bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic functional interrogation of human pseudogenes using CRISPRi
Authors: Sun Ming , Wang Yunfei , Zheng Caishang , Wei Yanjun , Hou Jiakai , Zhang Peng , He Wei , Lv Xiangdong , Ding Yao , Liang Han , Hon Chung-Chau , Chen Xi , Xu Han , Chen Yiwen 
Published: August 2021

AbstractBackgroundThe human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert important functions. However, to what extent human pseudogenes are functionally relevant remains unclear. There has been no large-scale characterization of pseudogene function because of technical challenges, including high sequence similarity between pseudogene and parent genes, and poor annotation of transcription start sites.ResultsTo overcome these technical obstacles, we develop an integrated computational pipeline to design the first genome-wide library of CRISPR interference (CRISPRi) single-guide RNAs (sgRNAs) that target human pseudogene promoter-proximal regions. We perform the first pseudogene-focused CRISPRi screen in luminal A breast cancer cells and reveal approximately 70 pseudogenes that affect breast cancer cell fitness. Among the top hits, we identify a cancer-testis unitary pseudogene, MGAT4EP, that is predominantly localized in the nucleus and interacts with FOXA1, a key regulator in luminal A breast cancer. By enhancing the promoter binding of FOXA1, MGAT4EP upregulates the expression of oncogenic transcription factor FOXM1. Integrative analyses of multi-omic data from the Cancer Genome Atlas (TCGA) reveal many unitary pseudogenes whose expressions are significantly dysregulated and/or associated with overall/relapse-free survival of patients in diverse cancer types.ConclusionsOur study represents the first large-scale study characterizing pseudogene function. Our findings suggest the importance of nuclear function of unitary pseudogenes and underscore their underappreciated roles in human diseases. The functional genomic resources developed here will greatly facilitate the study of human pseudogene function.
Genetic diversity and population structure of Rhipicephalus sanguineus sensu lato across different regions of Colombia
Authors: Páez-Triana Luisa , Muñoz Marina , Herrera Giovanny , Moreno-Pérez Darwin A. , Tafur-Gómez Gabriel A. , Montenegro Diego , Patarroyo Manuel A. , Paniz-Mondolfi Alberto , Ramírez Juan David 
Published: August 2021

Abstract
Background
There has been a long-standing debate over the taxonomic status of Rhipicephalus sanguineus sensu lato. Different studies worldwide have reported the occurrence of different well-defined lineages, in addition to Rhipicephalus sanguineus sensu stricto. To date, there are very few studies examining the diverse aspects of this tick in Colombia. We assessed the population structure and genetic diversity of R. sanguineus s.l. in eight departmental regions across Colombia.

Methods
A total of 170 ticks were collected from dogs in different departments of Colombia. All specimens were morphologically compatible with R. sanguineus s.l. and subjected to genetic analysis. DNA sequences were obtained for the 12S rDNA, cytochrome oxidase I (COI) and internal transcribed spacer 2 (ITS2) markers. A concatenated set of all mitochondrial markers was also constructed. Next, maximum likelihood phylogenetic trees were constructed using the sequences generated herein and sequences available in GenBank. Finally, we assessed different summary statistics and analysed population structure and divergence with Fst and Dxy and demographic changes with Tajima's D and Fu and Li’s statistical tests.

Results
Analysis of the 12S rDNA and COI revealed that all R. sanguineus s.l. specimens collected across different regions of Colombia clustered within the tropical lineage. Micro-geographical analyses showed that the tick population from Amazonas formed a distinct cluster separated from the other sequences, with moderate Fst and Dxy values. However, no signs of a robust population structure were found within the country. The results of Fu’s FS tests, together with the haplotype networks and diversity values, signal a possible population expansion of this tick species in Colombia.

Conclusions
Evidence provided herein supports the tropical lineage as the main circulating lineage in Colombia, exhibiting a general lack of genetic structure except for the Amazonas region.

Graphical Abstract
Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain
Authors: Liang Lindsay , Fazel Darbandi Siavash , Pochareddy Sirisha , Gulden Forrest O. , Gilson Michael C. , Sheppard Brooke K. , Sahagun Atehsa , An Joon-Yong , Werling Donna M. , Rubenstein John L. R. , Sestan Nenad , Bender Kevin J. , Sanders Stephan J. 
Published: August 2021

AbstractBackgroundGenetic variants in the voltage-gated sodium channelsSCN1A,SCN2A,SCN3A, andSCN8Aare leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes vary across development in the rodent brain, including mutually exclusive copies of the fifth protein-coding exon detected in the neonate (5N) and adult (5A). A second pair of mutually exclusive exons is reported inSCN8Aonly (18N and 18A). We aimed to quantify the expression of individual exons in the developing human brain.MethodsRNA-seq data from 783 human brain samples across development were analyzed to estimate exon-level expression. Developmental changes in exon utilization were validated by assessing intron splicing. Exon expression was also estimated in RNA-seq data from 58 developing mouse neocortical samples.ResultsIn the mature human neocortex, exon 5A is consistently expressed at least 4-fold higher than exon 5N in all four genes. ForSCN2A,SCN3A, andSCN8A, a brain-wide synchronized 5N to 5A transition occurs between 24 post-conceptual weeks (2nd trimester) and 6 years of age. In mice, the equivalent 5N to 5A transition begins at or before embryonic day 15.5. InSCN8A, over 90% of transcripts in the mature human cortex include exon 18A. Early in fetal development, most transcripts include 18N or skip both 18N and 18A, with a transition to 18A inclusion occurring from 13 post-conceptual weeks to 6 months of age. No other protein-coding exons showed comparably dynamic developmental trajectories.ConclusionsExon usage inSCN1A,SCN2A,SCN3A, andSCN8Achanges dramatically during human brain development. These splice isoforms, which alter the biophysical properties of the encoded channels, may account for some of the observed phenotypic differences across development and between specific variants. Manipulation of the proportion of splicing isoforms at appropriate stages of development may act as a therapeutic strategy for specific mutations or even epilepsy in general.
Pharmacy services for the 2019 Fédération Internationale de Natation (FINA) World Masters Championships in Gwangju, South Korea
Authors: Yang In Kyu , Shin Eun Ok , Kim Dong Gyun , Jung Hyun Cheol , Kim Kwang Joon , Ki Sung Hwan 
Published: August 2021

Abstract
Background
The role of sports pharmacists is being emphasized in international athletic events. This study aimed to describe the pharmacy services for the 2019 Fédération Internationale de Natation (FINA) World Masters Championships in Gwangju, South Korea.

Method
Research focused on athletes and coaching staff who received medications after visiting medical centers and pharmacies located in the athletes’ village from July 5 to July 29, 2019. We collected daily results of pharmacy operation and prescription interventions. The data were analyzed using Microsoft Excel, and were expressed as frequency (%).

Results
Throughout the tournament, 633 patients received medication at the athletes’ village pharmacy (gender: 338 men [53.4%], 295 women [46.6%]; nationality: 299 Korean [47.2%], 334 overseas players [52.8%]; patient type: 150 athletes [23.7%], 427 non-athletes [67.5%]). Therapy for musculoskeletal disorders was the most common (n = 29, 19.3%), and oral NSAIDs (n = 56, 22.0%) were the most frequently dispensed medication in athletes. Pharmacists intervened for 47 out of 491 prescriptions (9.6%), with dosage change (n = 21, 44.7%) being the most common intervention type.

Conclusion
Sports pharmacists at FINA World Masters Championships played a pivotal role in ensuring the safe usage of medications by all participants, especially athletes. This study results will be a useful reference for pharmacy services at future international or domestic sports competitions.
Complete genome sequence of Trueperella pyogenes strain Arash114, isolated from the uterus of a water buffalo (Bubalus bubalis) in Iran
Authors: Ashrafi Tamai Iradj , Mohammadzadeh Abdolmajid , Ghalyanchi Langeroudi Arash , Mahmoodi Pezhman , Ziafati Kafi Zahra , Pakbin Babak , Zahraei Salehi Taghi 
Published: August 2021

AbstractObjectiveTrueperella pyogeneshas been considered a major causative agent of metritis, abortion, and death in a broad range of domestic and wild animals, including cattle, swine, sheep, goats, camels, buffalo, deer, antelopes, reptiles, and birds.Data descriptionHere, we report the complete chromosome sequence ofTrueperella pyogenesstrain Arash114, isolated from the uterus of a water buffalo (Bubalus bubalis) died due to the infection caused by this pathogen. The genome assembly comprised 2,338,282 bp, with a 59.5% GC content. Annotation of the genome showed 46 tRNA genes, 6 rRNA, 1 CRISPR and 2059 coding sequences. Also, several genes coding for antimicrobial resistance such astetWand virulence factor includingplo,nanH,nanP,cbpand 4 fimbrial proteins were found. This study will advance our knowledge regarding the metabolism, virulence factors, antibiotic resistance and evolution of Arash114 strain and serve as an appropriate template for future researches.
Chronic and moderate consumption of reduced-alcohol wine confers cardiac benefits in a rat model of pulmonary arterial hypertension
Authors: Diaba-Nuhoho Patrick , Cour Martin , Hadebe Nkanyiso , Marais David , Lecour Sandrine , Blackhurst Dee 
Published: August 2021

Abstract
Objectives
In pulmonary arterial hypertension (PAH), right ventricular (RV) dysfunction develops via mechanisms involving oxidative stress. Moderate and chronic red wine (RW) consumption reduces oxidative stress and confers cardioprotection but its effect on PAH is unknown. We evaluated whether moderate and chronic consumption of reduced-alcohol RW (RARW) confers cardioprotection in a monocrotaline (MCT)-induced PAH rat model.

Results
Rats were randomly grouped: control; MCT; RARW; MCT + RARW. Wine was diluted to mimic moderate intake for humans, and consumed from 7 days before, until 28 days after MCT-injection. Echocardiography measured pulmonary artery acceleration time (PAAT) and RV thickness. Conjugated dienes (CD), and thiobarbituric acid reactive substances (TBARS) concentrations were assessed. MCT induced RV thickness and decreased PAAT compared to controls [1.22 ± 0.09 mm vs 0.46 ± 0.02 mm and 14 ± 1 vs 23 ± 2 m/s, respectively (p < 0.001)]. Chronic RARW consumption limited MCT-induced RV hypertrophy and increased PAAT. CD and TBARS increased in MCT-treated animals compared to controls (672 ± 43 nmol/L vs 453 ± 35 nmol/L; p < 0.01 and 13 ± 2 µmol/L vs 4 ± 0.3 µmol/L; p < 0.01). RARW reduced MCT-induced CD (472 ± 27 nmol/L vs 672 ± 43 nmol/L; p < 0.01).

Conclusion
Chronic and moderate intake of RARW ameliorates MCT-induced PAH in rats, which may be partly attributable to reduction of lipid peroxidation.
Endometrial stem/progenitor cells and their roles in immunity, clinical application, and endometriosis
Authors: Kong Yue , Shao Yang , Ren Chunxia , Yang Gong 
Published: August 2021

AbstractEndometrial stem/progenitor cells have been proved to exist in periodically regenerated female endometrium and can be divided into three categories: endometrial epithelial stem/progenitor cells, CD140b+CD146+ or SUSD2+ endometrial mesenchymal stem cells (eMSCs), and side population cells (SPs). Endometrial stem/progenitor cells in the menstruation blood are defined as menstrual stem cells (MenSCs). Due to their abundant sources, excellent proliferation, and autotransplantation capabilities, MenSCs are ideal candidates for cell-based therapy in regenerative medicine, inflammation, and immune-related diseases. Endometrial stem/progenitor cells also participate in the occurrence and development of endometriosis by entering the pelvic cavity from retrograde menstruation and becoming overreactive under certain conditions to form new glands and stroma through clonal expansion. Additionally, the limited bone marrow mesenchymal stem cells (BMDSCs) in blood circulation can be recruited and infiltrated into the lesion sites, leading to the establishment of deep invasive endometriosis. On the other hand, cell derived from endometriosis may also enter the blood circulation to form circulating endometrial cells (CECs) with stem cell-like properties, and to migrate and implant into distant tissues. In this manuscript, by reviewing the available literature, we outlined the characteristics of endometrial stem/progenitor cells and summarized their roles in immunoregulation, regenerative medicine, and endometriosis, through which to provide some novel therapeutic strategies for reproductive and cancerous diseases.
Serum-free medium and hypoxic preconditioning synergistically enhance the therapeutic effects of mesenchymal stem cells on experimental renal fibrosis
Authors: Ishiuchi Naoki , Nakashima Ayumu , Doi Shigehiro , Kanai Ryo , Maeda Satoshi , Takahashi Shinya , Nagao Masataka , Masaki Takao 
Published: August 2021

AbstractBackgroundMesenchymal stem cells (MSCs) repair injured tissue in a paracrine manner. To enhance their therapeutic properties, preconditioning with various factors has been researched. We have previously showed that MSCs cultured in serum-free medium (SF-MSCs) promote their immunosuppressive ability, thereby enhancing their anti-fibrotic effect. Here, we examined whether serum-free medium and hypoxic preconditioning synergistically enhance the therapeutic effects of MSCs on renal fibrosis in rats with ischemia–reperfusion injury (IRI).MethodsSF-MSCs were incubated under 1% O2conditions (hypo-SF-MSCs) or 21% O2conditions (normo-SF-MSCs) for 24 h before collection. After IRI procedure, hypo-SF-MSCs or normo-SF-MSCs were injected through the abdominal aorta. At 7 or 21 days post-injection, the rats were killed and their kidneys were collected to evaluate inflammation and fibrosis. In in vitro experiments, we investigated whether hypo-SF-MSCs enhanced secretion of anti-fibrotic humoral factors using transforming growth factor (TGF)-β1-stimulated HK-2 cells incubated with conditioned medium from hypo-SF-MSCs or normo-SF-MSCs.ResultsNormo-SF-MSCs showed attenuation of senescence, which increased their proliferative capacity. Although no significant difference in cellular senescence was found between normo-SF-MSCs and hypo-SF-MSCs, hypo-SF-MSCs further increased their proliferative capacity compared with normo-SF-MSCs. Additionally, administration of hypo-SF-MSCs more strongly ameliorated renal fibrosis than that of normo-SF-MSCs. Moreover, although hypo-SF-MSCs strongly attenuated infiltration of inflammatory cells compared with the control rats, which were treated with PBS, this attenuation was almost equal between normo-SF-MSCs and hypo-SF-MSCs. In vitro experiments revealed that hypo-SF-MSCs more significantly inhibited transforming growth factor (TGF)-β/Smad signaling compared with normo-SF-MSCs. Moreover, hypoxic preconditioning increased hepatocyte growth factor (HGF) secretion even under serum-free conditions, whereas knockdown of HGF in hypo-SF-MSCs attenuated inhibition of TGF-β/Smad signaling.ConclusionsThese results indicate that administration of ex vivo-expanded, hypoxia-preconditioned SF-MSCs may be a useful cell therapy to prevent renal fibrosis.
Antifibrotic effect of lung-resident progenitor cells with high aldehyde dehydrogenase activity
Authors: Takahashi Hiroshi , Nakashima Taku , Masuda Takeshi , Namba Masashi , Sakamoto Shinjiro , Yamaguchi Kakuhiro , Horimasu Yasushi , Miyamoto Shintaro , Iwamoto Hiroshi , Fujitaka Kazunori , Hamada Hironobu , Hattori Noboru 
Published: August 2021

Abstract
Background
Aldehyde dehydrogenase (ALDH) is highly expressed in stem/progenitor cells in various tissues, and cell populations with high ALDH activity (ALDHbr) are associated with tissue repair. However, little is known about lung-resident ALDHbr. This study was performed to clarify the characteristics of lung-resident ALDHbr cells and to evaluate their possible use as a tool for cell therapy using a mouse model of bleomycin-induced pulmonary fibrosis.

Methods
The characteristics of lung-resident/nonhematopoietic (CD45−) ALDHbr cells were assessed in control C57BL/6 mice. The kinetics and the potential usage of CD45−/ALDHbr for cell therapy were investigated in bleomycin-induced pulmonary fibrosis. Localization of transferred CD45−/ALDHbr cells was determined using mCherry-expressing mice as donors. The effects of aging on ALDH expression were also assessed using aged mice.

Results
Lung CD45−/ALDHbr showed higher proliferative and colony-forming potential than cell populations with low ALDH activity. The CD45−/ALDHbr cell population, and especially its CD45−/ALDHbr/PDGFRα+ subpopulation, was significantly reduced in the lung during bleomycin-induced pulmonary fibrosis. Furthermore, mRNA expression of ALDH isoforms was significantly reduced in the fibrotic lung. When transferred in vivo into bleomycin-pretreated mice, CD45−/ALDHbr cells reached the site of injury, ameliorated pulmonary fibrosis, recovered the reduced expression of ALDH mRNA, and prolonged survival, which was associated with the upregulation of the retinol-metabolizing pathway and the suppression of profibrotic cytokines. The reduction in CD45−/ALDHbr/PDGFRα+ population was more remarkable in aged mice than in young mice.

Conclusions
Our results strongly suggest that the lung expression of ALDH and lung-resident CD45−/ALDHbr cells are involved in pulmonary fibrosis. The current study signified the possibility that CD45−/ALDHbr cells could find application as novel and useful cell therapy tools in pulmonary fibrosis treatment.
Thrombocytopenia after meta-iodobenzylguanidine (MIBG) therapy in neuroblastoma patients may be caused by selective MIBG uptake via the serotonin transporter located on megakaryocytes
Authors: Blom Thomas , Meinsma Rutger , di Summa Franca , van den Akker Emile , van Kuilenburg André B. P. , Hansen Marten , Tytgat Godelieve A. M. 
Published: August 2021

Abstract
Background
The therapeutic use of [131I]meta-iodobenzylguanidine ([131I]MIBG) is often accompanied by hematological toxicity, primarily consisting of severe and persistent thrombocytopenia. We hypothesize that this is caused by selective uptake of MIBG via the serotonin transporter (SERT) located on platelets and megakaryocytes. In this study, we have investigated whether in vitro cultured human megakaryocytes are capable of selective plasma membrane transport of MIBG and whether pharmacological intervention with selective serotonin reuptake inhibitors (SSRIs) may prevent this radiotoxic MIBG uptake.

Methods
Peripheral blood CD34+ cells were differentiated to human megakaryocytic cells using a standardized culture protocol. Prior to [3H]serotonin and [125I]MIBG uptake experiments, the differentiation status of megakaryocyte cultures was assessed by flow cytometry. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to assess SERT and NET (norepinephrine transporter) mRNA expression. On day 10 of differentiation, [3H]serotonin and [125I]MIBG uptake assays were conducted. Part of the samples were co-incubated with the SSRI citalopram to assess SERT-specific uptake. HEK293 cells transfected with SERT, NET, and empty vector served as controls.

Results
In vitro cultured human megakaryocytes are capable of selective plasma membrane transport of MIBG. After 10 days of differentiation, megakaryocytic cell culture batches from three different hematopoietic stem and progenitor cell donors showed on average 9.2 ± 2.4 nmol of MIBG uptake per milligram protein per hour after incubation with 10–7 M MIBG (range: 6.6 ± 1.0 to 11.2 ± 1.0 nmol/mg/h). Co-incubation with the SSRI citalopram led to a significant reduction (30.1%—41.5%) in MIBG uptake, implying SERT-specific uptake of MIBG. A strong correlation between the number of mature megakaryocytes and SERT-specific MIBG uptake was observed.

Conclusion
Our study demonstrates that human megakaryocytes cultured in vitro are capable of MIBG uptake. Moreover, the SSRI citalopram selectively inhibits MIBG uptake via the serotonin transporter. The concomitant administration of citalopram to neuroblastoma patients during [131I]MIBG therapy might be a promising strategy to prevent the onset of thrombocytopenia.
Sulforaphane inhibits self-renewal of lung cancer stem cells through the modulation of sonic Hedgehog signaling pathway and polyhomeotic homolog 3
Authors: Wang Fanping , Sun Yanwei , Huang Xiaoyu , Qiao Caijuan , Zhang Wenrui , Liu Peijun , Wang Mingyong 
Published: August 2021

AbstractSulforaphane (SFN), an active compound in cruciferous vegetables, has been characterized by its antiproliferative capacity. We investigated the role and molecular mechanism through which SFN regulates proliferation and self-renewal of lung cancer stem cells. CD133+ cells were isolated with MACs from lung cancer A549 and H460 cells. In this study, we found that SFN inhibited the proliferation of lung cancer cells and self-renewal of lung cancer stem cells simultaneously. Meanwhile, the mRNA and protein expressions of Shh, Smo, Gli1 and PHC3 were highly activated in CD133+ lung cancer cells. Compared with siRNA-control group, Knock-down of Shh inhibited proliferation of CD133+ lung cancer cells, and decreased the protein expression of PHC3 in CD133+ lung cancer cells. Knock-down of PHC3 also affected the proliferation and decreased the Shh expression level in CD133+ lung cancer cells. In addition, SFN inhibited the activities of Shh, Smo, Gli1 and PHC3 in CD133+ lung cancer cells. Furthermore, the inhibitory effect of SFN on the proliferation of siRNA-Shh and siRNA-PHC3 cells was weaker than that on the proliferation of siRNA-control cells. Sonic Hedgehog signaling pathway might undergo a cross-talk with PHC3 in self-renewal of lung cancer stem cells. SFN might be an effective new drug which could inhibit self-renewal of lung cancer stem cells through the modulation of Sonic Hedgehog signaling pathways and PHC3. This study could provide a novel way to improve therapeutic efficacy for lung cancer stem cells.
Idiotype/anti-idiotype antibodies: as a glorious savior in COVID-19 pandemics
Authors: Naveed Ahsan , Naz Deeba , Rahman Sajjad ur 
Published: August 2021

AbstractThe idiotype network is experimentally modified to provide protective immunity against various microbial pathogens. Both internal and non-internal image-idiotype antibodies can trigger specific immune responses to antigens. The current outbreak of Severe Acute Respiratory Syndrome 2 (SARS-2) has provided a great opportunity to take advantage of idiotype / anti-idiotype antibodies as a protective regimen when no approved vaccine is available on earth. The current review identifies successful applications of idiotype/ anti-idiotype antibodies in various viral diseases and highlights their importance in COVID-19 pandemics. In the absence of vaccines and targeted therapies, polyclonal idiotype/ anti-idiotype antibodies against the viral structure may be a potential approach to the prevention and treatment of COVID-19 patients.