bluuebunny/crossref_metadata_2025 huggingface dataset:
Social Injustice by Prescription?
Authors: Kamugisha Gozibert Kamuhabwa , Nyakubega Peter
Published: November 2021

Since independence, Tanzania has instituted healthcare reforms in the quest for improving availability, quality, and social equity in access to public medical services. The extent to which the most recent healthcare reforms have impacted the existing patterns of medicinal prescription writing is largely opaque in the literature. This paper relies on data from two hospitals in Dar es Salaam. It emerges that the practice of categorising healthcare seekers into groups depending upon their varied health status and their entitlement to benefits has resulted in differential prescription allocations that might be interpreted as inequitable. The majority of very low income patients finance their healthcare through out-of-pocket payments and support of the Community Health Fund; this group receives a greater ratio of services with zero prescriptions, less poly-pharmacy and fewer prescribed generic medications than the proportion received by well-to-do patients with healthcare insurance. However, the medical and non-medical determinants of this differential in prescription allocation remain unclear, and so too, the ethical implications of such patterns in Tanzania’s out-patient medical service system are inconclusive.
Optical discs in zoological nomenclature: problems and proposed solution
Authors: DUBOIS ALAIN , ANEESH PANAKKOOL THAMBAN , BAUER AARON M. , CERÍACO LUIS M. P. , DANIEL GIMO M. , DELLAPÉ PABLO , ENGEL MICHAEL S. , FRÉTEY THIERRY , LÖBL IVAN , LORVELEC OLIVIER , MARINOV MILEN , OHLER ANNEMARIE , SCHMITT MICHAEL , WHITTINGTON ANDREW , YOUNG MARK , AESCHT ERNA
Published: November 2021

According to the Code currently in force, taxonomic works presenting nomenclatural novelties published on optical discs may be nomenclaturally available only if published between 1985 and 2013, and respecting some conditions allowing their nomenclatural promulgation. These works will remain accessible to readers only as long as the technologies allowing to read such discs are available to all, but will become inaccessible when these technologies become obsolete. In order to overcome this technology dependence, the Linz Zoocode Committee has decided to publish facsimiles of these works, both on paper and online. For this to be possible, a list of these works needs to be built. We are therefore sending an appeal to the international community to provide information on all taxonomic works including nomenclatural novelties published so far on optical discs, whether available or not under the current Code.
Nomenclatural status of Pyuridae and Bolteniidae (Tunicata, Ascidiacea) with comments on several included genera
Authors: SANAMYAN KAREN , SANAMYAN NADYA
Published: November 2021

Detailed discussion of the nomenclatural history of the Pyuridae, Bolteniidae and related families is provided. It is shown that the valid nomen for the family currently known as Pyuridae is Bolteniidae. The generic nomen "Claudenus Kott, 1998" is not available and Claudenus is re-established here as intentionally new nomen (Claudenus Sanamyan & Sanamyan gen. nov.) The generic nomen Cratostigma is not available but no replacement nomen is suggested because we suppose that this genus may be congeneric with Bolteniopsis. The generic nomen Eupera Michaelsen, 1904 is invalid being a junior homonym, but a new replacement nomen is not suggested because it is synonymized here with Culeolus.
It is high time that taxonomists follow the Code.
4. Amphibia of Indochina
Authors: DUBOIS ALAIN
Published: November 2021

A recent checklist of the Amphibia of Indochina contains several nomenclatural errors that should be corrected before they spread: two species-series and two genus-series treated as valid in this work are invalid; the authorships and dates of several family-series and of all class-series nomina mentioned are wrong; the information provided about onomatophores (nomen-bearing specimens and nomina) are incomplete and for some of them inaccurate. Besides, the ergotaxonomy (classification) adopted is methodologically poorly justified, supported mostly by ‘tradition’ and ‘stability’, and therefore arbitrary, heterogeneous and unreliable.
A cladistic revision of Tortopus Needham & Murphy with description of the new genus Tortopsis (Ephemeroptera: Polymitarcyidae)
Authors: MOLINERI CARLOS
Published: November 2021

The 12 species previously placed in Tortopus together with 3 species newly described here, are revised and included in a phylogenetic analysis. Based on synapomorphic characters on the nymphs and adults of both sexes, Tortopus is restricted to T. igaranus Needham & Murphy, T. circumfluus Ulmer, T. harrisi Traver, T. zottai (Navás), T. bellus Lugo-Ortiz & McCafferty, and T. arenales sp. nov., and the genus is defined by: female parastyli receptors with long furrows anterior to sockets; penes entirely flattened; male ninth abdominal sternum almost separated in two portions by a median notch; mesosternum with furcasternal protuberances contiguous only on basal corner; and nymphs with two subapical tubercles on mandibular tusks. Tortopsis is newly described for T. bruchianus (Navás), T. limoncocha sp. nov., T. obscuripennis (Domínguez), T. parishi (Banks), T. primus (McDunnough), T. puella (Pictet), T. sarae (Domínguez), T. spatula sp. nov., and T. unguiculatus (Ulmer). Tortopsis is characterized by: R sector of female fore wing without additional veins between R 2 and IR; female parastyli receptors C or V-shaped, with sockets opening towards median line; male gonopore associated with a claw-like structure; penes separated from the base; parastyli more than 5 times length of pedestals; parastyli curved in lateral view; nymphs with a single subapical tubercle on mandibular tusks. The study of available type material permitted inclusion of comparative diagnoses, with figures and redescriptions as needed. The male imago of the type species of Tortopus (T. igaranus Needham & Murphy) is described for the first time, as are the female adults of Tortopus bellus Lugo-Ortiz & McCafferty and T. harrisi Traver. Three new Neotropical species based on male and female adults are described: Tortopus arenales and Tortopsis limoncocha from Ecuador, and Tortopsis spatula from Colombia. Keys to separate the adults and nymphs of the genera of Polymitarcyidae, and for male and female adults of all the species of Tortopus and Tortopsis are presented, as well as line drawings, pictures and SEM photographs of important structures.
Revalidation and redescription of Bungona illiesi (Lugo-Ortiz & McCafferty) (Ephemeroptera: Baetidae) from Australia, based on mitochondrial and morphological evidence
Authors: WEBB J. M. , SUTER P. J.
Published: November 2021

Bungona illiesi (Lugo-Ortiz & McCafferty) n.comb. was described from a single specimen collected in northern Queensland, Australia, as a species of Cloeodes Traver. The distinguishing characteristics of a minute maxillary palp, the absence of spination on the mandibles between the mola and prostheca, narrow-elongate gills, and medially expanded labial palps were later found to occur in Bungona narilla Harker, and the two species were synonymized. Extensive collecting in northern Queensland yielded larvae and adults of Bungona that differ from B. narilla in all life stages. We believe our specimens are equivalent to B. illiesi because they were collected only a few kilometres from the type locality, at least one specimen had both minute and normally sized maxillary palps, nearly all specimens had medially expanded labial palps, and the dorsal abdominal colour pattern was similar. Sequences of a 657-bp fragment of the mitochondrial gene cytochrome oxidase I supported the recognition of two species and confirmed the association of larvae and adults of B. illiesi. Interspecific p-distances ranged from 18.8–19.4% and the maximum intraspecific divergence observed was 1.7%. Based on the combination of morphological, mitochondrial, and biogeographical data, we show B. illiesi should be recognised as a valid species distinct from B. narilla. Larvae of B. illiesi differ from those of B. narilla by having fewer robust setae on the femora and a small lateral tooth on the outer incisor of both mandibles. Male and female adults differ from those of B. narilla by having less extensive red colouration on the abdominal terga.
A taxonomic study of Chinese Empoascini (Hemiptera: Cicadellidae: Typhlocybinae) (I)
Authors: QIN DAO-ZHENG , LIU YANG , ZHANG YA-LIN
Published: November 2021

A new genus of Chinese Empoascini (Hemiptera: Cicadellidae: Typhlocybinae), Radicafurcus Qin & Zhang, gen. n. with one new species, R. breviprocessus Qin & Zhang, sp. n. from Sichuan Province (S.W. China) is described and illustrated. Baguoidea Mahmood 1967 is redescribed and a new species, B. yunnanensis Qin & Zhang, sp. n. is described from Yunnan Province (S.W. China). Two genera (Faiga Dworakowska 1980 and Sikkimasca Dworakowska 1994) are reported for the first time from China, and the type species of these genera are re-illustrated.
A new genus and new species of Baetidae (Ephemeroptera) from lakes and reservoirs in eastern North America
Authors: HILL MATTHEW A. , PFEIFFER JOHN , JACOBUS LUKE M.
Published: November 2021

Waynokiops dentatogriphus, new genus and new species (Ephemeroptera: Baetidae), is described from nymphs collected from seven lakes and reservoirs in the eastern United States of America, specifically from the states of Virginia, Kentucky, Ohio, Indiana and Arkansas (type locale), during sampling for the USEPA National Lakes Assessment. The lateral abdominal expansions and the dorsal abdominal armature of the new genus are unique among Cloeon complex genera. Abdominal tergal projections are unusual for a small minnow mayfly from lentic habitats.
Entero-Urachal Fistula: An Unusual Initial Presentation of Penetrating and Stricturing Crohn’s Disease
Authors: Herrick-Reynolds Kayleigh M. , Steinhauser Christina M. , Singla Manish , Kucera Walter B. , Wind Gary G. , Gerald Thomas S. , Altamar Hernan O. , O’Donnell Mary T.
Published: November 2021

Crohn’s disease (CD) has a wide variety of clinical presentations, ranging from abdominal pain to stricture and fistula. Fistulas involving the genitourinary tract can be severe and often require surgical intervention. Given the array of presenting symptoms, a delay in diagnosis can occur. We present the case of a healthy active duty soldier, with no previous medical history, found to have CD through an initial presentation of isolated umbilical drainage. Imaging workup identified an entero-uracho-cutaneous fistula with involvement of the transverse colon. Urachal anomalies are uncommon, and entero-urachal fistula as an initial presentation of CD is exceedingly rare. This case highlights the need to consider CD in the differential for patients with umbilical drainage despite a lack of concurrent more frequent presenting symptoms (abdominal pain, bloody diarrhea, and perianal fistula). Maintaining awareness of uncommon initial presentations of CD can minimize delay in diagnosis and thereby mitigate the risk of severe complications.
The Patterns of Bone Technology in Ancient Kashi (1300 bc to 300 ad)
Authors: Singh Anuradha
Published: November 2021

The political, socio-economic and cultural development of Kashi was never blocked. The history of technological development in Kashi state has been very flourished. The present study is an attempt to present historical and analytical studies regarding bone technology and its characteristics used in the region of ancient Kashi. The contribution of bone technology in the wisdom of Kashi and the development of a socio-economic perspective has also been discussed. Various bone tools obtained from Kashi’s archaeological sites and excavations reports have been studied. Archaeological and literary sources revealed that ancient Kashi was very developed in technology. The sources candidly depicted the prosperous societal life of its inhabitants in the backdrop of rich culture. Bone objects remains constitute an essential theme to study the integrated ecological aspect of human life.
India as a Global Power: The Strategic Culture Problems
Authors: Lunev Sergey I. , Shavlay Ellina P.
Published: November 2021

The article reviews India’s contested role of a great power in global politics. Although showing tangible results across all the aspects pertaining to the great power status, in international relations India is still largely underestimated and even overlooked. Politicians and scholars generally mention three main reasons behind that phenomenon: weak social and economic figures, the country’s relatively narrow global impact and the absence of strategic culture. We argue that the latter is key, and that it is in the process of being remedied. In fact, India already has all the prerequisites for being recognised as a ‘great power’, since it has political, military, economic and cultural capabilities corresponding to the status. It is simply a matter of time and coordinated efforts of the government to formulate and implement a consistent foreign policy and economic strategy as well as a change in Indian elite’s strategic thinking which will enable untapping India’s existing potential and successfully meeting the objective of increasing its influence in global politics.
Talent Development of Generation Y: Evidence from Sri Lanka
Authors: Kodagoda Thilakshi , Wijeratne Dulini
Published: November 2021

This study aims to understand the nature of Generation Y (Gen Y) and identify their understandings of talent development practices at the workplace. This research used open-ended interviews directed to 15 participants belonging to Gen Y in an automobile company in Sri Lanka. Job-hopping is an identifiable factor among the generation, as they continuously look for a change in their work and personal routines. The ‘Talk and chalk’ model is getting unpopular, whereas different approaches carrying new concepts have created a good impression among the Gen Y employees. Treasure hunts, talent shows, racing events, kaizen events, grooming and flexibility, were identified as non-traditional attractive talent development programmes. This research provided practical implications for employers to recognize how to Y-size their organizations by incorporating talent development as a critical strategy for retaining Gen Y. The present study has given attention to expanding the geographical scope of the literature on Gen Y.
Co-design in the Exascale Computing Project
Authors: Germann Timothy C
Published: November 2021

We provide an overview of the six co-design centers within the U.S. Department of Energy’s Exascale Computing Project, each of which is described in more detail in a separate paper in this special issue. We also give a perspective on the evolution of computational co-design.
The alleles of AGT and HIF1A gene affect the risk of hypertension in plateau residents
Authors: Li Zongjin , Hu Xi , Wan Jinping , Yang Jiyu , Jia Zeyu , Tian Liqin , Wu Xiaoming , Song Changxin , Yan Chengying
Published: November 2021

Plateau essential hypertension is a common chronic harmful disease of permanent residents in plateau areas. Studies have shown some single nucleotide polymorphisms (SNPs) associations with hypertension, but few have been verified in plateau area-lived people. In this paper, we examined some hypertension-related gene loci to analyze the relationship between risk SNPs and plateau essential hypertension in residents in Qinghai-Tibet plateau area. We screened hypertension-related SNPs from the literature, Clinvar database, GHR database, GTR database, and GWAS database, and then selected 101 susceptible SNPs for detection. Illumina MiSeq NGS platform was used to perform DNA sequencing on the blood samples from 185 Tibetan dwellings of Qinghai, and bioinformatic tools were used to make genotyping. Genetic models adjusted by gender and age were used to calculate the risk effects of genotypes. Four known SNPs as well as a new locus were found associated with PHE, which were rs2493134 (AGT), rs9349379 (PHACTR1), rs1371182 (CYP2C56P-PRPS1P1), rs567481079 (CYP2C56P-PRPS1P1), and chr14:61734822 (HIF1A). Among them, genotypes of rs2493134, rs9349379, and rs567481079 were risk factors, genotypes of rs1371182 and chr14:61734822 were protective factors. The rs2493134 in AGT was found associated with an increased risk of the plateau essential hypertension by 3.24-, 3.24-, and 2.06-fold in co-dominant, dominant, and Log-additive models, respectively. The rs9349379 in PHACTR1 is associated with a 2.61-fold increased risk of plateau essential hypertension according to the dominant model. This study reveals that the alleles of AGT, HIF1A, and PHACTR1 are closely related to plateau essential hypertension risk in the plateau Tibetan population.
Impact of Demographic Factors on Consumer’s Usage of Digital Payments
Authors: Lohana Sarika , Roy Deepankar
Published: November 2021

The post-demonetization phase in India has triggered more cashless transactions; a shortage of cash in the system had forced consumers to shift themselves from cash to cashless transactions. In the retail space, the thrust has shifted on costs, as banks continued their efforts towards migrating customers to lower-cost electronic and automated channels to reduce human intervention. On the contrary, it is also vital to check the customers’ demographic impact on the usage of digital payment services. The objective of the study is to analyse the changing customer dynamics and improve the customer experience from the outcome. This article aims to investigate the impact of demographic factors on consumer usage (CU) of Digital payments during post-demonetization. Further, exploring the impact of demographic factors (gender, age, education, marital status and income) on CU and satisfaction of 599 respondents towards various digital payment methods in tier I and tier II cities of India. The results show a significant impact of age, education, occupation, and income of respondents and no significant impact of gender and marital status of the respondents on consumers’ usage. The outcomes of the current work revealed useful insights into consumer’s usage and satisfaction with four prevailing digital payment methods vis-à-vis demographic factors. This study is significant as it empirically examines the impact of demographic factors on the CU of digital payment systems during the post-demonetization period in India.
Geeli Pucchi: An Account of the Inheritance of Trauma and the Desire of an Untouchable: A Critical Film Review
Authors: Barot Mitali Usha
Published: November 2021

The piece is a critical review of a part of a contemporary anthology. The film is written and directed by a contemporary Dalit filmmaker. The author discusses the portrayal of caste in the film while deconstructing the identity of both the protagonist and the antagonist, discusses their traumas and caste locations. The author further discusses how being Dalit, a woman and bearing an identity other than that of being heterosexual is a lethal combination in both rural and urban India even today. The author brings focus on caste and the power structures prevalent today and how they change the experience of love, intimacy and sexuality, how the bodies of Dalit folks are undesirable and continue to remain untouchable.
Development of Surgical and Visualization Procedures to Analyze Vasculatures by Mouse Tail Edema Model
Authors: Kumegawa Shinji , Yamada Gen , Hashimoto Daiki , Hirashima Tsuyoshi , Kajimoto Mizuki , Isono Kyoichi , Fujimoto Kota , Suzuki Kentaro , Uemura Kazuhisa , Ema Masatsugu , Asamura Shinichi
Published: November 2021

Background

Because of the high frequency of chronic edema formation in the current “aged” society, analyses and detailed observation of post-surgical edema are getting more required. Post-surgical examination of the dynamic vasculature including L.V. (Lymphatic Vasculature) to monitor edema formation has not been efficiently performed. Hence, procedures for investigating such vasculature are essential. By inserting transparent sheet into the cutaneous layer of mouse tails as a novel surgery model (theTailEdema bySilicone sheet mediatedTransparency protocol; TEST), the novel procedures are introduced and analyzed by series of histological analyses including video-based L.V. observation and 3D histological reconstruction of vasculatures in mouse tails.

Results

The dynamic generation of post-surgical main and fine (neo) L.V. connective structure during the edematous recovery process was visualized by series of studies with a novel surgery model. Snapshot images taken from live binocular image recording for TEST samples suggested the presence of main and elongating fine (neo) L.V. structure. After the ligation of L.V., the enlargement of main L.V. was confirmed. In the case of light sheet fluorescence microscopy (LSFM) observation, such L.V. connections were also suggested by using transparent 3D samples. Finally, the generation of neo blood vessels particularly in the region adjacent to the silicone sheet and the operated boundary region was suggested in 3D reconstruction images. However, direct detection of elongating fine (neo) L.V. was not suitable for analysis by such LSFM and 3D reconstruction procedures. Thus, such methods utilizing fixed tissues are appropriate for general observation for the operated region including of L.V.

Conclusions

The current surgical procedures and analysis on the post-surgical status are the first case to observe vasculatures in vivo with a transparent sheet. Systematic analyses including the FITC-dextran mediated snap shot images observation suggest the elongation of fine (neo) lymphatic vasculature. Post-surgical analyses including LSFM and 3D histological structural reconstruction, are suitable to reveal the fixed structures of blood and lymphatic vessels formation.
Promising self-emulsifying drug delivery system loaded with lycopene from red guava (Psidium guajava L.): in vivo toxicity, biodistribution and cytotoxicity on DU-145 prostate cancer cells
Authors: Vasconcelos Andreanne G. , Barros Ana Luisa A. N. , Cabral Wanessa F. , Moreira Daniel C. , da Silva Ingrid Gracielle M. , Silva-Carvalho Amandda É. , de Almeida Miguel P. , Albuquerque Lucas F. F. , dos Santos Raimunda C. , S. Brito Ana Karolinne , Saldanha-Araújo Felipe , Arcanjo Daniel D. R. , C. Martins Maria do Carmo , dos S. Borges Tatiana K. , Báo Sônia N. , Plácido Alexandra , Eaton Peter , Kuckelhaus Selma A. S. , Leite José Roberto S. A.
Published: November 2021

Background

Self-emulsifying drug delivery systems (SEDDSs) have attracted attention because of their effects on solubility and bioavailability of lipophilic compounds. Herein, a SEDDS loaded with lycopene purified from red guava (nanoLPG) was produced. The nanoemulsion was characterized using dynamic light scattering (DLS), zeta potential measurement, nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FTIR), lycopene content quantification, radical scavenging activity and colloidal stability in cell culture medium. Then, in vivo toxicity and tissue distribution in orally treated mice and cytotoxicity on human prostate carcinoma cells (DU-145) and human peripheral blood mononuclear cells (PBMC) were evaluated.

Results

NanoLPG exhibited physicochemical properties with a size around 200 nm, negative zeta-potential, and spherical morphology. The size, polydispersity index, and zeta potential parameters suffered insignificant alterations during the 12 month storage at 5 °C, which were associated with lycopene stability at 5 °C for 10 months. The nanoemulsion showed partial aggregation in cell culture medium at 37 °C after 24 h. NanoLPG at 0.10 mg/mL exhibited radical scavenging activity equivalent to 0.043 ± 0.002 mg Trolox/mL. The in vivo studies did not reveal any significant changes in clinical, behavioral, hematological, biochemical, and histopathological parameters in mice orally treated with nanoLPG at 10 mg/kg for 28 days. In addition, nanoLPG successfully delivered lycopene to the liver, kidney and prostate in mice, improved its cytotoxicity against DU-145 prostate cancer cells—probably by pathway independent on classical necrosis and apoptosis—and did not affect PBMC viability.

Conclusions

Thus, nanoLPG stands as a promising and biosafe lycopene delivery system for further development of nanotechnology-based health products.

Graphical Abstract
Identifying stress responsive genes using overlapping communities in co-expression networks
Authors: Riccio-Rengifo Camila , Finke Jorge , Rocha Camilo
Published: November 2021

Background

This paper proposes a workflow to identify genes that respond to specific treatments in plants. The workflow takes as input the RNA sequencing read counts and phenotypical data of different genotypes, measured under control and treatment conditions. It outputs a reduced group of genes marked as relevant for treatment response. Technically, the proposed approach is both a generalization and an extension of WGCNA. It aims to identify specific modules of overlapping communities underlying the co-expression network of genes. Module detection is achieved by using Hierarchical Link Clustering. The overlapping nature of the systems’ regulatory domains that generate co-expression can be identified by such modules. LASSO regression is employed to analyze phenotypic responses of modules to treatment.

Results

The workflow is applied to rice (Oryza sativa), a major food source known to be highly sensitive to salt stress. The workflow identifies 19 rice genes that seem relevant in the response to salt stress. They are distributed across 6 modules: 3 modules, each grouping together 3 genes, are associated to shoot K content; 2 modules of 3 genes are associated to shoot biomass; and 1 module of 4 genes is associated to root biomass. These genes represent target genes for the improvement of salinity tolerance in rice.

Conclusions

A more effective framework to reduce the search-space for target genes that respond to a specific treatment is introduced. It facilitates experimental validation by restraining efforts to a smaller subset of genes of high potential relevance.
Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig
Authors: Arora Devender , Park Jong-Eun , Lim Dajeong , Choi Bong-Hwan , Cho In-Cheol , Srikanth Krishnamoorthy , Kim Jaebum , Park Woncheoul
Published: November 2021

Background

DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation.

Results

A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genesC7orf50, ACTB and MLC1in backfat andTNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5AandHOXA5in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver.

Conclusions

In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.
Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies
Authors: Velluva Akhil , Radtke Maximillian , Horn Susanne , Popp Bernt , Platzer Konrad , Gjermeni Erind , Lin Chen-Ching , Lemke Johannes R. , Garten Antje , Schöneberg Torsten , Blüher Matthias , Abou Jamra Rami , Le Duc Diana
Published: November 2021

Background

RNA-seq emerges as a valuable method for clinical genetics. The transcriptome is “dynamic” and tissue-specific, but typically the probed tissues to analyze (TA) are different from the tissue of interest (TI) based on pathophysiology.

Results

We developed Phenotype-Tissue Expression and Exploration (PTEE), a tool to facilitate the decision about the most suitable TA for RNA-seq. We integrated phenotype-annotated genes, used 54 tissues from GTEx to perform correlation analyses and identify expressed genes and transcripts between TAs and TIs. We identified skeletal muscle as the most appropriate TA to inquire for cardiac arrhythmia genes and skin as a good proxy to study neurodevelopmental disorders. We also explored RNA-seq limitations and show that on-off switching of gene expression during ontogenesis or circadian rhythm can cause blind spots for RNA-seq-based analyses.

Conclusions

PTEE aids the identification of tissues suitable for RNA-seq for a given pathology to increase the success rate of diagnosis and gene discovery. PTEE is freely available athttps://bioinf.eva.mpg.de/PTEE/
Effects of nitrogen levels on gene expression and amino acid metabolism in Welsh onion
Authors: Zhao Chen , Ma Guanchu , Zhou Lin , Zhang Song , Su Le , Sun Xin , Borrás-Hidalgo Orlando , Li Kunlun , Yue Qiulin , Zhao Lin
Published: November 2021

Background

Welsh onion constitutes an important crop due to its benefits in traditional medicine. Nitrogen is an important nutrient for plant growth and yield; however, little is known about its influence on the mechanisms of Welsh onion regulation genes. In this study, we introduced a gene expression and amino acid analysis of Welsh onion treated with different concentrations of nitrogen (N0, N1, and N2 at 0 kg/ha, 130 kg/ha, and 260 kg/ha, respectively).

Results

Approximately 1,665 genes were differentially regulated with different concentrations of nitrogen. Gene ontology enrichment analysis revealed that the genes involved in metabolic processes, protein biosynthesis, and transportation of amino acids were highly represented. KEGG analysis indicated that the pathways were related to amino acid metabolism, cysteine, beta-alanine, arginine, proline, and glutathione. Differential gene expression in response to varying nitrogen concentrations resulted in different amino acid content. A close relationship between gene expression and the content of amino acids was observed.

Conclusions

This work examined the effects of nitrogen on gene expression and amino acid synthesis and provides important evidence on the efficient use of nitrogen in Welsh onion.
Integrated analyses of miRNA-mRNA expression profiles of ovaries reveal the crucial interaction networks that regulate the prolificacy of goats in the follicular phase
Authors: Liu Yufang , Zhou Zuyang , He Xiaoyun , Tao Lin , Jiang Yanting , Lan Rong , Hong Qionghua , Chu Mingxing
Published: November 2021

Background

Litter size is an important index of mammalian prolificacy and is determined by the ovulation rate. The ovary is a crucial organ for mammalian reproduction and is associated with follicular development, maturation and ovulation. However, prolificacy is influenced by multiple factors, and its molecular regulation in the follicular phase remains unclear.

Methods

Ten female goats with no significant differences in age and weight were randomly selected and divided into either the high-yielding group (n = 5, HF) or the low-yielding group (n = 5, LF). Ovarian tissues were collected from goats in the follicular phase and used to construct mRNA and miRNA sequencing libraries to analyze transcriptomic variation between high- and low-yield Yunshang black goats. Furthermore, integrated analysis of the differentially expressed (DE) miRNA-mRNA pairs was performed based on their correlation. The STRING database was used to construct a PPI network of the DEGs. RT–qPCR was used to validate the results of the predicted miRNA-mRNA pairs. Luciferase analysis and CCK-8 assay were used to detect the function of the miRNA-mRNA pairs and the proliferation of goat granulosa cells (GCs).

Results

A total of 43,779 known transcripts, 23,067 novel transcripts, 424 known miRNAs and 656 novel miRNAs were identified by RNA-seq in the ovaries from both groups. Through correlation analysis of the miRNA and mRNA expression profiles, 263 negatively correlated miRNA-mRNA pairs were identified in the LF vs. HF comparison. Annotation analysis of the DE miRNA-mRNA pairs identified targets related to biological processes such as “estrogen receptor binding (GO:0030331)”, “oogenesis (GO:0048477)”, “ovulation cycle process (GO:0022602)” and “ovarian follicle development (GO:0001541)”. Subsequently, five KEGG pathways (oocyte meiosis, progesterone-mediated oocyte maturation, GnRH signaling pathway, Notch signaling pathway and TGF-β signaling pathway) were identified in the interaction network related to follicular development, and a PPI network was also constructed. In the network, we found that CDK12, FAM91A1, PGS1, SERTM1, SPAG5, SYNE1, TMEM14A, WNT4, and CAMK2G were the key nodes, all of which were targets of the DE miRNAs. The PPI analysis showed that there was a clear interaction among the CAMK2G, SERTM1, TMEM14A, CDK12, SYNE1 and WNT4 genes. In addition, dual luciferase reporter and CCK-8 assays confirmed that miR-1271-3p suppressed the proliferation of GCs by inhibiting the expression of TXLNA.

Conclusions

These results increase the understanding of the molecular mechanisms underlying goat prolificacy. These results also provide a basis for studying interactions between genes and miRNAs, as well as the functions of the pathways in ovarian tissues involved in goat prolificacy in the follicular phase.
Quantitative flow chamber system for evaluating in vitro biofilms and the kinetics of S. aureus biofilm formation in human plasma media
Authors: Sutipornpalangkul Werasak , Nishitani Kohei , Schwarz Edward M.
Published: November 2021

Background

It has been well established that biofilm formation on orthopaedic implants is a critical event in the pathogenesis of orthopaedic infections, yet the natural history of this process with respect to bacterial adhesion, proliferation, and glycocalyx matrix production remains poorly understood. Moreover, there are no quantitative methods yet available to assess the differences in biofilm formation between different bacterial strains or implant materials. Consequently, this study aimed to investigate the natural history of S. aureus in in vitro biofilm formation in human plasma media using a flow chamber system. Bioluminescent S. aureus strains were used to better understand the bacterial growth and biofilm formation on orthopaedic materials. Also, the effects of human plasma media were assessed by loading the chamber with Tryptic Soy Broth with 10% human plasma (TSB + HP).

Results

Scanning electron microscopy (SEM) was utilized to assess the morphological appearance of the biofilms, revealing that S. aureus inoculation was required for biofilm formation, and that the phenotypes of biofilm production after 24 h inoculation with three tested strains (SH1000, UAMS-1, and USA300) were markedly different depending on the culture medium. Time course study of the bioluminescence intensity (BLI) and biofilm production on the implants due to the UAMS-1 and USA300 strains revealed different characteristics, whereby UAMS-1 showed increasing BLI and biofilm growth until peaking at 9 h, while USA300 showed a rapid increase in BLI and biofilm formation at 6 h. The kinetics of biofilm formation for both UAMS-1 and USA300 were also supported and confirmed by qRT-PCR analysis of the 16S rRNA gene. Biofilms grown in our flow chamber in the plasma media were also demonstrated to involve an upregulation of the biofilm-forming-related genes icaA, fnbA, and alt. The BLI and SEM results from K-wire experiments revealed that the in vitro growth and biofilm formation by UAMS-1 and USA300 on stainless-steel and titanium surfaces were virtually identical.

Conclusion

We demonstrated a novel in vitro model for S. aureus biofilm formation with quantitative BLI and SEM outcome measures, and then used this model to demonstrate the presence of strain-specific phenotypes and its potential use to evaluate anti-microbial surfaces.
Occurrence and multidrug resistance of Campylobacter spp. at duck farms and associated environmental and anthropogenic risk factors in Bangladesh
Authors: Uddin Md. Nasir , Neogi Sucharit Basu , Islam Sk Shaheenur , Ferdous Jannatul , Khan Md. Shahidur Rahman , Yamasaki Shinji , Kabir S. M. Lutful
Published: November 2021

Background

The alarming rise in multi-drug resistant (MDR) zoonotic pathogens, includingCampylobacterspp., has been threatening the health sector globally. In Bangladesh, despite rapid growth in poultry sector little is known about the potential risks of zoonotic pathogens in homestead duck flocks. The aim of this study was to understand the occurrence, species diversity, and multi-drug resistance inCampylobacterspp., and identify the associated risk factors in duck farms in Bangladesh.

Methods

The study involved 20 duck farms at 6 sub-districts of Mymensingh, Bangladesh. Monthly occurrence ofCampylobacterspp. in potential sources at the farms during February-September, 2018, was detected by culture and PCR-based methods.Campylobacterisolates were examined for resistance to different antimicrobials. Risk factors, concerning climatic and environmental disposition, farm management, and anthropogenic practices, ofCampylobacterinfection were estimated by participatory epidemiological tools.

Results

Occurrence ofCampylobacterspp. was detected in overall 36.90% (155/420) samples, more frequently in drinking water (60%, 30/50), followed by cloacal swab (37.50%, 75/200), egg surface swab (35%, 35/100) and soil of the duck resting places (30%, 15/50) but was not detected in feed samples (n = 20). PCR assays distinguished the majority (61.30%, 95/155) of the isolates asC. coli, while the rest (38.70%, 60/155) wereC. jejuni. Notably, 41.7% (25/60) and 31.6% (30/95) strains ofC. jejuniandC. coli, respectively, were observed to be MDR. The dynamics ofCampylobacterspp., distinctly showing higher abundance during summer and late-monsoon, correlated significantly with temperature, humidity, and rainfall, while sunshine hours had a negative influence. Anthropogenic management-related factors, including, inadequate hygiene practices, use of untreated river water, wet duck shed, flock age (1–6 months), and unscrupulous use of antimicrobials were identified to enhance the risk of MDRCampylobacterinfection.

Conclusion

The present study clearly demonstrates that duck farms contribute to the enhanced occurrence and spread of potentially pathogenic and MDRC. coliandC. jejunistrains and the bacterial dynamics are governed by a combined interaction of environmental and anthropogenic factors. A long-term holistic research at the environment-animal-human interface would be integral to divulge health risk reduction approaches tackling the spread ofCampylobacterspp. from duck farms.
Assessing the use of antibiotics and the burden of varicella in Belgium using a retrospective GP database analysis
Authors: Vandenhaute Jessica , Tsakeu Elyonore , Chevalier Pierre , Pawaskar Manjiri , Benčina Goran , Vertriest Jan
Published: November 2021

Background

Varicella is a highly contagious infection that typically occurs in childhood. While most cases have a generally benign outcome, infection results in a considerable healthcare burden and serious complications may occur.

Objectives

The objective of this study was to characterize the burden of varicella in a real-world primary care setting in Belgium, including the rate of varicella-related complications, medication management and general practitioner (GP) visits.

Methods

The study was a retrospective observational study using data from a longitudinal patient database in a primary care setting in Belgium. Patients with a GP visit and a varicella diagnosis between January 2016 and June 2019 were eligible and data one month prior and three months after the diagnosis were included. Outcomes included varicella-related complications, antibiotic use, antiviral use, and GP follow-up visits. Antibiotic use could be specified by class of antibiotic and linked to a diagnosis. Complications were identified based on concomitant diagnosis with varicella during the study period.

Results

3,847 patients with diagnosis of varicella were included, with a mean age of 8.4 years and a comparable distribution of gender. 12.6% of patients with varicella had a concomitant diagnosis of a varicella-related complication. During the follow-up period, 27.3% of patients with varicella were prescribed antibiotics, either systemic (19.8%) and/or topical (10.3%). The highest rate of antibiotic prescriptions was observed in patients with complications (63.5%) and in patients younger than 1 year (41.8%). Nevertheless, 5.3% of the patients were prescribed antibiotics without a concomitant diagnosis of another infection. The most commonly prescribed systemic antibiotics were amoxicillin alone or combined with beta-lactamase inhibitor, and thiamphenicol. Fusidic acid and tobramycin were the most prescribed topical antibiotics. Antivirals were prescribed for 2.7% of the study population. 4.7% of the patients needed a follow-up visit with their GP.

Conclusions

This study reports a substantial burden of varicella in a primary care setting in Belgium, with high rates of complications and antibiotic use.
The ratio of measured to estimated glomerular filtration rate may be a marker of early mortality and dialysis requirement
Authors: Heaf James G. , Yahya Rafal , Dahl Morten
Published: November 2021

Background

It has been suggested that, in patients with CKD stage 5, measured GFR (mGFR), defined as the mean of urea and creatinine clearance, as measured by a 24-h urine collection, is a better measure of renal function than estimated GFR (eGFR), based on the CKD-EPI formula. This could be due to reduced muscle mass in this group. Its use is recommended in the ERBP guidelines. Unplanned dialysis initiation (DI) is associated with increased morbidity, mortality, and reduced modality choice and is generally considered undesirable. We hypothesized that the ratio mGFR/eGFR (M/E) aids prediction of death and DI.

Methods

All 24-h measurements of urea and creatinine excretion were extracted from the clinical biochemistry databases in Zealand. Data concerning renal diagnosis, comorbidity, biochemistry, medical treatment, mortality and date of DI, were extracted from patient notes, the National Patient Registry and the Danish Nephrology Registry. Patients were included if their eGFR was < 30 ml/min/1.73m2. The last available value for each patient was included. Follow-up was 12 months.

Results

One thousand two hundred sixty-five patients were included. M/E was median 0.91 ± 0.43. It was highly correlated to previous determinations. It was negatively correlated to eGFR, comorbidity, high age and female sex. It was positively related to albumin and negatively to C-reactive protein. M/E was higher in patients treated with ACE inhibitors and diuretics but no other treatment groups.

On a multivariate analysis, M/E was negatively correlated with mortality and combined mortality/DI, but not DI. A post hoc analysis showed a negative correlation to DI at 3 months. For patients with an eGFR 10–15 ml/min/1.73m2, combined mortality and DI at 3 months was for low M/E (< 0.75) 36%, medium (0.75–1.25) 20%, high (> 1.25) 8%. A low M/E predicted increased need for unplanned DI.

A supplementary analysis in 519 patients where body surface area values were available, allowing BSA-corrected M/E to be analyzed, revealed similar results.

Conclusion

A low mGFR/eGFR ratio is associated with comorbidity, malnutrition, and inflammation. It is a marker of early DI, mortality, and unplanned dialysis initiation, independently of eGFR, age and comorbidity. Particular attention paid to patients with a low M/E may lower the incidence of unplanned dialysis requirement.
Cautious addition of targeted therapy to PD-1 inhibitors after initial progression of BRAF mutant metastatic melanoma on checkpoint inhibitor therapy
Authors: Samlowski Wolfram , Adajar Camille
Published: November 2021

Background

Virtually all metastatic patients with metastatic melanoma who progress after initial treatment with PD-1 or CTLA-4 directed antibodies will die of their disease. Salvage options are urgently needed. It is theoretically attractive to combine immunotherapy with targeted agents in progressing patients with BRAF mutation positive melanoma, but the toxicity of combined treatment has proven challenging.

Methods

We performed a retrospective analysis of our patient database and identified 23 patients who progressed on initial checkpoint inhibitor treatment, who subsequently had cautious addition of BRAF±MEK inhibitor therapy to continued PD-1 antibody treatment.

Results

We found an objective response rate of 55% in second line therapy, with a median progression-free survival of 33.4 months and median overall survival of 34.1 months, with 40% of patients in unmaintained remission at over 3 years. Ten of 12 responding patients were able to discontinue all therapy and continue in unmaintained remission. Toxicity of this approach was generally manageable (21.7% grade 3–5 toxicity). There was 1 early sudden death for unknown reasons in a responding patient.

Discussion

Our results suggest that 2nd line therapy with PD-1 inhibitors plus BRAF±MEK inhibitors has substantial activity and manageable toxicity. This treatment can induce additional durable complete responses in patients who have progressed on initial immunotherapy. These results suggest further evaluation be performed of sequential PD-1 antibody treatment with cautious addition of targeted therapy in appropriate patients.