bluuebunny/crossref_metadata_2025_split huggingface dataset:
A BioBricks toolbox for metabolic engineering of the tetracenomycin pathway
Authors: Nguyen Jennifer T. , Riebschleger Kennedy K. , Brown Katelyn V. , Gorgijevska Nina M. , Nybo S. Eric 
Published: October 2021

AbstractBackground/Goal/AimThe tetracenomycins are aromatic anticancer polyketides that inhibit peptide translation via binding to the large ribosomal subunit. Here, we expressed the elloramycin biosynthetic gene cluster in the heterologous host Streptomyces coelicolor M1146 to facilitate the downstream production of tetracenomycin analogs.Main Methods and Major ResultsWe developed a BioBricks genetic toolbox of genetic parts for substrate precursor engineering in S. coelicolor M1146::cos16F4iE. We cloned a series of integrating vectors based on the VWB, TG1, and SV1 integrase systems to interrogate gene expression in the chromosome. We genetically engineered three separate genetic constructs to modulate tetracenomycin biosynthesis: (1) the vhb hemoglobin from obligate aerobe Vitreoscilla stercoraria to improve oxygen utilization; (2) the accA2BE acetyl‐CoA carboxylase to enhance condensation of malonyl‐CoA; (3) lastly, the sco6196 acyltransferase, which is a “metabolic regulatory switch” responsible for mobilizing triacylglycerols to β‐oxidation machinery for acetyl‐CoA. In addition, we engineered the tcmO 8‐O‐methyltransferase and newly identified tcmD 12‐O‐methyltransferase from Amycolatopsis sp. A23 to generate tetracenomycins C and X. We also co‐expressed the tcmO methyltransferase with oxygenase urdE to generate the analog 6‐hydroxy‐tetracenomycin C.Conclusions and ImplicationsAltogether, this system is compatible with the BioBricks [RFC 10] cloning standard for the co‐expression of multiple gene sets for metabolic engineering of Streptomyces coelicolor M1146::cos16F4iE. This production platform improves access to potent analogs, such as tetracenomycin X, and sets the stage for the production of new tetracenomycins via combinatorial biosynthesis.
Experimental and numerical determination of the screw deformation in laminated beech veneer lumber as a result of moisture‐induced swelling
Authors: Gerstorfer Daniela , Forte Thomas , Füssl Josef 
Published: October 2021

AbstractThe strong hygroscopic behavior of wood can lead to severe moisture‐induced swelling deformations, especially perpendicular to the grain direction. Fully threaded screws arranged in this direction can be used as reinforcement and to constrain those deformations. Depending on the wood moisture content increase, tensile stresses in the screws and compression stresses in the surrounding solid wood evolve. A sufficiently accurate prediction of the maximum stresses occurring is important for reliable structural designs. For this reason, moisture‐induced swelling experiments for two different configurations of screw diameter and specimen dimensions were performed within this work. Due to its homogeneity and its high swelling rate perpendicular to the grain, beech laminated veneer lumber (LVL) was used. A moisture content increase from oven‐dry to about 7% led to screw tensile stresses in the magnitude of the yield strength and to highly nonlinear effects in the surrounding wood material. By means of a two‐dimensional finite‐element‐based numerical simulation model, taking into account orthotropic plasticity and moisture‐dependent material properties, the experiments could be simulated with high accuracy. The numerical results agree well with experimental observations. Based on a small parameter study, new insights into the complex interaction behavior between beech LVL and fully threaded screws could be gained.
Do crocodiles have a zona incerta?
Authors: Pritz Michael B. 
Published: October 2021

AbstractIn mammals, the zona incerta is thought to be involved in a number of behaviors: visceral activity, arousal, attention, and posture and locomotion. These diverse and complex features suggested that the zona incerta functions as a global or integrative node. Nevertheless, despite multiple investigations into its anatomy, physiology, and behavior in a variety of mammals, no specific character identifies the zona incerta besides its appearance in fiber‐stained material and its relationship to surrounding structures. One such structure is the thalamic reticular nucleus whose caudal pole often contains some intermingled cells of the zona incerta. In crocodilians, the entopeduncular nucleus (ep) abuts the caudal pole of the thalamic reticular nucleus and displays different immunohistochemical properties and soma size when compared with neurons in the thalamic reticular nucleus itself. To determine if neurons in the ep differed from those in the thalamic reticular nucleus in Alligator mississippiensis, the ep was investigated using Golgi methodology. The morphology and soma size of neurons in the ep differed from those in the thalamic reticular nucleus and indicated that these two areas are indeed separate neuronal aggregates. Based on these data and the known relationships of the zona incerta to surrounding structures in mammals, the ep of crocodilians is suggested to be the counterpart of the zona incerta of mammals.
Modeling and simulation of cell migration on the basis of force equilibrium
Authors: Chang Chia‐Yu , Dai Zhi‐Xuan , Shih Po‐Jen 
Published: October 2021

AbstractTo study cell behavior, we developed a cell model to simulate cell movements and the interacting forces among cells and between cells and obstacles. The developed model simulates several cells simultaneously and examines correlations among characteristic parameters between cells and substrates during migration. We modified Odde's model to develop fundamental model, applied Gillespie's stochastic algorithm to design time during in the migration simulation, and employed Keren's membrane theory to analyze the equilibrium at the leading edges. Thus, the proposed model can analyze stresses due to substrate, the intracellular body, and the external interaction between cells and obstacles. Simulation results indicate that cell–cell interaction depends on the equilibrium between the forces at the leading edge of the membrane, namely the cell–substrate interaction force, cell–cell interaction forces, and the cell membrane force. These results also indicate that the migration direction is dependent on the resultant forces. The membrane force and substrate force directions are “low correlation,” and the polymerization rate exhibits “little correlative” with the migration direction. We propose a modified cell migration model for simulating allocation and interaction among multiple cells. This model helps indicate the weightings of characteristic parameters that affect the cell migration direction and velocity.
Recent approach for preventing complications in upper gastrointestinal endoscopic submucosal dissection
Authors: Hatta Waku , Koike Tomoyuki , Abe Hiroko , Ogata Yohei , Saito Masahiro , Jin Xiaoyi , Kanno Takeshi , Uno Kaname , Asano Naoki , Imatani Akira , Masamune Atsushi 
Published: October 2021

AbstractAlthough endoscopic submucosal dissection (ESD) is a minimally invasive treatment method for upper gastrointestinal (GI) tumors, patients undergoing upper GI ESD sometimes fall into a serious condition from complications. Thus, it is important to fully understand how to prevent complications when performing upper GI ESD. One of the major complications in esophageal and gastric ESD is intraoperative perforation. To prevent this complication, blind dissection should be avoided. Traction‐assisted ESD is a useful technique for maintaining good endoscopic view. This method was proven to reduce the incidence of intraoperative perforation, which would become a standard technique in esophageal and gastric ESD. In gastric ESD, delayed bleeding is the most common complication. Recently, a novel prediction model (BEST‐J score) consisting of 10 factors with four risk categories for delayed bleeding in gastric ESD was established, and a free mobile application is now available. For reducing delayed bleeding in gastric ESD, vonoprazan ≥20 mg/day is the sole reliable method in the current status. Duodenal ESD is still challenging with a much higher frequency of complications, such as perforation and delayed bleeding, than ESD in other organs. However, with the development of improved devices and techniques, the frequency of complications in duodenal ESD has been decreasing. To prevent intraoperative perforation, some ESD techniques, such as using the distal tips of the Clutch Cutter, were developed. An endoscopic mucosal defect closure technique would be mandatory for preventing delayed complications. However, several unresolved issues, including standardization of duodenal ESD, remain and further studies are demanded.
Utility of autologous fecal microbiota transplantation and elucidation of microbiota in diversion colitis
Authors: Tominaga Kentaro , Tsuchiya Atsunori , Mizusawa Takeshi , Matsumoto Asami , Minemura Ayaka , Oka Kentaro , Takahashi Motomichi , Yoshida Tomoaki , Kojima Yuichi , Ogawa Kohei , Kawata Yuzo , Nakajima Nao , Kimura Naruhiro , Abe Hiroyuki , Setsu Toru , Takahashi Kazuya , Sato Hiroki , Ikarashi Satoshi , Hayashi Kazunao , Mizuno Ken‐ichi , Yokoyama Junji , Tajima Yosuke , Nakano Masato , Shimada Yoshifumi , Kameyama Hitoshi , Wakai Toshifumi , Terai Shuji 
Published: October 2021

AbstractObjectivesDiversion colitis (DC) is an inflammatory disorder caused by interruption of the fecal stream and subsequent nutrient deficiency from luminal bacteria. The utility of fecal microbiota transplantation (FMT) for DC was recently investigated; however, the precise pathogenesis of this condition remains unclear. This study aimed to evaluate the utility of autologous FMT in DC and to determine the related changes in the intestinal microbiota.MethodsAutologous FMT was performed to reestablish the intestinal microbiota in five patients (average age, 64.6 ± 8.3 years) with DC. They underwent double‐ended colostomy. We assessed the diverted colon by endoscopy and evaluated the microbiota before and after FMT using the 16S rRNA gene sequencing method.ResultsAll five patients had mild inflammation (ulcerative colitis endoscopic index of severity [UCEIS] 2–3) in the diverted colon based on the colonoscopic findings. Three patients presented with symptoms, such as tenesmus, mucoid stool, and bloody stool. With FMT treatment, all patients achieved endoscopic remission (UCEIS score of 0 or 1) and symptomatic improvement. We observed a significantly decreased α‐diversity in DC patients compared to healthy controls. The frequency of aerobic bacteria, such as Enterobacteriaceae, in the diverted colon decreased after autologous FMT.ConclusionsThis study was the first to show that the microbiota in the diverted colon was significantly affected by autologous FMT. Since interruption of the fecal stream is central to the development of DC, FMT can be considered a promising treatment.
An RNA Interference/Adeno‐Associated Virus Vector–Based Combinatorial Gene Therapy Approach Against Hepatitis E Virus
Authors: Zhang Cindy , Freistaedter Andrew , Schmelas Carolin , Gunkel Manuel , Dao Thi Viet Loan , Grimm Dirk 
Published: October 2021

Hepatitis E virus (HEV) is a major public health problem with limited therapeutic options. Here, we engineered adeno‐associated viral vectors of serotype 6 (AAV6) to express short hairpin RNAs (shRNAs) against HEV transcripts with the prospect of down‐regulating HEV replication in vivo. We designed 20 different shRNAs, targeting the genome of the HEV genotype 3 (GT3) Kernow‐C1 p6 strain, for delivery upon AAV6 transduction. Using an original selectable HEV GT3 reporter replicon, we identified three shRNAs that efficiently down‐regulated HEV replication. We further confirmed their inhibitory potency with full‐length HEV infection. Seventy‐two hours following transduction, HEV replication in both systems decreased by up to 95%. The three most potent inhibitory shRNAs identified were directed against the methyltransferase domain, the junction region between the open reading frames (ORFs), and the 3´ end of ORF2. Targeting all three regions by multiplexing the shRNAs further enhanced their inhibitory potency over a prolonged period of up to 21 days following transduction. Conclusion: Combining RNA interference and AAV vector–based gene therapy has great potential for suppressing HEV replication. Our strategy to target the viral RNA with multiplexed shRNAs should help to counteract viral escape through mutations. Considering the widely documented safety of AAV vector–based gene therapies, our approach is, in principle, amenable to clinical translation.
Impact of water source dynamics on dissolved reactive phosphorus loadings in heterogenous karst agroecosystems with phosphatic limestones
Authors: Radcliff Cory , Ford William I. , Nazari Saeid , Shepard Christopher 
Published: October 2021

AbstractKarst landscapes underlain with phosphatic limestones are now recognized to be an important contributor of fluvial phosphorus (P) to coastal waters. Specifically, karst agroecosystems may be a hotspot for dissolved reactive P (DRP) due to chronic over‐application of organic and inorganic fertilizers that create legacy P accumulation in surface soils. Nevertheless, few studies have assessed the hydrologic controls on DRP transport in these systems at the watershed scale, which is the focus of this study. We analysed soil moisture, soil water extractable P, and storm event hydrologic and water quality data from a small heterogenous karst watershed (10.7 km2) in the Inner‐Bluegrass Region of Central Kentucky, USA. Four storm events were sampled in winter, 2020 and were analysed for flow pathways using hydrograph recession analysis and water source connectivity using a tracer‐based unmixing model. Based on hydrograph separation results, multiple linear regression analysis was performed to assess drivers of DRP concentrations and loadings. Soil water extractable P results showed stark vertical gradients with greater concentrations at both the surface and deeper soil zones, and minimum concentrations in the root zone. Results for the storm event analysis showed that water source connectivity provided superior prediction of DRP concentrations over the flow pathway analysis, which reflected the heterogeneity of karst maturity masking intermediate flow pathways. Findings from the MLR and loading analysis suggest waters sourced from the soil/epikarst produced significantly higher loadings compared with phreatic and precipitation water source in the three largest events, although concentrations fell between the phreatic (low) and precipitation (high) sources. Findings highlight variable activation of matrix‐macropore exchange at different depths throughout the event. Collectively these results suggest existing models and approaches to assess karst hydrology need revision to improve management strategies in this critical landscape.
Butanol recovery using ionic liquids as green solvents
Authors: Motghare Kalyani A , Shende Diwakar Z , Wasewar Kailas L 
Published: October 2021

AbstractBACKGROUNDConsistent rising energy demand due to depleting conventional resources leads to the development of alternative energy sources. Biobutanol is a promising fuel because of its high energy content. However, the fermentative technique of butanol generation by the acetone−butanol−ethanol procedure utilizing solventogenic Clostridium has serious constraints. It represses microbial movement (ordinarily ≥10 g L−1) and influences its production. To extricate butanol from aging broth, there are different separation techniques. To conquer these issues, ionic liquids can be utilized as novel extractants replacing ordinary unstable solvents.RESULTSIn the present paper, separation of butanol (simulated) from aqueous media utilizing typical hydrophobic ionic liquids – 1‐hexyl‐3‐methylimidazolium bis(trifluoromethanesulfonimide) (HMIM[NTF2]), 1‐hexyl‐3‐methylimidazolium hexafluorophosphate (HMIM[PF6]) and other solvents; oleyl alcohol (OA), tri‐n‐butyl phosphate (TBP) and their blends – has been carried at 298 ± 1 K. Results were compared with TBP, which was taken as a conventional reference solvent. Extraction efficiency was observed in the range TBP > 85–87% for OA > 55–85 for HMIM[NTF2] > 26–66% for HMIM[PF6], respectively. From the equilibrium experiments, distribution coefficients (Kd) values were observed in the range of TBP (7–23) > OA (5–7) > HMIM[NTF2] (1.2–5.6) > HMIM[PF6] (0.36–1.94), respectively.CONCLUSIONThe present study shows how extractant–diluent combinations can be used to obtain a non‐toxic extractant to tune characteristics of ionic liquids and improve fluid properties by significantly increasing distribution coefficients and extraction efficiencies. This could be helpful for separation of butanol from aqueous phase. © 2021 Society of Chemical Industry (SCI).
International Expert Consensus on Precision Anatomy for minimally invasive distal pancreatectomy: PAM‐HBP Surgery Project
Authors: Ban Daisuke , Nishino Hitoe , Ohtsuka Takao , Nagakawa Yuichi , Abu Hilal Mohammed , Asbun Horacio J. , Boggi Ugo , Goh Brian K. P. , He Jin , Honda Goro , Jang Jin‐Young , Kang Chang Moo , Kendrick Michael L. , Kooby David A. , Liu Rong , Nakamura Yoshiharu , Nakata Kohei , Palanivelu Chinnusamy , Shrikhande Shailesh V. , Takaori Kyoichi , Tang Chung‐Ngai , Wang Shin‐E , Wolfgang Christopher L. , Yiengpruksawan Anusak , Yoon Yoo‐Seok , Ciria Ruben , Berardi Giammauro , Garbarino Giovanni Maria , Higuchi Ryota , Ikenaga Naoki , Ishikawa Yoshiya , Kozono Shingo , Maekawa Aya , Murase Yoshiki , Watanabe Yusuke , Zimmitti Giuseppe , Kunzler Filipe , Wang Zi‐Zheng , Sakuma Leon , Osakabe Hiroaki , Takishita Chie , Endo Itaru , Tanaka Masao , Yamaue Hiroki , Tanabe Minoru , Wakabayashi Go , Tsuchida Akihiko , Nakamura Masafumi 
Published: October 2021

AbstractBackgroundSurgical views with high resolution and magnification have enabled us to recognize the precise anatomical structures that can be used as landmarks during minimally invasive distal pancreatectomy (MIDP). This study aimed to validate the usefulness of anatomy‐based approaches for MIDP before and during the Expert Consensus Meeting: Precision Anatomy for Minimally Invasive HBP Surgery (February 24, 2021).MethodsTwenty‐five international MIDP experts developed clinical questions regarding surgical anatomy and approaches for MIDP. Studies identified via a comprehensive literature search were classified using Scottish Intercollegiate Guidelines Network methodology. Online Delphi voting was conducted after experts had drafted the recommendations, with the goal of obtaining >75% consensus. Experts discussed the revised recommendations in front of the validation committee and an international audience of 384 attendees. Finalized recommendations were made after a second round of online Delphi voting.ResultsFour clinical questions were addressed, resulting in 10 recommendations. All recommendations reached at least a 75% consensus among experts.ConclusionsThe expert consensus on precision anatomy for MIDP has been presented as a set of recommendations based on available evidence and expert opinions. These recommendations should guide experts and trainees in performing safe MIDP and foster its appropriate dissemination worldwide.
Histology and ultrastructure of the gastrointestinal tract in four temperate marine herbivorous fishes
Authors: Johnson Kate S. , Clements Kendall D. 
Published: October 2021

AbstractWhile alimentary tract anatomy in many terrestrial herbivorous vertebrates is well documented, the digestive systems of marine herbivorous fishes are poorly characterised. The gastrointestinal tract (GIT) of four species of marine herbivorous fishes from northeastern New Zealand, butterfishOdax pullus(Labridae), marblefishAplodactylus arctidens(Aplodactylidae), notch‐head marblefishA. etheridgii(Aplodactylidae) and silver drummerKyphosus sydneyanus(Kyphosidae), were examined using histology and transmission electron microscopy (TEM) to provide a detailed histological and ultrastructural description of gut anatomy. Gastric glands were distributed over rugae in the stomach ofA. arctidens,A. etheridgiiandK. sydneyanus. The luminal surface of the stomach of these three species was lined by columnar mucous cells, and oxynticopeptic cells lined the glands in the stomach. Villi were present along the length of the intestine in all four species. The anterior intestine had thin musculature, and was lined by absorptive cells with long microvilli and numerous small vesicles in the apical cytoplasm. The posterior intestine was lined by absorptive columnar cells with long microvilli, invaginations between microvilli with electron‐dense membranes, and pinocytotic vesicles. Surface area generally decreased from the anterior to posterior intestine. Histological and ultrastructural results were consistent with lipid absorption occurring in the anterior GIT and protein absorption in the posterior GIT. The results of this study indicate clear differences in GIT structure among the study species, and digestion models based on chemical reactor theory were developed to characterise these differences.
Influence of temperature on secretion and functionality of lupin seed γ‐conglutin
Authors: Czubinski Jaroslaw 
Published: October 2021

AbstractBACKGROUNDBasic 7S globulins, a group of proteins commonly found in legumes, undergo the intriguing phenomenon of release from the seeds into hot water. γ‐Conglutin is a representative of this group of proteins found in lupin seeds. The physiological significance and the molecular mechanism of the selective release of γ‐conglutin from lupin seeds remain unknown. Therefore, the presented study aimed to determine changes in the functionality of this protein in response to the high temperature occurring during lupin seed incubation.RESULTSIt was confirmed that the main protein fraction released from the seeds during high‐temperature incubation was γ‐conglutin. The incubation condition favours the occurrence of this protein in a monomeric form, and the temperature used corresponds to its midpoint unfolding temperature. Subsequent analysis carried out on the γ‐conglutin monomer revealed changes in its functionality after heat shock. The thermally treated protein shows a considerable increase in its interaction strength with flavonoids. Moreover, the inhibitory activity against glycoside hydrolases was enhanced when γ‐conglutin monomer was exposed to specific temperatures.CONCLUSIONThe results of the present study provide a potential explanation of the physiological relevance of γ‐conglutin and shed new light on a possible mechanism of its activation upon specific heat treatment. This knowledge will help characterise homologous proteins, which are commonly found in other legumes and undergo a similar heat‐induced secretion phenomenon. © 2021 Society of Chemical Industry.