bluuebunny/crossref_metadata_2025 huggingface dataset:
INFLUENCE OF INTERNAL LABOR FACTORS ON WORK ACCIDENTS OF XX TOLL ROAD CONSTRUCTION PROJECT
Authors: Riskijah Sitti Safiatus
Published: July 2021

Abstract The XX Toll Road Construction Project is a national project with high risk and high complexity, given the nature of the work that requires clearing new land on hills and valley areas which requires retaining wall works. During its implementation, work accident occurence can be caused by many factors, including labor factors. This study aims to determine the effect of internal labor factors on work accidents occurred at XX Toll Road Construction Project. The data required in the form of primary data obtained from questionnaires about occupational safety and health, and fitness measurements using the Balke method. The data analysis used Multiple Regression analysis with SPSS. The results showed that the internal factors of the workforce, namely the factors of work safety, occupational health, and workforce fitness simultaneously have strong and significant effect on the occurrence of work accidents in the project. Hence, these internal factors partially bring significant effect. Keywords: labor, safety, health, fitness, accidents
Occult adenocarcinoma in adenomas. Possibilities of diagnostic methods
Authors: Chernyshov S. V. , Khomyakov E. A. , Sinitsyn R. K. , Vaganov Yu. E. , Trubacheva Yu. L. , Eligulashvili R. R. , Maynovskaya O. A. , Rybakov E. G.
Published: July 2021

Aim: to analyze the diagnostic value of the digital rectal examination, colonoscopy, MRI and ERUS for detecting occult adenocarcinoma in rectal adenomas.

Patients and methods: the study included 100 patients with newly identified epithelial rectal neoplasms, which undergone transanal endoscopic microsurgery from December 2019 to December 2020. All the patients underwent digital rectal examination, colonoscopy, ERUS with sonoelastography, and pelvic MRI. The diagnostics value of this methods was estimated with determination of sensitivity and specificity.

Results: the study included 67 (67%) females and 33 (33%) males. The mean age of the patients was 64.4 ± 10.7 years. The median distance from the tumor to the anal verge was 6.0 ± 2.9 cm. The sensitivity of the digital rectal examination in the occult malignancy verification was 0.44 (95% CI 0.24–0.65), specificity — 0.93 (95% CI 0.85–0.97). The sensitivity of the colonoscopy — 0.56 (95% CI 0.34–0.75), the specificity — 0.84 (95% CI 0.73–0.91). The sensitivity of MRI — 0.40 (95% CI 0.21–0.61), specificity — 0.89 (95% CI 0.80–0.95). The sensitivity of ERUS was 0.48 (95% CI 0.27–0.68), the specificity — 0.73 (95% CI 0.61–0.82). Pair wise comparison of diagnostic methods revealed the absence of significant differences in their diagnostic value (p > 0.05).

Conclusion: at least one of diagnostic methods allows to verify the presence of malignant transformation in 100% of cases. So, only combination of diagnostic methods can help to choose the optimal treatment option.
Vladimir L. Dzhimbeev. OBITUARY
Authors: Editorial Article
Published: July 2021

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Factors limiting the endoscopic submucosal dissection in colorectal tumors
Authors: Likutov A. A. , Mtvralashvili D. A. , Nagudov M. A. , Yugai O. M. , Vaganov Yu. E. , Chernyshov S. V. , Mainovskaya O. A.
Published: July 2021

Aim:to identify the risk factors for conversion of endoscopic submucosal dissection to abdominal surgery.

Patients and methods: the prospective cohort study included 405 patients: 166 (40.9%) males and 239 (59.1%) females. The median age was 66 (59; 72) years old; the patients underwent endoscopic submucosal dissection of colorectal epithelial neoplasms.

Results:the median size of the removed neoplasms was 3.0 (2.4; 4) cm, tumor was removed en bloc in 324/363 (89.2%) cases; and R0 resection margins were detected in 218/324 (67.3%) cases. Significant risk factors for conversion were: the tumor size ≥ 3.2 cm (OR 2.9, 95% CI 1.2–7.1, p = 0.017), lifting ≤ 3 mm (OR 41, 95% CI 15–105, p = 0.000002) and the tumor vascular pattern IIIa according Sano’s capillary pattern classification (OR 4.0, 95% CI 1.3–11.9, p = 0.013).

Conclusion:endoscopic submucosal dissection is a safe way to remove colorectal neoplasms. However, the presence of conversion risk factors can influence the outcome of endoscopic treatment.
Rehabilitation of patients with low anterior resection syndrome
Authors: Nafedzov I. O. , Chernyshov S. V. , Ponomarenko A. A. , Fomenko O. Yu. , Alekseev M. V. , Khomyakov E. A. , Belousova S. V. , Rybakov E. G.
Published: July 2021

Aim: to develop a conservative rehabilitation program for patients with severe symptoms of LARS.

Patients and methods: since January 2019, 50 patients after low anterior resection were included in the study. The main group included 25 patients who underwent biofeedback therapy and tibial neuromodulation in 3–6 months after surgery. Functional results before and after treatment were evaluated by anorectal manometry. The control group included 25 patients, according to the Propensity score matching.

Results: the median score on the LARS scale, in the main group was 41.0 ± 2.8 points, in the control — 38 ± 4. With sphincterometry, the median pressure at rest before treatment was 30.0 ± 7.8, with a voluntary contraction of 140.6 ± 56.0 mm Hg. After the conservative treatment, patients in the main group had significantly better results: the median score on the LARS scale decreased from 41 ± 2.8 to 17 ± 8 points (p < 0.0001), the median pressure after treatment increased from 30.0 ± 7.8 to 36.0 ± 8.0 (p = 0.004), with a voluntary contraction from 140.6 ± 56.0 to 157.5 ± 53.2 mmHg (p = 0.008). Comparing the results of the questionnaire of the main group with the control group after the stoma closure and after 12 months, it turned out that in the main group there was a significant decrease in the severity of LARS: 17.0 ± 8.0 scores vs. 35.0 ± 4.5 (p = 0.0003), which shows an improvement in the tone and contractility of the sphincter after conservative treatment.

Conclusion: comprehensive biofeedback therapy and tibial neuromodulation improves the functional results of patients with severe LARS.
Population characteristics of colorectal cancer in the Ulyanovsk region according to the regional cancer register
Authors: Bogomolova I. A. , Antoneeva I. I. , Abakumova T. V. , Gening T. P.
Published: July 2021

Aim:to analyze the structure and changes of colorectal cancer (CRC) epidemiology in the Ulyanovsk region in 2005–2019 according to the regional cancer register.

Materials and methods:the study is based on statistical data on the primary detection of CRC in the districts of the Ulyanovsk region (form No. 7) in 2005–2019. Standardized rates of morbidity and mortality were evaluated. Data on the number, gender and age of the regional population were obtained in Ulyanovsk State Statistics Service.

Results:the incidence of CRC in the region increased by 1.51 times over the analyzed period (from 31.12 to 49.58 per 100 thousand people). From the total number of newly diagnosed CRC in 2019, the urban population was 25%, and the rural population — 75%. The incidence rates in the districts of the region were assessed. The highest morbidity in males was detected at the age of 60–64 years old, and it was 1.58 times higher than in females. In the adult population under 30 years old, only few cases of colorectal cancer were detected. The main histological type of tumors was adenocarcinoma. Poorly differentiated tumors accounted for about 3%. The highest age-standardized rates for rectal tumors were 10.1 and 12.8 per 100 thousand people in 2005 and 2019, respectively; for the recto sigmoid tumors — 0.9 and 2.3 per 100 thousand people; and for the anal cancer — 0.4 cases per 100 thousand people in 2019. The male/female ratio of deaths from CRC in 2019 was 1.005:1.000.

Conclusion:there has been a trend to an increase in the incidence of colorectal cancer among the Ulyanovsk region population in the period from 2005 to 2019. We identified some areas of the region that significantly differ in the incidence of colorectal cancer.
Potential of Pulse Flours as Partial Meat Replacers in Heat-Treated Emulsion-Type Meat Sausages
Authors: Mateo Javier , Caro Irma , Kasiayan Seyedalireza , Salvá Bettit K. , Carhuallanqui Andrea , Ramos Daphne D.
Published: July 2021

Reformulation approaches in the meat industry are required to promote nutritional improvement, health functionality, and reduce environmental impact. A relevant approach among these is to reduce the amount of meat in meat products. Reduced-meat products should maintain or improve the sensory characteristics and nutritive value compared to conventional meat products. Among meat products, heat-treated emulsion-meat sausages are widely consumed and especially suitable for reformulation approaches. Due to its high protein content, with high functionally and biological value, pulse flour has a high potential to be used as meat replacer. Most studies regarding the replacement of meat with pulses have been made on fresh meat preparations where amounts of up to 15% of pulse flour did not negatively affect sensory quality while increased yield and firmness. However, studies using pulse flour in emulsion-type sausages are scarce. Further research is warranted to optimize the reformulation of these meat products using flour pulses. The topics to be addressed are the following: effects of pulse type, pulse pretreatments, such as soaking or germination, pulse flour treatments before incorporation into the meat mix, combination of pulses with other proper ingredients, and heat treatment intensity on the pulse antinutrient inactivation and the technological and edible quality traits of the pulse-containing sausages.
Pan-Cancer Survey of Tumor Mass Dormancy and Underlying Mutational Processes
Authors: Wiecek Anna Julia , Jacobson Daniel Hadar , Lason Wojciech , Secrier Maria
Published: July 2021

Tumor mass dormancy is the key intermediate step between immune surveillance and cancer progression, yet due to its transitory nature it has been difficult to capture and characterize. Little is understood of its prevalence across cancer types and of the mutational background that may favor such a state. While this balance is finely tuned internally by the equilibrium between cell proliferation and cell death, the main external factors contributing to tumor mass dormancy are immunological and angiogenic. To understand the genomic and cellular context in which tumor mass dormancy may develop, we comprehensively profiled signals of immune and angiogenic dormancy in 9,631 cancers from the Cancer Genome Atlas and linked them to tumor mutagenesis. We find evidence for immunological and angiogenic dormancy-like signals in 16.5% of bulk sequenced tumors, with a frequency of up to 33% in certain tissues. Mutations in the CASP8 and HRAS oncogenes were positively selected in dormant tumors, suggesting an evolutionary pressure for controlling cell growth/apoptosis signals. By surveying the mutational damage patterns left in the genome by known cancer risk factors, we found that aging-induced mutations were relatively depleted in these tumors, while patterns of smoking and defective base excision repair were linked with increased tumor mass dormancy. Furthermore, we identified a link between APOBEC mutagenesis and dormancy, which comes in conjunction with immune exhaustion and may partly depend on the expression of the angiogenesis regulator PLG as well as interferon and chemokine signals. Tumor mass dormancy also appeared to be impaired in hypoxic conditions in the majority of cancers. The microenvironment of dormant cancers was enriched in cytotoxic and regulatory T cells, as expected, but also in macrophages and showed a reduction in inflammatory Th17 signals. Finally, tumor mass dormancy was linked with improved patient survival outcomes. Our analysis sheds light onto the complex interplay between dormancy, exhaustion, APOBEC activity and hypoxia, and sets directions for future mechanistic explorations.
Cell Death Induction and Protection by Activation of Ubiquitously Expressed Anion/Cation Channels. Part 2: Functional and Molecular Properties of ASOR/PAC Channels and Their Roles in Cell Volume Dysregulation and Acidotoxic Cell Death
Authors: Okada Yasunobu , Sato-Numata Kaori , Sabirov Ravshan Z. , Numata Tomohiro
Published: July 2021

For survival and functions of animal cells, cell volume regulation (CVR) is essential. Major hallmarks of necrotic and apoptotic cell death are persistent cell swelling and shrinkage, and thus they are termed the necrotic volume increase (NVI) and the apoptotic volume decrease (AVD), respectively. A number of ubiquitously expressed anion and cation channels play essential roles not only in CVR but also in cell death induction. This series of review articles address the question how cell death is induced or protected with using ubiquitously expressed ion channels such as swelling-activated anion channels, acid-activated anion channels, and several types of TRP cation channels including TRPM2 and TRPM7. In the Part 1, we described the roles of swelling-activated VSOR/VRAC anion channels. Here, the Part 2 focuses on the roles of the acid-sensitive outwardly rectifying (ASOR) anion channel, also called the proton-activated chloride (PAC) anion channel, which is activated by extracellular protons in a manner sharply dependent on ambient temperature. First, we summarize phenotypical properties, the molecular identity, and the three-dimensional structure of ASOR/PAC. Second, we highlight the unique roles of ASOR/PAC in CVR dysfunction and in the induction of or protection from acidotoxic cell death under acidosis and ischemic conditions.
A Tale of Two States: Pluripotency Regulation of Telomeres
Authors: Novo Clara Lopes
Published: July 2021

Inside the nucleus, chromatin is functionally organized and maintained as a complex three-dimensional network of structures with different accessibility such as compartments, lamina associated domains, and membraneless bodies. Chromatin is epigenetically and transcriptionally regulated by an intricate and dynamic interplay of molecular processes to ensure genome stability. Phase separation, a process that involves the spontaneous organization of a solution into separate phases, has been proposed as a mechanism for the timely coordination of several cellular processes, including replication, transcription and DNA repair. Telomeres, the repetitive structures at the end of chromosomes, are epigenetically maintained in a repressed heterochromatic state that prevents their recognition as double-strand breaks (DSB), avoiding DNA damage repair and ensuring cell proliferation. In pluripotent embryonic stem cells, telomeres adopt a non-canonical, relaxed epigenetic state, which is characterized by a low density of histone methylation and expression of telomere non-coding transcripts (TERRA). Intriguingly, this telomere non-canonical conformation is usually associated with chromosome instability and aneuploidy in somatic cells, raising the question of how genome stability is maintained in a pluripotent background. In this review, we will explore how emerging technological and conceptual developments in 3D genome architecture can provide novel mechanistic perspectives for the pluripotent epigenetic paradox at telomeres. In particular, as RNA drives the formation of LLPS, we will consider how pluripotency-associated high levels of TERRA could drive and coordinate phase separation of several nuclear processes to ensure genome stability. These conceptual advances will provide a better understanding of telomere regulation and genome stability within the highly dynamic pluripotent background.
Gold-Catalyzed Complementary Nitroalkyne Internal Redox Process: A DFT Study
Authors: Vipin Raj K. , Dhote Pawan S. , Vanka Kumar , Ramana Chepuri V.
Published: July 2021

Gold-catalysis, in this century, is one of the most emerging and promising new areas of research in organic synthesis. During the last two decades, a wide range of distinct synthetic methodologies have been unveiled employing homogeneous gold catalysis and aptly applied in the synthesis of numerous natural products and biologically active molecules. Among these, the reactions involving α-oxo gold carbene/α-imino gold carbene intermediates are of contemporary interest, in view of their synthetic potential and also due to the need to understand the bonding involved in these complexes. In this manuscript, we document the theoretical investigations on the regio-selectivity dependence of substitution on the gold-catalyzed cycloisomerization of o-nitroarylalkyne derivatives. We have also studied the relative stabilities of α-oxo gold carbene intermediates.
Conformational Change of H64 and Substrate Transportation: Insight Into a Full Picture of Enzymatic Hydration of CO2 by Carbonic Anhydrase
Authors: Fu Yuzhuang , Fan Fangfang , Zhang Yuwei , Wang Binju , Cao Zexing
Published: July 2021

The enzymatic hydration of CO2 into HCO3− by carbonic anhydrase (CA) is highly efficient and environment-friendly measure for CO2 sequestration. Here extensive MM MD and QM/MM MD simulations were used to explore the whole enzymatic process, and a full picture of the enzymatic hydration of CO2 by CA was achieved. Prior to CO2 hydration, the proton transfer from the water molecule (WT1) to H64 is the rate-limiting step with the free energy barrier of 10.4 kcal/mol, which leads to the ready state with the Zn-bound OH−. The nucleophilic attack of OH− on CO2 produces HCO3− with the free energy barrier of 4.4 kcal/mol and the free energy release of about 8.0 kcal/mol. Q92 as the key residue manipulates both CO2 transportation to the active site and release of HCO3−. The unprotonated H64 in CA prefers in an inward orientation, while the outward conformation is favorable energetically for its protonated counterpart. The conformational transition of H64 between inward and outward correlates with its protonation state, which is mediated by the proton transfer and the product release. The whole enzymatic cycle has the free energy span of 10.4 kcal/mol for the initial proton transfer step and the free energy change of −6.5 kcal/mol. The mechanistic details provide a comprehensive understanding of the entire reversible conversion of CO2 into bicarbonate and roles of key residues in chemical and nonchemical steps for the enzymatic hydration of CO2.
Review: Effect of Gut Microbiota and Its Metabolite SCFAs on Radiation-Induced Intestinal Injury
Authors: Li Yangyang , Zhang Yiming , Wei Kongxi , He Jinpeng , Ding Nan , Hua Junrui , Zhou Ting , Niu Fan , Zhou Gucheng , Shi Tongfan , Zhang Liying , Liu Yongqi
Published: July 2021

Gut microbiota is regarded as the second human genome and forgotten organ, which is symbiotic with the human host and cannot live and exist alone. The gut microbiota performs multiple physiological functions and plays a pivotal role in host health and intestinal homeostasis. However, the gut microbiota can always be affected by various factors and among them, it is radiotherapy that results in gut microbiota12dysbiosis and it is often embodied in a decrease in the abundance and diversity of gut microbiota, an increase in harmful bacteria and a decrease in beneficial bacteria, thereby affecting many disease states, especially intestine diseases. Furthermore, gut microbiota can produce a variety of metabolites, among which short-chain fatty acids (SCFAs) are one of the most abundant and important metabolites. More importantly, SCFAs can be identified as second messengers to promote signal transduction and affect the occurrence and development of diseases. Radiotherapy can lead to the alterations of SCFAs-producing bacteria and cause changes in SCFAs, which is associated with a variety of diseases such as radiation-induced intestinal injury. However, the specific mechanism of its occurrence is not yet clear. Therefore, this review intends to emphasize the alterations of gut microbiota after radiotherapy and highlight the alterations of SCFAs-producing bacteria and SCFAs to explore the mechanisms of radiation-induced intestinal injury from the perspective of gut microbiota and its metabolite SCFAs.
Global CpG DNA Methylation Footprint in Kaposi’s Sarcoma
Authors: Journo Guy , Ahuja Anuj , Dias-Polak David , Eran Yonatan , Bergman Reuven , Shamay Meir
Published: July 2021

Kaposi’s sarcoma-associated herpesvirus (KSHV), also familiar as human herpesvirus 8 (HHV-8), is one of the well-known human cancer-causing viruses. KSHV was originally discovered by its association with Kaposi’s sarcoma (KS), a common AIDS-related neoplasia. Additionally, KSHV is associated with two B-lymphocyte disorders; primary effusion lymphoma (PEL) and Multicentric Castlemans Disease (MCD). DNA methylation is an epigenetic modification that is essential for a properly functioning human genome through its roles in chromatin structure maintenance, chromosome stability and transcription regulation. Genomic studies show that expressed promoters tend to be un-methylated whereas methylated promoters tend to be inactive. We have previously revealed the global methylation footprint in PEL cells and found that many cellular gene promoters become differentially methylated and hence differentially expressed in KSHV chronically infected PEL cell lines. Here we present the cellular CpG DNA methylation footprint in KS, the most common malignancy associated with KSHV. We performed MethylationEPIC BeadChip to compare the global methylation status in normal skin compared to KS biopsies, and revealed dramatic global methylation alterations occurring in KS. Many of these changes were attributed to hyper-methylation of promoters and enhancers that regulate genes associated with abnormal skin morphology, a well-known hallmark of KS development. We observed six-fold increase in hypo-methylated CpGs between early stage of KS (plaque) and the more progressed stage (nodule). These observations suggest that hyper-methylation takes place early in KS while hypo-methylation is a later process that is more significant in nodule. Our findings add another layer to the understanding of the relationship between epigenetic changes caused by KSHV infection and tumorigenesis.
Preparation of the Endometrium for Frozen Embryo Transfer: A Systematic Review
Authors: Mumusoglu Sezcan , Polat Mehtap , Ozbek Irem Yarali , Bozdag Gurkan , Papanikolaou Evangelos G. , Esteves Sandro C. , Humaidan Peter , Yarali Hakan
Published: July 2021

Despite the worldwide increase in frozen embryo transfer, the search for the best protocol to prime endometrium continues. Well-designed trials comparing various frozen embryo transfer protocols in terms of live birth rates, maternal, obstetric and neonatal outcome are urgently required. Currently, low-quality evidence indicates that, natural cycle, either true natural cycle or modified natural cycle, is superior to hormone replacement treatment protocol. Regarding warmed blastocyst transfer and frozen embryo transfer timing, the evidence suggests the 6th day of progesterone start, LH surge+6 day and hCG+7 day in hormone replacement treatment, true natural cycle and modified natural cycle protocols, respectively. Time corrections, due to inter-personal differences in the window of implantation or day of vitrification (day 5 or 6), should be explored further. Recently available evidence clearly indicates that, in hormone replacement treatment and natural cycles, there might be marked inter-personal variation in serum progesterone levels with an impact on reproductive outcomes, despite the use of the same dose and route of progesterone administration. The place of progesterone rescue protocols in patients with low serum progesterone levels one day prior to warmed blastocyst transfer in hormone replacement treatment and natural cycles is likely to be intensively explored in near future.
Open-Source Code-Based Tidal Modeling of Tropical and Temperate Waters
Authors: Srikanth Narasimalu , Kannappan Lakshmanan
Published: July 2021

Tidal energy is the most reliable and predictable form of renewable energy capable of ensuring energy security in coastal regions of the world. Many developing countries are prone to energy self-sufficiency due to a lack of tidal data, expensive commercial tidal modeling tools, and program codes. In the present study, an open-source finite element code along with available open-source data was used to predict the tidal resource potential of sites in both temperate and coastal waters. This paper also investigates the suitability of open-source code towards accurate tidal resource prediction and provides a comparative study on tidal resource prediction of sites in both temperate and coastal waters. Based on knowledge gained from tidal experts all around the globe, the straits of the Alderney race were selected as a temperate water site because of their high tidal flow conditions and high tidal energy resource potential. Singapore was selected as a tropical water site because of its low tidal flow conditions and lack of open-source tidal resource data in the tropical belt. From the results, temperate waters such as Alderney Race experience high tidal velocity in the range of 3.5–4.5 m/s with an average power density of about 15 kW/m2 in comparison with tropical waters such as Singapore that experiences tidal velocity in the range of 1–1.5 m/s with an average power density of about 1.5 kW/m2. The thrusting force behind the coastal dynamics is mainly due to tides, their interactions, and changes in seabed topography. The seabed roughness profile creates a drag force on the flow on the velocity field. Lack of understanding of the effects of seabed friction on tidal modeling might reduce the accuracy of the model prediction. Thus, the present study also focuses on the effects of seabed roughness on tidal prediction of Alderney race straits using the open-source finite element-based 2-dimensional depth average ocean model. It can be found that an increase in seabed friction reduces the flow velocity and thus the average power density of the location due to its major energy dissipating phenomenon for the energetic ocean flow.
Cancer Risk Levels for Sediment- and Soil-Bound Polycyclic Aromatic Hydrocarbons in Coastal Areas of South Korea
Authors: Roy Debananda , Jung Woosik , Kim Jayun , Lee Minjoo , Park Joonhong
Published: July 2021

The increasing cancer risk (CR) due to sediment- and soil-bound polycyclic aromatic hydrocarbons (PAHs) is one of the major threats to public health. The CR of sediment- and soil-bound carcinogenic PAHs was estimated for the first time in coastal and residential areas near an industrial zone in Korea. Monte Carlo probabilistic simulations and sensitivity tests were conducted to calculate the CR and to identify the most sensitive parameters. The CR was found to be highest in the coastal areas of Korea. Ulsan, which is located on the southeastern coast of Korea, was classified as a high cancer risk zone according to United States Environmental Protection Agency standards, while the western coast and Mohang Harbor were classified as moderate cancer risk zones. Fish consumption was identified as the main contributor (94–99%) to the total risk levels in the coastal areas. The biota-to-sediment accumulation factor (43–76%) and PAH levels (8–44%) in sediment were identified as the parameters that were most sensitive to the CR. In the residential area, the CR was found to be within the range of 10–6–10–4, which categorized it as a low cancer risk zone. Furthermore, the CR for residents in the industrial area was estimated to be 12 and 5 times higher than that for residents in the rural and urban areas, respectively. The exposure duration (55–85%) and skin adherence factor for soil (35–42%) were identified as the most sensitive parameters for the overall CR in the residential area. Korea generally has high fish and seafood consumption, which has been recognized as the most significant exposure route for CR in the studied coastal areas. Thus, the consumption of fish and seafood from coastal areas, especially those near Ulsan, might be responsible for the increasing number of cancer patients in Korea.
Learning and Animal Movement
Authors: Lewis Mark A. , Fagan William F. , Auger-Méthé Marie , Frair Jacqueline , Fryxell John M. , Gros Claudius , Gurarie Eliezer , Healy Susan D. , Merkle Jerod A.
Published: July 2021

Integrating diverse concepts from animal behavior, movement ecology, and machine learning, we develop an overview of the ecology of learning and animal movement. Learning-based movement is clearly relevant to ecological problems, but the subject is rooted firmly in psychology, including a distinct terminology. We contrast this psychological origin of learning with the task-oriented perspective on learning that has emerged from the field of machine learning. We review conceptual frameworks that characterize the role of learning in movement, discuss emerging trends, and summarize recent developments in the analysis of movement data. We also discuss the relative advantages of different modeling approaches for exploring the learning-movement interface. We explore in depth how individual and social modalities of learning can matter to the ecology of animal movement, and highlight how diverse kinds of field studies, ranging from translocation efforts to manipulative experiments, can provide critical insight into the learning process in animal movement.
Phytolith Palaeoenvironments at Mumba Rock Shelter
Authors: Mercader Julio , Clarke Siobhán , Itambu Makarius , Mohamed Abdallah , Mwitondi Musa , Siljedal Gunnar , Soto María , Bushozi Pastory
Published: July 2021

The rock shelter site of Mumba in northern Tanzania plays a pivotal role in the overall study of the late Pleistocene archaeology of East Africa with an emphasis on the Middle to Later Stone Age transition. We used phytolith analysis to reconstruct general plant habitat physiognomy around the site from the onset of the late Pleistocene to recent times, tallying 4246 individual phytoliths from 19 archaeological samples. Statistical analysis explored phytolith richness, diversity, dominance, and evenness, along with principal components to compare phytolith distributions over the site’s sequence with known plant habitats today. Generally, the phytolith record of Mumba signifies paleoenvironments with analogs in the Somalia – Masai bushland and grassland, as well as Zambezian woodlands.
Host Plant Volatile Lures Attract Apanteles polychrosidis (Hymenoptera: Braconidae) to Ash Trees Infested With Caloptilia fraxinella (Lepidoptera: Gracillariidae)
Authors: McPike Sarah M. , Evenden Maya L.
Published: July 2021

Caloptilia fraxinella Ely (Lepidoptera: Gracillariidae), the ash leaf-cone roller, is an aesthetic pest of horticultural ash trees (Oleaceae, Genus Fraxinus) in prairie communities across Canada. Because pesticide use is undesirable in urban centers, biological control of C. fraxinella is a preferred approach. The native parasitoid wasp, Apanteles polychrosidis Vierek (Hymenoptera: Braconidae), has shifted hosts and is the primary parasitoid of C. fraxinella in Edmonton, Alberta, Canada, and has potential as a biological control agent. Here, in an effort to increase parasitism of C. fraxinella, lures releasing methyl salicylate (MeSA) and two green leaf volatiles (GLVs), [(Z)-3-hexenol, and (Z)-3-hexenyl-acetate], at both low and high release rates, were tested to enhance attraction and retention of A. polychrosidis in infested ash trees. Attraction of A. polychrosidis to baited trees was measured by capture on yellow sticky cards positioned in the tree canopy, and wasp activity was assessed by the parasitism rate of C. fraxinella. More male and female A. polychrosidis were captured on yellow sticky traps positioned in trees baited with the low dose of both MeSA + GLVs than to unbaited, infested ash trees. The increased attraction of wasps did not correlate with an increase in parasitism of C. fraxinella. The high release rate lures did not enhance attraction of A. polychrosidis to infested ash trees. Parasitism rate, however, was negatively correlated with host density in both field experiments. There was no evidence of close-range attraction to lures in an olfactometer assay. Synthetic HIPVs attract A. polychrosidis to ash trees infested with C. fraxinella, but the effect of wasp attraction on parasitism rate requires further research if HIPVs are to be used to enhance biological control in this system.
Identification of Single Nucleotide Polymorphism in TaSBEIII and Development of KASP Marker Associated With Grain Weight in Wheat
Authors: Irshad Ahsan , Guo Huijun , Ur Rehman Shoaib , Wang Xueqing , Gu Jiayu , Xiong Hongchun , Xie Yongdun , Zhao Linshu , Zhao Shirong , Wang Chaojie , Liu Luxiang
Published: July 2021

Manipulation of genes involved in starch synthesis could significantly affect wheat grain weight and yield. The starch-branching enzyme (SBE) catalyzes the formation of branch points by cleaving the α-1,4 linkage in polyglucans and reattaching the chain via an α-1,6 linkage. Three types of SBE isoforms (SBEI, SBEII, and SBEIII) exist in higher plants, with the number of SBE isoforms being species-specific. In this study, the coding sequence of the wheat TaSBEIII gene was amplified. After the multiple sequence alignment of TaSBEIII genome from 20 accessions in a wheat diversity panel, one SNP was observed in TaSBEIII-A, which formed the allelic marker allele-T. Based on this SNP at 294 bp (C/T), a KASP molecular marker was developed to distinguish allelic variation among the wheat genotypes for thousand grain weight (TGW). The results were validated using 262 accessions of mini core collection (MCC) from China, 153 from Pakistan, 53 from CIMMYT, and 17 diploid and 18 tetraploid genotypes. Association analysis between TaSBEIII-A allelic variation and agronomic traits found that TaSBEIII-A was associated with TGW in mini core collection of China (MCC). The accessions possessing Allele-T had higher TGW than those possessing Allele-C; thus, Allele-T was a favorable allelic variation. By analyzing the frequency of the favorable allelic variation Allele-T in MCC, it increased from pre-1950 (25%) to the 1960s (45%) and increased continuously from 1960 to 1990 (80%). The results suggested that the KASP markers can be utilized in grain weight improvement, which ultimately improves wheat yield by marker-assisted selection in wheat breeding. The favorable allelic variation allele-T should be valuable in enhancing grain yield by improving the source and sink simultaneously. Furthermore, the newly developed KASP marker validated in different genetic backgrounds could be integrated into a breeding kit for screening high TGW wheat.
Inflammation Determines the Capacity of Allogenic Endothelial Cells to Regulate Human Treg Expansion
Authors: Cross Amy Rachael , Lion Julien , Poussin Karine , Glotz Denis , Mooney Nuala
Published: July 2021

During allotransplantation, the endothelium acts as semi-professional antigen-presenting cells with the ability to activate proliferation and to promote differentiation of CD4+-T subsets. These abilities are dependent on the luminal expression of HLA class II antigens by microvascular endothelial cells, which is regulated by inflammatory cytokines. The upregulation of HLA-DR and HLA-DQ during rejection implies significant intragraft inflammation. Furthermore, the microvascular inflammation is an independent determinant for renal allograft failure. In this study, the potential of inflammation to modify endothelial regulation of peripheral CD4+Treg cells was examined. Microvascular endothelial cells were exposed to pro-inflammatory cytokines for varying durations before co-culture with PBMC from non-HLA matched donors. Proliferation and expansion of CD4+Treg and soluble factor secretion was determined. Early interactions were detected by phosphorylation of Akt. Video microscopy was used to examine spatial and temporal endothelial-CD4+T interactions. Highly inflammatory conditions led to increased endothelial expression of HLA-DR, the adhesion molecule ICAM-1, the costimulatory molecule PD-L1 andde novoexpression of HLA-DQ. Treg differentiation was impaired by exposure of endothelial cells to a high level of inflammation. Neither IL-6, IL-2 nor TGFβ were implicated in reducing Treg numbers. High PD-L1 expression interfered with early endothelial cell interactions with CD4+T lymphocytes and led to modified TCR signaling. Blocking endothelial PD-L1 resulted in a partial restoration of Treg. The allogenic endothelial cell-mediated expansion of Treg depends on a critical threshold of inflammation. Manipulation of the PD-L1/PD-1 pathway or endothelial activation post-transplantation may promote or interfere with this intrinsic mechanism of allospecific Treg expansion.
A Pan-Cancer Analysis of CD161, a Potential New Immune Checkpoint
Authors: Zhou Xiaohan , Du Jun , Liu Chengdong , Zeng Hanyi , Chen Yuting , Liu Li , Wu Dehua
Published: July 2021

Background

CD161, encoded by killer cell lectin-like receptor B1 gene, is a newly reported candidate inhibitor of tumour-infiltrating T cells. Antibody-mediated CD161 blockade enhances T cell-mediated killing of cancer cells in vitro and in vivo in several tumour types. We evaluated the role of CD161 using The Cancer Genome Atlas (TCGA) Pan-Cancer Data.

Methods

CD161 expression was analysed using RNAseq data from TCGA and the Genotype-Tissue Expression (GTEx) database. HPA, GeneCards, and String database were used to explore the protein information of CD161. The prognostic value of CD161 was analysed using clinical survival data from the TCGA. Enrichment analysis of CD161 was conducted using the R package “clusterProfiler”. We downloaded the immune cell infiltration score of TCGA samples from published articles and online databases and performed a correlation analysis between immune cell infiltration levels and CD161 expression. We further assessed the association between CD161 and immune checkpoints, immune activating genes, immunosuppressive genes, chemokines, and chemokine receptors.

Findings

CD161 was differentially expressed and predicted better survival status in most tumour types in TCGA. In addition, CD161 expression was significantly associated with immunoregulatory interactions between lymphoid and non-lymphoid cells. CD161 expression was closely correlated with T cell infiltration, immune checkpoints, immune activating genes, immunosuppressive genes, chemokines, and chemokine receptors.

Interpretation

Our results suggest that CD161 is a potential cancer biomarker. CD161 might synergize with other immune checkpoints to regulate the immune microenvironment, which could be applied in the development of new-targeted drugs for immunotherapy.

Funding

This work was supported by the National Nature Science Foundation of China (grant numbers 81773008, 81672756, 81872399, 81972897), the Guangdong Province Universities and Colleges Pearl River Scholar Funded Scheme (2015), the Natural Science Foundation of Guangdong Province (grant number 2017A030311023), the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program: 2017BT01S131 and the Guangzhou Technology Project (grant number 201804010044), National Key R&D Program of China (Grant Nos. 2020YFC2006400), Key-Area Research and Development Program of Guangdong Province (2019B020227004).
Enhanced Dry Process Method for Modified Asphalt Containing Plastic Waste
Authors: Radeef Hasanain Radhi , Abdul Hassan Norhidayah , Abidin Ahmad Razin Zainal , Mahmud Mohd Zul Hanif , Yusoffa Nur Izzi Md. , Idham Mohd Satar Mohd Khairul , Warid Muhammad Naqiuddin Mohd
Published: July 2021

In recent years, the proliferation of plastic waste has become a global problem. A potential solution to this problem is the dry process, which incorporates plastic waste into asphalt mixtures. However, the dry process often has inconsistent performance due to poor interaction with binder and improper distribution of plastic waste particles in the mixture skeleton. This inconsistency may be caused by inaccurate mixing method, shredding size, mixing temperature and ingredient priorities. Thus, this study aims to improve the consistency of the dry process by comparing the control asphalt mixture and two plastic waste-modified asphalt mixtures prepared using the dry process. This study used crushed granite aggregate with the nominal maximum aggregate size of 14 mm whereas the shredded plastic bag is in the range of 5–10 mm. Quantitative sieving analysis and performance tests were carried out to examine the effects of plastic waste added into the asphalt mixture. The volumetric and performance properties combined with image analysis of the modified mixtures were obtained and compared with the control mixture. In addition, the moisture damage, resilient modulus, creep deformation and rutting were evaluated. This study also highlighted in detail the distribution of plastic particles in the final skeleton of the asphalt mixture. Based on the analysis, an enhanced dry process of mixing procedure was proposed and evaluated. Results showed that the addition of plastic particles using the conventional dry process leads to the deviation in the aggregate structure as high plastic content is added. Furthermore, the enhanced dry process developed in this study presents substantial enhancement in the asphalt performance, particularly with plastic waste that accounts for 20% of the weight of the asphalt binder.
Compensating Complete Loss of Signal Recognition Particle During Co-translational Protein Targeting by the Translation Speed and Accuracy
Authors: Zhao Liuqun , Fu Gang , Cui Yanyan , Xu Zixiang , Cai Tao , Zhang Dawei
Published: July 2021

Signal recognition particle (SRP) is critical for delivering co-translational proteins to the bacterial inner membrane. Previously, we identified SRP suppressors in Escherichia coli that inhibit translation initiation and elongation, which provided insights into the mechanism of bypassing the requirement of SRP. Suppressor mutations tended to be located in regions that govern protein translation under evolutionary pressure. To test this hypothesis, we re-executed the suppressor screening of SRP. Here, we isolated a novel SRP suppressor mutation located in the Shine–Dalgarno sequence of the S10 operon, which partially offset the targeting defects of SRP-dependent proteins. We found that the suppressor mutation decreased the protein translation rate, which extended the time window of protein targeting. This increased the possibility of the correct localization of inner membrane proteins. Furthermore, the fidelity of translation was decreased in suppressor cells, suggesting that the quality control of translation was inactivated to provide an advantage in tolerating toxicity caused by the loss of SRP. Our results demonstrated that the inefficient protein targeting due to SRP deletion can be rescued through modulating translational speed and accuracy.
Protective Effect of Lactobacillus plantarum P8 on Growth Performance, Intestinal Health, and Microbiota in Eimeria-Infected Broilers
Authors: Wang Yang , Lv Xiaoguo , Li Xuemin , Zhao Jinshan , Zhang Kai , Hao Xiaojing , Liu Kaidong , Liu Huawei
Published: July 2021

Coccidiosis is one of the major parasitic diseases in the commercial broiler industry. Probiotics can protect poultry against Eimeria infection. However, the mechanisms are not fully known. Therefore, Lactobacillus plantarum P8 (P8) was used to investigate its anti-coccidial property and mechanism. Five hundred broilers were allocated to five treatments: control diet (NC), control diet + Eimeria infection (IC), control diet containing 1 × 107 cfu/g P8 + Eimeria infection (P8L), control diet containing 1 × 108 cfu/g P8 + Eimeria infection (P8H), and control diet + Eimeria infection + Diclazuril (DIC). At day 14, all treatments except NC were inoculated with sporulated oocysts. Results indicated that Eimeria infection increased the mortality and oocysts shedding, and declined the growth performance as well as the intestinal barrier in Eimeria-treated broilers. On the contrary, dietary supplementation of low level P8, high level P8 and DIC decreased the mortality and oocysts shedding, but improved the growth performance and intestinal barrier. The impaired intestinal morphology in the IC group was also improved by P8H and DIC treatments. Besides, the elevated oxidative stress and pro-inflammation in Eimeria-infected broilers were reduced by P8L, P8H, and DIC treatments. Metagenomic analysis indicated P8 altered the structure of the gut microbiota, and the alteration was more obvious at day 21 than day 42. Notably, IC also increased the abundances of Eimeriidae, Eimeria and Eimeria tenella at day 21, while P8L and DIC decreased the abundances. Correlation analysis revealed that bacteria in Eimeria-treated broilers positively correlated with the intestinal permeability, oxidative stress and inflammation, while bacteria in broilers receiving P8L and DIC negatively correlated with the aforementioned pathological indices. Functional prediction demonstrated that the metagenomes of Eimeria-infected broilers were involved in several diseases. But the metagenomes of P8L-treated broilers were involved in energy metabolism and replication repair. In conclusion, dietary P8 supplementation inhibited oocyst shedding and improved the growth performance as well as the intestinal health of broilers infected with Eimeria, which was closely related to the regulation of gut microbiota. Moreover, the effects of P8 may be more effective in the early infection of coccidia.
Indole-Terpenoids With Anti-inflammatory Activities From Penicillium sp. HFF16 Associated With the Rhizosphere Soil of Cynanchum bungei Decne
Authors: Pan Guojun , Zhao Yanfen , Ren Shuang , Liu Fengyang , Xu Qicai , Pan Weibin , Yang Tongtao , Yang Mingtian , Zhang Xinru , Peng Chuanyue , Hao Gangping , Kong Fandong , Zhou Liman , Xiao Na
Published: July 2021

Four new indole-terpenoids (1–4) named encindolene A, 18-O-methyl-encindolene A, encindolene B, and encindolene C, as well as three known analogs (5–7), were isolated from the fungus Penicillium sp. HFF16 from the rhizosphere soil of Cynanchum bungei Decne. The structures of compounds including absolute configurations were elucidated by spectroscopic data and electronic circular dichroism (ECD) analysis. Anti-inflammatory activity evaluation revealed that compounds 1–7 inhibit the production of nitric oxide with IC50 values of 79.4, 49.7, 81.3, 40.2, 86.7, 90.1, and 54.4 μM, respectively, and decrease the levels of tumor necrosis factor-α, interleukin-6 contents in lipopolysaccharide-induced RAW264.7 macrophages.