis at high fracture risk.MethodsThis was a randomized, double-blind, placebo-controlled study conducted in Japan. Postmenopausal women and men with osteoporosis with high fracture risk were given daily subcutaneous 80 µg abaloparatide or placebo for 78 weeks (18 months). The primary end point was percentage change in lumbar spine (LS) BMD from baseline at the last visit. Secondary end points included time-course changes in LS, total hip (TH), and femoral neck (FN) BMDs and bone turnover markers, and cumulative number of fractures.ResultsAbaloparatide increased LS, TH, and FN BMDs (mean [95% CI]) by 12.5% (10.3%-14.8%; P &lt; .001), 4.3% (3.3%-5.3%), and 4.3% (2.9%-5.6%), respectively, vs placebo. Serum procollagen type I N-terminal propeptide increased rapidly to ~ 140% above baseline at 6 weeks and gradually decreased but was approximately 25% higher than baseline at 78 weeks. Serum carboxy-terminal cross-linking telopeptide of type I collagen gradually increased to 50% above baseline at 24 weeks and decreased gradually to the placebo-group level from 60 weeks. Four vertebrae of 3 participants in the placebo group, but none in the abaloparatide group, developed new vertebral fractures. The safety profile was similar to that in the ACTIVE study.ConclusionIn Japanese patients with postmenopausal and male osteoporosis with high fracture risk, abaloparatide for 78 weeks robustly increased LS, TH, and FN BMDs, suggesting a similar efficacy in Japanese patients vs the ACTIVE study population.
Circulating Exosomal circRNA_0063476 Impairs Expression of Markers of Bone Growth Via the miR-518c-3p/DDX6 Axis in ISS
Authors: Du Zhi , Yuan Jinghong , Wu Zhiwen , Chen Qi , Liu Xijuan , Jia Jingyu 
Published: August 2022

Abstract

Objectives
Idiopathic short stature (ISS), a disorder of unknown cause, accounts for approximately 80% of the clinical diagnoses of children with short stature. Exosomal circular RNA in plasma has been implicated in various disease processes. However, the role of exosome-derived circRNA in ISS has not been elucidated yet.

Methods
Plasma exosomes of ISS and normal children were cocultured with human chondrocytes. Microarray analysis and RT-PCR identified the differential expression of circRNA in exosomes between ISS and normal children. Hsa_circ_0063476 was upregulated or downregulated in human chondrocytes. Subsequently, overexpression rats of hsa_circ_0063476 was constructed via adenoviral vector to further validate the role of hsa_circ_0063476 on longitudinal bone growth via in vivo experiment.

Results
The plasma exosome of ISS children suppressed the expression of markers of chondrocyte hypertrophy and endochondral ossification. Subsequently, upregulation of hsa_circ_0063476 in ISS exosome was identified. In vitro experiments demonstrated that chondrocyte proliferation, cell cycle and endochondral ossification were suppressed, and apoptosis was increased following hsa_circ_0063476 overexpression in human chondrocytes. Conversely, silencing hsa_circ_0063476 in human chondrocytes can show opposite outcomes. Our study further revealed hsa_circ_0063476 overexpression in vitro can enhance chondrocyte apoptosis and inhibit the expression of markers of chondrocyte proliferation and endochondral ossification via miR-518c-3p/DDX6 axis. Additionally, the rats with hsa_circ_0063476 overexpression showed a short stature phenotype.

Conclusions
The authors identified a novel pathogenesis in ISS that exosome-derived hsa_circ_0063476 retards the expression of markers of endochondral ossification and impairs longitudinal bone growth via miR-518c-3p/DDX6 axis, which may provide a unique therapeutic avenue for ISS.
A clinically relevant model of acute respiratory distress syndrome in human-size swine
Authors: Kaslow Sarah R. , Reimer Jonathan A. , Pinezich Meghan R. , Hudock Maria R. , Chen Panpan , Morris Mariya G. , Kain Mandy L. , Leb Jay S. , Ruzal-Shapiro Carrie B. , Marboe Charles C. , Bacchetta Matthew , Dorrello N. Valerio , Vunjak-Novakovic Gordana 
Published: August 2022

ABSTRACT
Despite over 30 years of intensive research for targeted therapies, treatment of acute respiratory distress syndrome (ARDS) remains supportive in nature. With mortality upwards of 30%, a high-fidelity pre-clinical model of ARDS, on which to test novel therapeutics, is urgently needed. We used the Yorkshire breed of swine to induce a reproducible model of ARDS in human-sized swine to allow the study of new therapeutics, from both mechanistic and clinical standpoints. For this, animals were anesthetized, intubated and mechanically ventilated, and pH-standardized gastric contents were delivered bronchoscopically, followed by intravenous infusion of Escherichia coli-derived lipopolysaccharide. Once the ratio of arterial oxygen partial pressure (PaO2) to fractional inspired oxygen (FIO2) had decreased to &lt;150, the animals received standard ARDS treatment for up to 48 h. All swine developed moderate to severe ARDS. Chest radiographs taken at regular intervals showed significantly worse lung edema after induction of ARDS. Quantitative scoring of lung injury demonstrated time-dependent increases in interstitial and alveolar edema, neutrophil infiltration, and mild to moderate alveolar membrane thickening. This pre-clinical model of ARDS in human-sized swine recapitulates the clinical, radiographic and histopathologic manifestations of ARDS, providing a tool to study therapies for this highly morbid lung disease.
Study on the Translational Diffusion of Transient Species in 1-Alkyl-3-methylimidazolium-Based Ionic Liquids by Transient Grating Spectroscopy
Authors: Nakajima Satoshi , Sumida Hiroki , Endo Takatsugu , Kimura Yoshifumi 
Published: August 2022

Abstract
Translational diffusion coefficients of two transient species in 1-alkyl-3-methylimidazolium-based ionic liquids (Cnmim+) with different alkyl chain lengths (n = 4, 8, 12) and the bis(trifluoromethanesulfonyl)imide anion were measured by transient grating spectroscopy. The systems of interest are the benzophenone ketyl radical (BPK) produced by the hydrogen-abstraction reaction of benzophenone (BP) and the zwitterionic merocyanine dye (MC) produced by the photoisomerization of 1,3,3-trimethylindolino-6′-nitrobenzopyrylospiran (SP). The diffusion coefficients of BPK and MC closely obey the Stokes-Einstein (SE) relation in the ionic liquids regardless of the alkyl chain lengths of the cations, whereas the diffusion coefficients of BP are larger than those predicted by the SE equation. The temperature dependences of the translational diffusion coefficients of BP, BPK, and MC reveal that the diffusional activation energies of BPK and MC are larger than those of BP in all solvents. The origin of this difference is discussed in terms of intermolecular interactions within the ionic-liquid solvents.
Individualized Endurance Training Based on Recovery and Training Status in Recreational Runners
Authors: NUUTTILA OLLI-PEKKA , NUMMELA ARI , KORHONEN ELISA , HÄKKINEN KEIJO , KYRÖLÄINEN HEIKKI 
Published: August 2022

ABSTRACT

Purpose
Long-term development of endurance performance requires a proper balance between strain and recovery. Because responses and adaptations to training are highly individual, this study examined whether individually adjusted endurance training based on recovery and training status would lead to greater adaptations compared with a predefined program.

Methods
Recreational runners were divided into predefined (PD; n = 14) or individualized (IND; n = 16) training groups. In IND, the training load was decreased, maintained, or increased twice a week based on nocturnal heart rate variability, perceived recovery, and heart rate–running speed index. Both groups performed 3-wk preparatory, 6-wk volume, and 6-wk interval periods. Incremental treadmill tests and 10-km running tests were performed before the preparatory period (T
0) and after the preparatory (T
1), volume (T
2), and interval (T
3) periods. The magnitude of training adaptations was defined based on the coefficient of variation between T
0 and T
1 tests (high >2×, low <0.5×).

Results
Both groups improved (P < 0.01) their maximal treadmill speed and 10-km time from T
1 to T
3. The change in the 10-km time was greater in IND compared with PD (−6.2% ± 2.8% vs −2.9% ± 2.4%, P = 0.002). In addition, IND had more high responders (50% vs 29%) and fewer low responders (0% vs 21%) compared with PD in the change of maximal treadmill speed and 10-km performance (81% vs 23% and 13% vs 23%), respectively.

Conclusions
PD and IND induced positive training adaptations, but the individualized training seemed more beneficial in endurance performance. Moreover, IND increased the likelihood of high response and decreased the occurrence of low response to endurance training.