bluuebunny/crossref_metadata_2025 huggingface dataset:
Combination of transcatheter arterial chemoembolization and portal vein embolization for patients with hepatocellular carcinoma: a review
Authors: Shao Zhiying , Liu Xin , Peng Chanjuan , Wang Liping , Xu Dong
Published: October 2021

Background

Transcatheter arterial chemoembolization has been widely used in patients with hepatocellular carcinoma. However, double blood supply and the existence of portal vein tumor thrombus influence the efficacy of transcatheter arterial chemoembolization.

Main body

Theoretically, portal vein embolization combined with transcatheter arterial chemoembolization may bring a breakthrough in the therapeutic effect of hepatocellular carcinoma. The feasibility, efficacy, long-term survival benefits, and side effects of the combined treatment have been explored in previous studies. Chemotherapeutic agents may also be added in the portal vein embolization procedure to further improve the treatment response.

Conclusion

In this study, we review the existing data and studies on the combined treatment in patients with hepatocellular carcinoma and provide an overall view of the strategy.
Mapping a mammalian adult adrenal gland hierarchy across species by microwell-seq
Authors: Lai Shujing , Ma Lifeng , E Weigao , Ye Fang , Chen Haide , Han Xiaoping , Guo Guoji
Published: October 2021

Recently, single-cell RNA-seq technologies have been rapidly updated, leading to a revolution in biology. We previously developed Microwell-seq, a cost-effective and high-throughput single cell RNA sequencing(scRNA-seq) method with a very simple device. Most cDNA libraries are sequenced using an expensive Illumina platform. Here, we present the first report showing combined Microwell-seq and BGI MGISEQ2000, a less expensive sequencing platform, to profile the whole transcriptome of 11,883 individual mouse adult adrenal gland cells and identify 18 transcriptionally distinct clusters. Moreover, we performed a single-cell comparative analysis of human and mouse adult adrenal glands to reveal the conserved genetic networks in these mammalian systems. These results provide new insights into the sophisticated adrenal gland hierarchy and provide a benchmark, low-cost strategy for high-throughput single-cell RNA study.
CRISPR/Cas: a potential gene-editing tool in the nervous system
Authors: Gao Yanxia , Gao Kexin , Yang Hui
Published: October 2021

The rapidly developmental RNA-guided CRISPR/Cas system is a powerful tool for RNA and DNA editing in a variety of cells from different species and makes a great contribution to gene function research, disease model generation and gene therapy development in the past few years. The ease of use, low cost and high efficiency of CRISPR/Cas make it commonly used in various conditions. In this review, we introduce the CRISPR/Cas system and its diverse applications in nervous system briefly, which provides a better understanding for its potential application values.
Capn3 depletion causes Chk1 and Wee1 accumulation and disrupts synchronization of cell cycle reentry during liver regeneration after partial hepatectomy
Authors: Chen Feng , Huang Delai , Shi Hui , Gao Ce , Wang Yingchun , Peng Jinrong
Published: October 2021

Recovery of liver mass to a healthy liver donor by compensatory regeneration after partial hepatectomy (PH) is a prerequisite for liver transplantation. Synchronized cell cycle reentry of the existing hepatocytes after PH is seemingly a hallmark of liver compensatory regeneration. Although the molecular control of the PH-triggered cell cycle reentry has been extensively studied, little is known about how the synchronization is achieved after PH. The nucleolus-localized protein cleavage complex formed by the nucleolar protein Digestive-organ expansion factor (Def) and cysteine proteinase Calpain 3 (Capn3) has been implicated to control wounding healing during liver regeneration through selectively cleaving the tumor suppressor p53 in the nucleolus. However, whether the Def-Capn3 complex participates in regulating the synchronization of cell cycle reentry after PH is unknown. In this report, we generated a zebrafish capn3b null mutant (capn3b∆19∆14). The homozygous mutant was viable and fertile, but suffered from a delayed liver regeneration after PH. Delayed liver regeneration in capn3b∆19∆14 was due to disruption of synchronized cell proliferation after PH. Mass spectrometry (MS) analysis of nuclear proteins revealed that a number of negative regulators of cell cycle are accumulated in the capn3b∆19∆14 liver after PH. Moreover, we demonstrated that Check-point kinase 1 (Chk1) and Wee1, two key negative regulators of G2 to M transition, are substrates of Capn3. We also demonstrated that Chk1 and Wee1 were abnormally accumulated in the nucleoli of amputated capn3b∆19∆14 liver. In conclusion, our findings suggest that the nucleolar-localized Def-Capn3 complex acts as a novel regulatory pathway for the synchronization of cell cycle reentry, at least partially, through inactivating Chk1 and Wee1 during liver regeneration after PH.
Consistent apparent Young’s modulus of human embryonic stem cells and derived cell types stabilized by substrate stiffness regulation promotes lineage specificity maintenance
Authors: Guo Anqi , Wang Bingjie , Lyu Cheng , Li Wenjing , Wu Yaozu , Zhu Lu , Bi Ran , Huang Chenyu , Li Jiao Jiao , Du Yanan
Published: October 2021

Background

Apparent Young’s modulus (AYM), which reflects the fundamental mechanical property of live cells measured by atomic force microscopy and is determined by substrate stiffness regulated cytoskeletal organization, has been investigated as potential indicators of cell fate in specific cell types. However, applying biophysical cues, such as modulating the substrate stiffness, to regulate AYM and thereby reflect and/or control stem cell lineage specificity for downstream applications, remains a primary challenge during in vitro stem cell expansion. Moreover, substrate stiffness could modulate cell heterogeneity in the single-cell stage and contribute to cell fate regulation, yet the indicative link between AYM and cell fate determination during in vitro dynamic cell expansion (from single-cell stage to multi-cell stage) has not been established.

Results

Here, we show that the AYM of cells changed dynamically during passaging and proliferation on substrates with different stiffness. Moreover, the same change in substrate stiffness caused different patterns of AYM change in epithelial and mesenchymal cell types. Embryonic stem cells and their derived progenitor cells exhibited distinguishing AYM changes in response to different substrate stiffness that had significant effects on their maintenance of pluripotency and/or lineage-specific characteristics. On substrates that were too rigid or too soft, fluctuations in AYM occurred during cell passaging and proliferation that led to a loss in lineage specificity. On a substrate with ‘optimal’ stiffness (i.e., 3.5 kPa), the AYM was maintained at a constant level that was consistent with the parental cells during passaging and proliferation and led to preservation of lineage specificity. The effects of substrate stiffness on AYM and downstream cell fate were correlated with intracellular cytoskeletal organization and nuclear/cytoplasmic localization of YAP.

Conclusions

In summary, this study suggests that optimal substrate stiffness regulated consistent AYM during passaging and proliferation reflects and contributes to hESCs and their derived progenitor cells lineage specificity maintenance, through the underlying mechanistic pathways of stiffness-induced cytoskeletal organization and the downstream YAP signaling. These findings highlighted the potential of AYM as an indicator to select suitable substrate stiffness for stem cell specificity maintenance during in vitro expansion for regenerative applications.
Organoid based personalized medicine: from bench to bedside
Authors: Li Yaqi , Tang Peiyuan , Cai Sanjun , Peng Junjie , Hua Guoqiang
Published: October 2021

Three-dimensional cultured organoids have become a powerful in vitro research tool that preserves genetic, phenotypic and behavioral trait of in vivo organs, which can be established from both pluripotent stem cells and adult stem cells. Organoids derived from adult stem cells can be established directly from diseased epithelium and matched normal tissues, and organoids can also be genetically manipulated by CRISPR-Cas9 technology. Applications of organoids in basic research involve the modeling of human development and diseases, including genetic, infectious and malignant diseases. Importantly, accumulating evidence suggests that biobanks of patient-derived organoids for many cancers and cystic fibrosis have great value for drug development and personalized medicine. In addition, organoids hold promise for regenerative medicine. In the present review, we discuss the applications of organoids in the basic and translational research.
Protein quality control of cell stemness
Authors: Yan Pengze , Ren Jie , Zhang Weiqi , Qu Jing , Liu Guang-Hui
Published: October 2021

Protein quality control (PQC) systems play essential roles in the recognition, refolding and clearance of aberrant proteins, thus ensuring cellular protein homeostasis, or proteostasis. Especially, continued proliferation and differentiation of stem cells require a high rate of translation; therefore, accurate PQC systems are essential to maintain stem cell function. Growing evidence suggested crucial roles of PQC systems in regulating the stemness and differentiation of stem cells. This review focuses on current knowledge regarding the components of the proteostasis network in stem cells, and the importance of proteostasis in maintaining stem cell identity and regenerative functions. A complete understanding of this process might uncover potential applications in aging intervention and aging-related diseases.
Proteins in DNA methylation and their role in neural stem cell proliferation and differentiation
Authors: Sun Jiaqi , Yang Junzheng , Miao Xiaoli , Loh Horace H. , Pei Duanqing , Zheng Hui
Published: October 2021

Background

Epigenetic modifications, namely non-coding RNAs, DNA methylation, and histone modifications such as methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation play a significant role in brain development. DNA methyltransferases, methyl-CpG binding proteins, and ten-eleven translocation proteins facilitate the maintenance, interpretation, and removal of DNA methylation, respectively. Different forms of methylation, including 5-methylcytosine, 5-hydroxymethylcytosine, and other oxidized forms, have been detected by recently developed sequencing technologies. Emerging evidence suggests that the diversity of DNA methylation patterns in the brain plays a key role in fine-tuning and coordinating gene expression in the development, plasticity, and disorders of the mammalian central nervous system. Neural stem cells (NSCs), originating from the neuroepithelium, generate neurons and glial cells in the central nervous system and contribute to brain plasticity in the adult mammalian brain.

Main body

Here, we summarized recent research in proteins responsible for the establishment, maintenance, interpretation, and removal of DNA methylation and those involved in the regulation of the proliferation and differentiation of NSCs. In addition, we discussed the interactions of chemicals with epigenetic pathways to regulate NSCs as well as the connections between proteins involved in DNA methylation and human diseases.

Conclusion

Understanding the interplay between DNA methylation and NSCs in a broad biological context can facilitate the related studies and reduce potential misunderstanding.
The interaction of Notch and Wnt signaling pathways in vertebrate regeneration
Authors: Gao Junying , Fan Lixia , Zhao Long , Su Ying
Published: October 2021

Regeneration is an evolutionarily conserved process in animal kingdoms, however, the regenerative capacities differ from species and organ/tissues. Mammals possess very limited regenerative potential to replace damaged organs, whereas non-mammalian species usually have impressive abilities to regenerate organs. The regeneration process requires proper spatiotemporal regulation from key signaling pathways. The canonical Notch and Wnt signaling pathways, two fundamental signals guiding animal development, have been demonstrated to play significant roles in the regeneration of vertebrates. In recent years, increasing evidence has implicated the cross-talking between Notch and Wnt signals during organ regeneration. In this review, we summarize the roles of Notch signaling and Wnt signaling during several representative organ regenerative events, emphasizing the functions and molecular bases of their interplay in these processes, shedding light on utilizing these two signaling pathways to enhance regeneration in mammals and design legitimate therapeutic strategies.
Some approximation properties of new $( p,q ) $-analogue of Balázs–Szabados operators
Authors: Hamal Hayatem , Sabancigil Pembe
Published: October 2021

In this paper, a new$( p,q ) $(p,q)-analogue of the Balázs–Szabados operators is defined. Moments up to the fourth order are calculated, and second order and fourth order central moments are estimated. Local approximation properties of the operators are examined and a Voronovskaja type theorem is given.
Students’ low proficiency in spoken English in private universities in Bangladesh: reasons and remedies
Authors: Islam Md Shaiful , Stapa Mahani Bt
Published: October 2021

Students of private universities in Bangladesh are often found to be less competent in spoken English. Since the universities have adopted EMI (English medium instruction) policy, the prevailing linguistic condition on the campus is an “English only environment.” In this context, students are required to communicate in English both inside and outside their classroom, but they desperately struggle to cope with this environment. This study attempted to understand and explain this problem; hence, it set three aims: to evaluate students’ current level of proficiency in spoken English, to investigate the reasons, and to offer remedies. Initially, selected students were given an IELTS-style speaking test in order to determine the overall proficiency in spoken English. Then, involving teachers and students, semistructured email interviews were conducted. The findings report that students’ current level of proficiency is around IELTS band score 5. Reasons for low development of spoken English among students include complex nature of speaking, inappropriate application of instructional methods, teachers’ low proficiency in spoken English and controlling behavior, students’ psychological factors, sociocultural factors, students’ inadequate linguistic resources, L1 interference, and large class size. Remedies suggested by the participants entail integrating TBL (task-based learning) and CL (cooperative learning) teaching-learning, making students aware of noticing, learning speaking through listening, teaching collocations, promoting self-regulated learning, and strengthening teacher education. The reasons investigated and the remedies explored have significant implications that might guide the members of the operating trusts of the private universities, members of the curriculum development and revision committees, and the practitioners to adopt practical approaches to ensure effective learning of spoken English by the students.
Development and validation of a metamemory maturity questionnaire in the context of English as a foreign language
Authors: Nour Payam , Esfandiari Rajab , Zarei Abbas Ali
Published: October 2021

To determine the inherent components of language learners’ capacity for metamemory maturity, the researchers drafted a metamemory maturity (MMM) questionnaire based on Hultsch et al.’s (Memory self-knowledge and self-efficacy in the aged, Springer-Verlag 65–92, 1988) model. The volunteer participants were a heterogeneous sample of 356 male and female English as a Foreign Language (EFL) teachers and student teachers with various age ranges, teaching experiences, and educational backgrounds. Through a series of factor analytic procedures and structural equation modeling, the final draft of the questionnaire with 30 binary Likert-scale items was validated. Statistics confirmed acceptable measures of internal consistency as well as convergent and discriminant validity. The newly designed MMM questionnaire consisted of three main components of memory strategy use (12 items), memory attentiveness (6 items), memory factual awareness (6 items), and a moderator component of confidence and affect (6 items). The researchers highlight the implications of this questionnaire to provide the teachers with an instrument to analyze the needs of EFL learners for metamemory enhancement strategies.
A new reinforcement method for the conservation of fragile, double-sided, printed paper cultural relics
Authors: Liu Jiaojiao , Xing Huiping , Wang Juanli , Cao Jing , Chao Xiaolian , Jia Zhihui , Li Yuhu
Published: October 2021

Paper cultural relics such as double-sided printed newspapers and periodicals represent modern cultural heritage. Severe damage such as embrittlement, decay, and dreg generally occur to paper; hence, it urgently needs conservation and restoration. Therefore, herein, a new reinforcement method for the fragile double-sided printed paper cultural relics is proposed with cotton mesh and adhesive PVA217 as reinforcement materials. Using a computer measured and controlled folding endurance tester, a pendulum tensile strength tester, pH meter, pulp viscosimeter, and other instruments, the physical properties of newspaper samples before and after aging were evaluated. In addition, the mechanical properties, chromatic aberration and surface morphology of simulated samples before and after the cotton mesh reinforcement and Japanese washi paper reinforcement were assessed. The experimental results indicate that this new reinforcement method could effectively improve the physical strength, chromatic aberration and durability of the simulated samples. Widespread applications of this cotton mesh reinforcement method for the reinforcement and protection of the red revolutionary cultural relics such as double-sided printed newspaper and periodicals during the Republic of China era are foreseeable.
Three-dimensional volumetric evaluation of the different mandibular segments using CBCT in patients affected by juvenile idiopathic arthritis: a cross-sectional study
Authors: Cavagnetto Davide , Abate Andrea , Caprioglio Alberto , Cressoni Paolo , Maspero Cinzia
Published: October 2021

Background

There is currently no information on how different mandibular segments are affected by juvenile idiopathic arthritis. The aim of this paper is to assess volumetric differences of different mandibular segments in subjects with unilateral and bilateral JIA and to compare them with non-JIA control volumes.

Materials and methods

Forty subjects with unilateral TMJ involvement and 48 with bilateral TMJ involvement were selected for the case group and 45 subjects with no known rheumatic comorbidities for the control group. The mandible of each subject was divided according to a validated method into different paired volumes (hemimandible, condyle, ramus and hemibody).

Results

The ANOVA test revealed a statistically significant difference in all the groups for condylar and ramus volumes, and the pairwise comparison evidenced a statistically significant higher condylar and ramus volume in the control group (1444.47 mm3; 5715.44 mm3) than in the affected side in the unilateral JIA group (929.46 mm3; 4776.31 mm3) and the bilateral JIA group (1068.54 mm3; 5715.44 mm3). Moreover, there was also a higher condylar volume in the unaffected side in the unilateral JIA group (1419.39 mm3; 5566.24 mm3) than in the bilateral JIA group and the affected side in the unilateral JIA group.

Conclusions

The affected side of unilateral JIA patients showed statistically significant lower volumes in the hemimandible, in the condyle and in the ramus. The largest total mandibular volume was observed in the control group, followed by the unilateral JIA group and, lastly, by the bilateral JIA group.
From byproduct to design factor: on validating the interpretation of process indicators based on log data
Authors: Goldhammer Frank , Hahnel Carolin , Kroehne Ulf , Zehner Fabian
Published: October 2021

International large-scale assessments such as PISA or PIAAC have started to provide public or scientific use files for log data; that is, events, event-related attributes and timestamps of test-takers’ interactions with the assessment system. Log data and the process indicators derived from it can be used for many purposes. However, the intended uses and interpretations of process indicators require validation, which here means a theoretical and/or empirical justification that inferences about (latent) attributes of the test-taker’s work process are valid. This article reviews and synthesizes measurement concepts from various areas, including the standard assessment paradigm, the continuous assessment approach, the evidence-centered design (ECD) framework, and test validation. Based on this synthesis, we address the questions of how to ensure the valid interpretation of process indicators by means of an evidence-centered design of the task situation, and how to empirically challenge the intended interpretation of process indicators by developing and implementing correlational and/or experimental validation strategies. For this purpose, we explicate the process of reasoning from log data to low-level features and process indicators as the outcome of evidence identification. In this process, contextualizing information from log data is essential in order to reduce interpretative ambiguities regarding the derived process indicators. Finally, we show that empirical validation strategies can be adapted from classical approaches investigating the nomothetic span and construct representation. Two worked examples illustrate possible validation strategies for the design phase of measurements and their empirical evaluation.
Vertical disease programs and their effect on integrated disease surveillance and response: perspectives of epidemiologists and surveillance officers in Nigeria
Authors: Onwe Francis Idenyi , Okedo-Alex Ijeoma Nkem , Akamike Ifeyinwa Chizoba , Igwe-Okomiso Dorothy Ogechi
Published: October 2021

Background

Integrated Disease Surveillance and Response (IDSR) is a cost-effective surveillance system designed to curb the inefficiency associated with vertical (disease-specific) programs. The study determined the existence and effect of vertical programs on disease surveillance and response in Nigeria.

Methods

A cross-sectional study involving 14 State epidemiologists and Disease Notification Surveillance Officers (DSNOs) in 12 states located within the 6 geopolitical zones in Nigeria. Data was collected using mailed electronic semi-structured self-administered questionnaires. Response rate was 33.3%. The data was analyzed using SPSS version 20.

Results

Half of the respondents were males (50.0%) and State epidemiologists (50.0%). Malaria, HIV/AIDS, tuberculosis, and other diseases were ongoing vertical programs in the States surveyed. In over 90% of cases, vertical programs had different personnel, communication channels and supportive supervision processes different from the IDSR system. Although less than 50% acknowledged the existence of a forum for data harmonization, this forum was ineffectively utilized in 83.3% of cases. Specific disease funding was higher than that of IDSR (92.9%) and only 42.9% reported funding for IDSR activities from development partners in the State. Poor data management, low priority on IDSR priority diseases, and donor-driven programming were major negative effects of vertical programs. Improved funding, political ownership, and integration were major recommendations preferred by the respondents.

Conclusion

We found that vertical programs in the surveyed States in the Nigerian health system led to duplication of efforts, inequitable funding, and inefficiencies in surveillance. We recommend integration of existing vertical programs into the IDSR system, increased resource allocation, and political support to improve IDSR.
Forecasting the volatility of EUA futures with economic policy uncertainty using the GARCH-MIDAS model
Authors: Liu Jian , Zhang Ziting , Yan Lizhao , Wen Fenghua
Published: October 2021

This study investigates the impact of economic policy uncertainty (EPU) on the volatility of European Union (EU) carbon futures prices and whether it has predictive power for the volatility of carbon futures prices. The GARCH-MIDAS model is applied for evaluating the impact of different EPU indexes on the price volatility of European Union Allowance (EUA) futures. We then compare the predictive power for the volatility of the two GARCH-MIDAS models based on different EPU indexes and six GARCH-type models. Our empirical results show that the GARCH-MIDAS models, which exhibit superior out-of-sample predictive ability, outperform GARCH-type models. The results also indicate that EPU has noticeable effect on the volatility of EUA futures. Specifically, the forecast accuracy of the EU EPU index is significantly higher than that of the global EPU index. Robustness checks further confirm that the EPU index (especially the EPU index of the EU) has strong predictive power for EUA futures prices. Additionally, using the volatility forecasting methods that GARCH-MIDAS models combine with the EPU index, investors can construct their portfolios to realize economic returns.
Adaptive e-learning environment based on learning styles and its impact on development students' engagement
Authors: El-Sabagh Hassan A.
Published: October 2021

Adaptive e-learning is viewed as stimulation to support learning and improve student engagement, so designing appropriate adaptive e-learning environments contributes to personalizing instruction to reinforce learning outcomes. The purpose of this paper is to design an adaptive e-learning environment based on students' learning styles and study the impact of the adaptive e-learning environment on students’ engagement. This research attempts as well to outline and compare the proposed adaptive e-learning environment with a conventional e-learning approach. The paper is based on mixed research methods that were used to study the impact as follows: Development method is used in designing the adaptive e-learning environment, a quasi-experimental research design for conducting the research experiment. The student engagement scale is used to measure the following affective and behavioral factors of engagement (skills, participation/interaction, performance, emotional). The results revealed that the experimental group is statistically significantly higher than those in the control group. These experimental results imply the potential of an adaptive e-learning environment to engage students towards learning. Several practical recommendations forward from this paper: how to design a base for adaptive e-learning based on the learning styles and their implementation; how to increase the impact of adaptive e-learning in education; how to raise cost efficiency of education. The proposed adaptive e-learning approach and the results can help e-learning institutes in designing and developing more customized and adaptive e-learning environments to reinforce student engagement.
Assessing the bioactivity of cannabis extracts in larval zebrafish
Authors: Nixon Jessica , Abramovici Hanan , Cabecinha Ashley , Martinez-Farina Camilo , Hui Joseph , Ellis Lee
Published: October 2021

Background

Whole-plant cannabis extracts are consumed by the public for medical and non-medical (“recreational”) purposes but are poorly researched compared to pure cannabinoids. There is emerging evidence that cannabis extracts comprising complex mixtures of cannabinoids may have different biological effects from that of pure cannabinoids. In the current study, we sought to assess the effect of whole-plant cannabis extracts produced from different chemotypes of cannabis on the normal behavior of zebrafish larvae.

Methods

Three cannabis plant chemotypes were used in this study that contained either high amounts of THC, high amounts of CBD, high but equal amounts of THC and CBD, or low but equal amounts of THC and CBD. Following solvent extraction, liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) was performed for the detection and quantitation of target cannabinoids. Larval zebrafish behavioral models were subsequently used to assess the effect of the four different whole-plant cannabis extracts on the normal larval behavior using the DanioVision behavioral tracking systems and software. To compare, changes in the behavior activity levels for 30 min periods were compared to controls using 2-way ANOVA with multiple comparisons followed by a Bonferroni post hoc test.

Results

It was found that the whole-plant extracts that contained high levels of THC had similar effects on larval behavior, while the high CBD and low THC:CBD extracts produced distinct effects on normal larval behavior. Exposure of larvae to concentration-matched levels of THC and CBD found in the extracts revealed that a subset of the cannabis extracts tested had similar behavioral profiles to the pure cannabinoids while others did not.

Conclusions

To our knowledge, this is the first study to test and compare the bioactivity of different whole-plant cannabis extracts in larval zebrafish. This work will provide a framework for future studies of distinct cannabis extracts and will be useful for comparing the bioactivity of extracts from different cannabis chemotypes as well as extracts made through various heating processes. It will also act as the first stage of assessment before testing the extracts against zebrafish models of toxicity and disease.
Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts
Authors: Bornbusch Sally L. , Harris Rachel L. , Grebe Nicholas M. , Roche Kimberly , Dimac-Stohl Kristin , Drea Christine M.
Published: October 2021

Background

Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases.

Results

Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups.

Conclusions

Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.
Introduction to this special section: Quantitative interpretation
Authors: Das Agnibha , Sengupta Mita
Published: October 2021

Quantitative interpretation (QI) is the geophysicist's endeavor to go beyond reservoir architecture. It is the effort to use geophysical measurements in understanding reservoir properties such as rock type, porosity, and fluid composition. QI often refers to the use of seismic amplitude analysis to predict lithology, porosity, and pore fluids away from the wellbore in oil and gas reservoirs. However, we can generalize and expand the concept of QI beyond seismic methods and beyond oil and gas reservoirs. In this special section, we feature five papers and cover not only seismic and well-log data, but also gravity and magnetic data. We address a hydrothermal reservoir in addition to several oil and gas reservoirs.
Basin-wide rock-physics analysis in Campeche Basin, Gulf of Mexico — Phase II: Reservoir rock and fluid properties
Authors: Liu Yangjun (Kevin) , Ellis Michelle , El-Toukhy Mohamed , Hernandez Jonathan
Published: October 2021

We present a basin-wide rock-physics analysis of reservoir rocks and fluid properties in Campeche Basin. Reservoir data from discovery wells are analyzed in terms of their relationship between P-wave velocity, density, porosity, clay content, Poisson's ratio (PR), and P-impedance (IP). The fluid properties are computed by using in-situ pressure, temperature, American Petroleum Institute gravity, gas-oil ratio, and volume of gas, oil, and water. Oil- and gas-saturated reservoir sands show strong PR anomalies compared to modeled water sand at equivalent depth. This suggests that PR anomalies can be used as a direct hydrocarbon indicator in the Tertiary sands in Campeche Basin. However, false PR anomalies due to residual gas or oil exist and compose about 30% of the total anomalies. The impact of fluid properties on IP and PR is calibrated using more than 30 discovery wells. These calibrated relationships between fluid properties and PR can be used to guide or constrain amplitude variation with offset inversion for better pore fluid discrimination.
Serum Testosterone to Androstenedione Ratio Predicts Metabolic Health in Normal-Weight Polycystic Ovary Syndrome Women
Authors: Dumesic Daniel A , Tulberg Ayli , McNamara Megan , Grogan Tristan R , Abbott David H , Naik Rajanigandha , Lu Gwyneth , Chazenbalk Gregorio D
Published: October 2021

Context

Increased aldo-keto reductase 1C3 (AKR1C3)-mediated conversion of androstenedione (A4) to testosterone (T) promotes lipid storage in subcutaneous (SC) abdominal adipose in overweight/obese polycystic ovary syndrome (PCOS) women.

Objective

This work examines whether an elevated serum T/A4 ratio, as a marker of enhanced AKR1C3 activity in SC abdominal adipose, predicts metabolic function in normal-weight PCOS women.

Methods

This prospective cohort study took place in an academic center and comprised 19 normal-weight PCOS women and 21 age- and body mass index–matched controls. Interventions included circulating hormone/metabolic determinations, intravenous glucose tolerance testing, total body dual-energy x-ray absorptiometry, and SC abdominal fat biopsy. Serum T/A4 ratios, hormone/metabolic measures, and AKR1C3 expression of adipocytes matured in vitro were compared between female types; serum T/A4 ratios were correlated with serum lipids, adipose insulin resistance (adipose-IR), homeostatic model assessment of insulin resistance (HOMA-IR) and insulin sensitivity (Si).

Results

Increased serum T/A4 ratios (P = .040) and log adipose-IR values (P = .002) in PCOS women vs controls were accompanied by AKR1C3 messenger RNA overexpression of PCOS adipocytes matured in vitro (P = .016). Serum T/A4 ratios in PCOS women, but not controls, negatively correlated with log triglycerides (TGs: R = –0.65, P = .002) and the TG index (R = –0.57, P = .011). Adjusting for serum free T, serum T/A4 ratios in PCOS women remained negatively correlated with log TG (R = –0.57, P = .013) and TG index (R = –0.50, P = .036), respectively, without significant relationships with other metabolic measures.

Conclusion

An elevated serum T/A4 ratio, as a marker of enhanced AKR1C3 activity in SC abdominal adipose, predicts healthy metabolic function in normal-weight PCOS women.
Tissue clearing and 3D imaging in developmental biology
Authors: Vieites-Prado Alba , Renier Nicolas
Published: October 2021

Tissue clearing increases the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these methodologies requires a good grasp of sample processing, imaging and the possibilities offered by image analysis. In this Primer, we highlight how tissue clearing can revolutionize the histological analysis of developmental processes and we advise on how to implement effective clearing protocols, imaging strategies and analysis methods for developmental biology.
Hypothesis on the pathophysiology of syringomyelia based on analysis of phase-contrast magnetic resonance imaging of Chiari-I malformation patients
Authors: Chang Han Soo
Published: October 2021

Background: Despite a number of hypotheses, our understanding of the pathophysiology of syringomyelia is still limited. The current prevailing hypothesis assumes that the piston-like movement of the cerebellar tonsils drives the cerebrospinal fluid (CSF) into the syrinx through the spinal perivascular space. However, it still needs to be verified by further experimental data. A major unexplained problem is how CSF enters and remains in the syrinx that has a higher pressure than the subarachnoid space.

Methods: I analyzed phase-contrast MRI scans of 18 patients with Chiari-I malformation with syringomyelia undergoing foramen magnum decompression and 21 healthy volunteers. I analyzed the velocity waveforms of the CSF and the brain in various locations. The obtained velocity waveforms were post-processed using a technique called synchronization in situ. I compared between the preoperative data and the control data (case-control study), as well as between the preoperative and postoperative data (cohort study).

Results: The syrinx shrank in 17 (94%) patients with good clinical improvement. In Chiari-I patients, the velocity of the tonsil was significantly larger than controls, but was significantly smaller than that of the CSF in the subarachnoid space, suggesting passive rather than active movement. The abnormal tonsillar movement disappeared after surgery, but the velocity waveform of the spinal subarachnoid CSF did not change. These results, contradicting the above mentioned hypothesis, required an alternative explanation. I thus hypothesized that there is a CSF channel between the fourth ventricle and the syrinx. This channel assumes one-way valve function when mildly compressed by the cyclical movement of the cerebellar tonsil. The decompression of the tonsils switches off the one-way valve, collapsing the syrinx.

Conclusions: My hypothesis reasonably explained my data that clearly contradicted the existing hypothesis, and successfully addressed the above-mentioned theoretical problem. It will serve as a working hypothesis for further study of syringomyelia pathophysiology.
Performance evaluation of a multinational data platform for critical care in Asia
Authors:   Collaboration for Research, Implementation and Training in Critical Care - Asia Investigators, Pisani Luigi , Rashan Thalha , Shamal Maryam , Ghose Aniruddha , Kumar Tirupakuzhi Vijayaraghavan Bharath , Tripathy Swagata , Aryal Diptesh , Hashmi Madiha , Nor Basri , Lam Minh Yen , Dondorp Arjen M. , Haniffa Rashan , Beane Abi
Published: October 2021

Background: The value of medical registries strongly depends on the quality of the data collected. This must be objectively measured before large clinical databases can be promoted for observational research, quality improvement, and clinical trials. We aimed to evaluate the quality of a multinational intensive care unit (ICU) network of registries of critically ill patients established in seven Asian low- and middle-income countries (LMICs).

Methods: The Critical Care Asia federated registry platform enables ICUs to collect clinical, outcome and process data for aggregate and unit-level analysis. The evaluation used the standardised criteria of the Directory of Clinical Databases (DoCDat) and a framework for data quality assurance in medical registries. Six reviewers assessed structure, coverage, reliability and validity of the ICU registry data. Case mix and process measures on patient episodes from June to December 2020 were analysed.

Results: Data on 20,507 consecutive patient episodes from 97 ICUs in Afghanistan, Bangladesh, India, Malaysia, Nepal, Pakistan and Vietnam were included. The quality level achieved according to the ten prespecified DoCDat criteria was high (average score 3.4 out of 4) as was the structural and organizational performance -- comparable to ICU registries in high-income countries. Identified strengths were types of variables included, reliability of coding, data completeness and validation. Potential improvements included extension of national coverage, optimization of recruitment completeness validation in all centers and the use of interobserver reliability checks.

Conclusions: The Critical Care Asia platform evaluates well using standardised frameworks for data quality and equally to registries in resource-rich settings.
August Rauber’s ideas for the creation of an Anatomy Museum in Lithuania (1920–1940)
Authors: Rudžianskaitė Angelė , Dabužinskienė Anita , Green Lena , Kriaučiūnienė Vega
Published: October 2021

Professor August Rauber (1841–1917) created the most important school of anatomy in the Baltic region. His students continued his educational and research work in their native countries. One of them was Professor Jurgis Žilinskas (1885–1957) who laid the foundation to Lithuanian anatomy and anthropology. From 1906–1912, he studied medicine at the University of Yuryev (Tartu) where Prof. A. Rauber worked for 25 years as Head of the Institute of Anatomy. In 1890, A. Rauber opened the Anatomy Museum there. In the university, J. Žilinskas maintained close contacts with Professors A. Rauber (1841–1917), N. N. Burdenko (1876–1946), W. Zoege-Manteuffel (1857–1926) and E. Landau (1878–1959). After graduation from the university, J. Žilinskas as a talented student was invited to work as an assistant at the Department of Hospital Surgery at Yuryev University. After Lithuania restored its independence on 16 February 1918, Prof. J. Žilinskas participated actively in the organization of medical studies in Lithuania (1922–1940) and was one of the creators and the principal patron of the Museum of Anatomy. Returning to Lithuania, J. Žilinskas brought along the most advanced ideas of his professors, especially of his honoured Prof. A. Rauber. During this period, the collection of the museum increased to 3,890 specimens. Osteological specimens comprised 1,925 (around 50%) of the specimens, wet specimens – 753 (19.3%), corrosion specimens – 467 (12%), transparent specimens – 201 (5.2%), dry specimens – 107 (2.8%) and models – 437. Professor J. Žilinskas’ collection constitutes 50% of the present exhibits at the Anatomy Museum of the Lithuanian University of Health Sciences.
One cannot know anatomy too well: Jēkabs Prīmanis and anatomy for artists
Authors: Zariņš Uldis , Lībiete Ieva
Published: October 2021

In recent years the scholars have stressed the role of anatomical collections and their histories as crucial to new interdisciplinary studies that investigate the interaction between arts and sciences. This could be attributed as well to the new exposition of Anatomy museum of Rīga Stradiņš University, that was opened to visitors in 2021. Museum galleries reveal the interplay between anatomists, artists and museum specialists, both in historical and contemporary contexts. Between the specimen jars and human bones, the anatomical drawings of both medical and art students are displayed. Sculpture-like life casts of congenital deformities made by anatomists contrast the ideal but skinless muscle man L’Ecorche Combattant. Historical artefacts interact with modern anatomical 3D illustration and multimedial solutions created by contemporary artists. No doubt, artists were and are important for visualising, explaining and displaying anatomy. But what about the role of anatomists in arts? This article aims to investigate an episode in the biography of long-time museum director anatomist and anthropologist professor Jēkabs Prīmanis (1892–1971) and his role in teaching the so-called plastic anatomy to the students of the Art Academy of Latvia.
Theatrum Anatomicum Rigense MCMXX and the historical collection of teaching and research exponates in the Institute of Anatomy and Anthropology of Riga Stradiņš University
Authors: Pilmane Māra
Published: October 2021

The Institute of Anatomy and Anthropology (AAI) of Riga Stradiņš University (RSU) displays a remarkable historical collection of educational and scientific materials on anatomy and embryology, 8381 items in total. The creation of the collection started in 2002, and nowadays it integrates 16 sub-collections: the main exhibits of P. Stradiņš’s collection; the collection of pathological exhibits from Gailezers Hospital with 542 items; the collection of the Children’s Clinical University Hospital with 21 exhibits; Anatomy Laboratory collection with 105 exhibits; Professor A. Amelin’s collection with 134 exhibits; the animal collection with 64 exhibits; the collection of embryological exhibits with 138 specimens together with 59 exhibits of the reproductive system; the bone collection from archaeological excavations in Riga with 986 exhibits; the collection of bone preparations and skulls, 4714 exhibits; V. Derums’ bone collection of 94 items. A separate collection contains 67 exhibits from the first Latvian anatomical excavations conducted under the guidance of Professor J. Prīmanis and Polish archaeological excavations of the Order of the Brothers of the Sword in St. George’s Church and the Convent yard, which includes 48 historical finds; the above is supplemented by 26 finds from anthropological material and a collection of bone specimens with 82 exhibits and a collection of skulls with 159 exhibits. A separate section at the AAI exhibition displays a collection of animal bones, which includes 58 exhibits and is used for comparative studies. Since 2003, the historical collection has been used to teach Latvians and foreigners who are interested to understand death, diseased tissues, to teach sympathy and how to protect oneself and others from diseases. The historical material is used for regular student training as well as for students’ research needs. Finally, digitization of unique exhibits, description in Latvian and English, and placing in the RSU repository has started, and, so far, 240 exhibits have been processed.