bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling the dynamics of the breast milk microbiome: impact of lactation stage and gestational age
Authors: Singh Parul , Al Mohannadi Noora , Murugesan Selvasankar , Almarzooqi Fajr , Kabeer Basirudeen Syed Ahamed , Marr Alexandra Katharina , Kino Tomoshige , Brummaier Tobias , Terranegra Annalisa , McGready Rose , Nosten François , Chaussabel Damien , Al Khodor Souhaila 
Published: November 2023

Abstract
Background
Breast milk (BM) provides complete nutrition for infants for the first six months of life and is essential for the development of the newborn’s immature immune and digestive systems. While BM was conventionally believed to be sterile, recent advanced high throughput technologies have unveiled the presence of diverse microbial communities in BM. These insights into the BM microbiota have mainly originated from uncomplicated pregnancies, possibly not reflecting the circumstances of mothers with pregnancy complications like preterm birth (PTB).

Methods
In this article, we investigated the BM microbial communities in mothers with preterm deliveries (before 37 weeks of gestation). We compared these samples with BM samples from healthy term pregnancies across different lactation stages (colostrum, transitional and mature milk) using 16S rRNA gene sequencing.

Results
Our analysis revealed that the microbial communities became increasingly diverse and compositionally distinct as the BM matured. Specifically, mature BM samples were significantly enriched in Veillonella and lactobacillus (Kruskal Wallis; p < 0.001) compared to colostrum. The comparison of term and preterm BM samples showed that the community structure was significantly different between the two groups (Bray Curtis and unweighted unifrac dissimilarity; p < 0.001). Preterm BM samples exhibited increased species richness with significantly higher abundance of Staphylococcus haemolyticus, Propionibacterium acnes, unclassified Corynebacterium species. Whereas term samples were enriched in Staphylococcus epidermidis, unclassified OD1, and unclassified Veillonella among others.

Conclusion
Our study underscores the significant influence of pregnancy-related complications, such as preterm birth (before 37 weeks of gestation), on the composition and diversity of BM microbiota. Given the established significance of the maternal microbiome in shaping child health outcomes, this investigation paves the way for identifying modifiable factors that could optimize the composition of BM microbiota, thereby promoting maternal and infant health.
LncRNA-XR_002792574.1-mediated ceRNA network reveals potential biomarkers in myopia-induced retinal ganglion cell damage
Authors: Wang Xuejun , Lin Qinghong , Liu Shengtao , Li Xiaoying , Kong Xiehe , Wang Yuliang , Ten Weijung , Huang Yangyi , Yang Yanting , Zhao Jing , Ma Xiaopeng , Zhou Xingtao 
Published: November 2023

Abstract
Background
Long noncoding RNAs (lncRNAs) play a key role in the occurrence and progression of myopia. However, the function of lncRNAs in retinal ganglion cells (RGCs) in the pathogenesis of myopia is still unknown. The aim of our study was to explore the lncRNA-mediated competing endogenous RNA (ceRNA) network in RGCs during the development of myopia.

Methods
RNA sequencing was performed to analyze lncRNA and mRNA expression profiles in RGCs between guinea pigs with form-deprived myopia (FDM) and normal control guinea pigs, and related ceRNA networks were constructed. Then, potentially important genes in ceRNA networks were verified by qRT‒PCR, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore biological functions in the RGCs of FDM guinea pigs. The important genes and related signaling pathways were further verified by qRT‒PCR, immunohistochemistry, immunofluorescence and Western blot in myopia in FDM guinea pigs, FDM mice, and highly myopic adults.

Results
The distribution of RGCs was uneven, the number of RGCs was decreased, and RGC apoptosis was increased in FDM guinea pigs. In total, 873 lncRNAs and 2480 mRNAs were determined to be differentially expressed genes in RGCs from normal control and FDM guinea pigs. Via lncRNA-mediated ceRNA network construction and PCR verification, we found that lncRNA-XR_002792574.1 may be involved in the development of myopia through the miR-760-3p/Adcy1 pathway in RGCs. Further verification in FDM guinea pigs, FDM mice, and highly myopic adults demonstrated that the lncRNA-XR_002792574.1/miR-760-3p/Adcy1 axis in RGCs might be related to cGMP/PKG, the apelin signaling pathway and scleral remodeling.

Conclusion
We demonstrated that the lncRNA-XR_002792574.1/miR-760-3p/Adcy1 axis in RGCs might be related to myopia. On the one hand, the lncRNA-XR_002792574.1/miR-760-3p/Adcy1 axis might inhibit the cGMP/PKG and apelin signaling pathways in RGCs, thereby causing RGC damage in myopia. On the other hand, the lncRNA-XR_002792574.1/miR-760-3p/Adcy1 axis may cause myopic scleral remodeling through the ERK-MMP-2 pathway. These findings may reveal novel potential targets in myopia and provide reference value for exploration and development of gene editing therapeutics for hereditary myopia.
Mertk-expressing microglia influence oligodendrogenesis and myelin modelling in the CNS
Authors: Nguyen Linda T. , Aprico Andrea , Nwoke Eze , Walsh Alexander D. , Blades Farrah , Avneri Raphael , Martin Elodie , Zalc Bernard , Kilpatrick Trevor J. , Binder Michele D. 
Published: November 2023

Abstract
Background
Microglia, an immune cell found exclusively within the CNS, initially develop from haematopoietic stem cell precursors in the yolk sac and colonise all regions of the CNS early in development. Microglia have been demonstrated to play an important role in the development of oligodendrocytes, the myelin producing cells in the CNS, as well as in myelination. Mertk is a receptor expressed on microglia that mediates immunoregulatory functions, including myelin efferocytosis.

Findings
Here we demonstrate an unexpected role for Mertk-expressing microglia in both oligodendrogenesis and myelination. The selective depletion of Mertk from microglia resulted in reduced oligodendrocyte production in early development and the generation of pathological myelin. During demyelination, mice deficient in microglial Mertk had thinner myelin and showed signs of impaired OPC differentiation. We established that Mertk signalling inhibition impairs oligodendrocyte repopulation in Xenopus tadpoles following demyelination.

Conclusion
These data highlight the importance of microglia in myelination and are the first to identify Mertk as a regulator of oligodendrogenesis and myelin ultrastructure.
Oil candidate genes in seeds of cotton (Gossypium hirsutum L.) and functional validation of GhPXN1
Authors: Gao Chenxu , Han Xiao , Xu Zhenzhen , Yang Zhaoen , Yan Qingdi , Zhang Yihao , Song Jikun , Yu Hang , Liu Renju , Yang Lan , Hu Wei , Yang Jiaxiang , Wu Man , Liu Jisheng , Xie Zongming , Yu Jiwen , Zhang Zhibin 
Published: November 2023

Abstract
Background
Cottonseed oil is a promising edible plant oil with abundant unsaturated fatty acids. However, few studies have been conducted to explore the characteristics of cottonseed oil. The molecular mechanism of cottonseed oil accumulation remains unclear.

Results
In the present study, we conducted comparative transcriptome and weighted gene co-expression network (WGCNA) analysis for two G. hirsutum materials with significant difference in cottonseed oil content. Results showed that, between the high oil genotype 6053 (H6053) and the low oil genotype 2052 (L2052), a total of 412, 507, 1,121, 1,953, and 2,019 differentially expressed genes (DEGs) were detected at 10, 15, 20, 25, and 30 DPA, respectively. Remarkably, a large number of the down-regulated DEGs were enriched in the phenylalanine metabolic processes. Investigation into the dynamic changes of expression profiling of genes associated with both phenylalanine metabolism and oil biosynthesis has shed light on a significant competitive relationship in substrate allocation during cottonseed development. Additionally, the WGCNA analysis of all DEGs identified eight distinct modules, one of which includes GhPXN1, a gene closely associated with oil accumulation. Through phylogenetic analysis, we hypothesized that GhPXN1 in G. hirsutum might have been introgressed from G. arboreum. Overexpression of the GhPXN1 gene in tobacco leaf suggested a significant reduction in oil content compared to the empty-vector transformants. Furthermore, ten other crucial oil candidate genes identified in this study were also validated using quantitative real-time PCR (qRT-PCR).

Conclusions
Overall, this study enhances our comprehension of the molecular mechanisms underlying cottonseed oil accumulation.
MGI short-read genome assemblies of Pythium insidiosum (reclassified as Pythium periculosum) strains Pi057C3 and Pi050C3
Authors: Krajaejun Theerapong , Patumcharoenpol Preecha , Rujirawat Thidarat , Kittichotirat Weerayuth , Tangphatsornruang Sithichoke 
Published: November 2023

Abstract
Objectives
Pythium insidiosum causes a difficult-to-treat infectious condition called pythiosis, with high morbidity and mortality. So far, genome data of at least 10 strains of P. insidiosum, primarily classified in the phylogenetic clades I and II, have been sequenced using various next-generation sequencing platforms. The MGI short-read platform was employed to obtain genome data of 2 clade-III strains of P. insidiosum (recently reclassified as Pythium periculosum) from patients in Thailand and the United States. This work is a part of our attempt to generate a comprehensive genome database from diverse pathogen strains.

Data description
A 150-bp paired-end library was prepared from a gDNA sample of P. insidiosum (P. periculosum) strains Pi057C3 and Pi050C3 (also known as ATCC90586) to generate draft genome sequences using an MGISEQ-2000RS sequencer. As a result, for the strain Pi057C3, we obtained a 42.5-Mb assembled genome (164x coverage) comprising 14,134 contigs, L50 of 241, N50 of 45,748, 57.6% CG content, and 12,147 ORFs. For the strain Pi050C3, we received a 43.3-Mb draft genome (230x coverage) containing 14,511 contigs, L50 of 245, N50 of 45,208, 57.7% CG content, and 12,249 ORFs. The genome sequences have been deposited in the NCBI/DDBJ databases under the accession numbers JAKCXM000000000.1 (strain Pi057C3) and JAKCXL000000000.1 (strain Pi050C3).
Quantitative estimate of cognitive resilience and its medical and genetic associations
Authors: Phongpreecha Thanaphong , Godrich Dana , Berson Eloise , Espinosa Camilo , Kim Yeasul , Cholerton Brenna , Chang Alan L. , Mataraso Samson , Bukhari Syed A. , Perna Amalia , Yakabi Koya , Montine Kathleen S. , Poston Kathleen L. , Mormino Elizabeth , White Lon , Beecham Gary , Aghaeepour Nima , Montine Thomas J. 
Published: November 2023

Abstract
Background
We have proposed that cognitive resilience (CR) counteracts brain damage from Alzheimer’s disease (AD) or AD-related dementias such that older individuals who harbor neurodegenerative disease burden sufficient to cause dementia remain cognitively normal. However, CR traditionally is considered a binary trait, capturing only the most extreme examples, and is often inconsistently defined.

Methods
This study addressed existing discrepancies and shortcomings of the current CR definition by proposing a framework for defining CR as a continuous variable for each neuropsychological test. The linear equations clarified CR’s relationship to closely related terms, including cognitive function, reserve, compensation, and damage. Primarily, resilience is defined as a function of cognitive performance and damage from neuropathologic damage. As such, the study utilized data from 844 individuals (age = 79 ± 12, 44% female) in the National Alzheimer’s Coordinating Center cohort that met our inclusion criteria of comprehensive lesion rankings for 17 neuropathologic features and complete neuropsychological test results. Machine learning models and GWAS then were used to identify medical and genetic factors that are associated with CR.

Results
CR varied across five cognitive assessments and was greater in female participants, associated with longer survival, and weakly associated with educational attainment or APOE ε4 allele. In contrast, damage was strongly associated with APOE ε4 allele (P value < 0.0001). Major predictors of CR were cardiovascular health and social interactions, as well as the absence of behavioral symptoms.

Conclusions
Our framework explicitly decoupled the effects of CR from neuropathologic damage. Characterizations and genetic association study of these two components suggest that the underlying CR mechanism has minimal overlap with the disease mechanism. Moreover, the identified medical features associated with CR suggest modifiable features to counteract clinical expression of damage and maintain cognitive function in older individuals.
Endoscopic stent placement for the management of gastro-pleural and gastro-cutaneous fistula post laparoscopic sleeve gastrectomy: a case report
Authors: Parkash Om , Sohail Zahabia , Khalid Natasha 
Published: November 2023

Abstract
Background
Gastro-pleural and gastro-cutaneous fistulae formation are rare yet life-threatening complications post-bariatric surgery. To our knowledge so far only limited cases of gastro-pleural and gastro-cutaneous fistulae post gastric sleeve surgery have been reported in the literature with their corresponding management. Therefore, we are reporting a case of placement of an endoscopic stent in the management of gastro-cutaneous fistula post laparoscopic sleeve gastrectomy.

Case presentation
A 42 years old Pakistani, female morbidly obese patient, underwent laparoscopic sleeve gastrectomy. Within a week after the procedure, the patient presented with dyspnea. Workup showed a gastric leak for which percutaneous drain placement was done. Later, gastro-pleural and gastro-cutaneous fistulae were formed for which endoscopic fistula closure was done using a metallic stent.

Conclusion
Endoscopic stent placement is an emerging field and it is considered safe and effective for the management of complications related to bariatric surgery.
New dawn for keratoconus treatment: potential strategies for corneal stromal regeneration
Authors: Dou Shengqian , Liu Xiaoxue , Shi Weiyun , Gao Hua 
Published: November 2023

AbstractKeratoconus is a progressive, ectatic and blinding disorder of the cornea, characterized by thinning of corneal stroma. As a highly prevalent among adolescents, keratoconus has been a leading indication for corneal transplantation worldwide. However, the severe shortage of donor corneas is a global issue, and the traditional corneal transplantation surgeries may superinduce multiple complications, necessitating efforts to develop more effective strategies for keratoconus treatment. In this review, we summarized several strategies to promote corneal stromal regeneration or improve corneal stromal thickness, including cell-based therapies, biosynthetic alternatives for inducing corneal regeneration, minimally invasive intrastromal implantation and bioengineered tissues for implantation. These strategies provided more accessible but safer alternatives from various perspectives for keratoconus treatment, paving the way for arresting the keratoconus progression in its earlier stage. For the treatments of corneal ectatic diseases beyond keratoconus, these approaches will provide important references and widen the therapy options in a donor tissue-independent manner.
Cell-based passive immunization for protection against SARS-CoV-2 infection
Authors: Sawula Evan , Miersch Shane , Jong Eric D. , Li Chengjin , Chou Fang-Yu , Tang Jean Kit , Saberianfar Reza , Harding Jeffrey , Sidhu Sachdev S. , Nagy Andras 
Published: November 2023

Abstract
Background
Immunologically impaired individuals respond poorly to vaccines, highlighting the need for additional strategies to protect these vulnerable populations from COVID-19. While monoclonal antibodies (mAbs) have emerged as promising tools to manage infectious diseases, the transient lifespan of neutralizing mAbs in patients limits their ability to confer lasting, passive prophylaxis from SARS-CoV-2. Here, we attempted to solve this problem by combining cell and mAb engineering in a way that provides durable immune protection against viral infection using safe and universal cell therapy.

Methods
Mouse embryonic stem cells equipped with our FailSafe™ and induced allogeneic cell tolerance technologies were engineered to express factors that potently neutralize SARS-CoV-2, which we call ‘neutralizing biologics’ (nBios). We subcutaneously transplanted the transgenic cells into mice and longitudinally assessed the ability of the cells to deliver nBios into circulation. To do so, we quantified plasma nBio concentrations and SARS-CoV-2 neutralizing activity over time in transplant recipients. Finally, using similar cell engineering strategies, we genetically modified FailSafe™ human-induced pluripotent stem cells to express SARS-CoV-2 nBios.

Results
Transgenic mouse embryonic stem cells engineered for safety and allogeneic-acceptance can secrete functional and potent SARS-CoV-2 nBios. As a dormant, subcutaneous tissue, the transgenic cells and their differentiated derivatives long-term deliver a supply of protective nBio titers in vivo. Moving toward clinical relevance, we also show that human-induced pluripotent stem cells, similarly engineered for safety, can secrete highly potent nBios.

Conclusions
Together, these findings show the promise and potential of using ‘off-the-shelf’ cell products that secrete neutralizing antibodies for sustained protective immunity against current and future viral pathogens of public health significance.
Diagnosis of testicular torsion with preserved blood flow detected by color Doppler ultrasonography
Authors: Kikkawa Kazuro , Ueda Yuko , Yamashita Shimpei , Kohjimoto Yasuo , Hara Isao 
Published: November 2023

Abstract
Background
To diagnose testicular torsion promptly and accurately when diagnosis of testicular torsion is difficult by color Doppler ultrasonography owing to testicular blood flow, we assess the helpfulness of physical findings to aid diagnosis of testicular torsion in cases with preserved testicular blood flow.

Methods
We retrospectively collected data of 45 patients below 18 years of age with suspected diagnosis of testicular torsion and underwent surgery. The clinical data of testicular torsion with normal testicular blood flow were compared to testicular torsion with normal testicular blood flow or no-testicular torsion for accurate diagnosis of testicular torsion.

Results
Testicular torsion was diagnosed in 34 of the 45 patients, and normal testicular blood flow was detected in six of the 34 patients. In testicular torsion with normal flow, duration of symptoms was significantly shorter, and the degree of torsion was significantly more mild than decreased blood flow. All testicular torsion with normal testicular flow had abnormal testicular findings. Duration of symptoms in patients with testicular torsion with normal flow was also significantly shorter than non-testicular torsion.

Conclusions
If testicular blood flow is detected, the presence of abnormal testicular findings and short duration of symptom are highly suspicious for testicular torsion.
Ruptured sinus of Valsalva aneurysm coexisted with congenital ventricular septal defect: a case series
Authors: Sari Ni Made Ayu Wulan , Dewangga Made Satria Yudha , Wibhuti Ida Bagus Rangga , Suastika Luh Oliva Saraswati , Badung I Dewa Gede Surya Mahardika , de Liyis Bryan Gervais , Kosasih Anastasya Maria , Prana Jagannatha Gusti Ngurah 
Published: November 2023

Abstract
Background
Ruptured sinus of Valsalva aneurysm (RSoVA) is an uncommon cardiac anomaly that may occasionally coexist with additional congenital heart disease (CHD). The presence of such congenital cardiac anomalies, frequently involving a ventricular septal defect (VSD), is of significant clinical importance and warrants vigilant detection during echocardiographic assessments to prevent oversight.

Case presentation
Three cases of RSoVA accompanied by VSD are presented in which all patients manifested symptoms of shortness of breath (SOB). In the first patient, right and left heart catheterization was undertaken; however, the images failed to reveal any evidence of VSD flow due to the occlusion of a small VSD by the prolapsed right coronary cusp (RCC). Prior to surgical intervention, multimodal imaging was conducted, revealing the presence of RSoVA extending into the right ventricle (RV) along with the VSD. The second patient had a prior childhood diagnosis of VSD but had not undergone further medical intervention. Transoesophageal echocardiography (TEE) was subsequently performed, identifying the presence of RSoVA, a small VSD, and valvular heart disease. The third patient presented with heart failure, exacerbated during her second pregnancy. TEE was also administered to this patient, revealing the presence of RSoVA accompanied by a small subaortic VSD with a left-to-right shunt. All three patients were scheduled for surgical repair of the ruptured sinus of Valsalva and closure of the VSD.

Conclusions
The coexistence of RSoVA and CHD, typically VSD, is frequently observed in patients experiencing symptoms of SOB. Recognizing the presence of CHD in individuals with RSoVA is of paramount importance, as it can significantly influence their medical management and treatment strategies.
The Lower Silurian Longmaxi rapid-transgressive black shale and organic matter distribution on the Upper Yangtze Platform, China
Authors: Shi Zhensheng , Zhou Tianqi , Qi Ling 
Published: November 2023

The characteristics and formation of maximum flooding (MF) black shales are important aspects in defining the geology of fine-grained reservoirs. The MF black shales are located at the bottom of the Longmaxi Formation on the Upper Yangtze Platform, corresponding to graptolite zone LM1. Seismic interpretation, X-ray diffraction entire rock analysis, total organic carbon (TOC) tests, and field emission scanning electron microscopy analysis indicate that the MF black shales have an average content of 49.3% quartz (85% clay size), 10.5% calcite, 8.4% dolomite, and 23.4% clay minerals. The quartz content increases basinward, whereas the clay mineral content decreases. The shale has developed during rapid sea level rise, with a thickness of 0.5–2.8 m that gradually thickens basinward. The TOC content, averaging 5.4%, gradually decreases basinward, with four distinct stacking patterns. The mineral composition and thickness of the Longmaxi shale are related closely to rapid transgression, biology, and volcanism during the period of sedimentation. Rapid transgression has led to a decrease in terrestrial input and shale thickness. In addition, biological activity and volcanism have caused the prevalence of microcrystalline quartz. Shales with high TOC content are related to anoxic conditions, along with low sedimentation rates and high primary productivity. The combination of an anoxic water column, weak dilution, and enhanced organic matter (OM) supply have enhanced the preservation of the OM. The four TOC stacking patterns are related to the water depth. The supply of clay minerals decreases with increasing water depth, whereas the degradation and recycling of OM decrease the TOC content. The sediment accommodation increases with increasing water depth, resulting in four TOC stacking patterns.