bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers
Authors: Mawla Alex M. , Meulen Talitha van der , Huising Mark O.
Published: October 2022

Background: High throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approaches have furthered our understanding of expression patterns that define healthy or diseased islet cell types and helped explicate some of the intricacies between major islet cell crosstalk and glucose regulation. All three endocrine cell types derive from a common pancreatic progenitor, yet alpha and beta cells have partially opposing functions, and delta cells modulate and control insulin and glucagon release. While gene expression signatures that define and maintain cellular identity have been widely explored, the underlying epigenetic components are incompletely characterized and understood. However, chromatin accessibility and remodeling is a dynamic attribute that plays a critical role to determine and maintain cellular identity.
Results: Here, we compare and contrast the chromatin landscape between mouse alpha, beta, and delta cells using ATAC-Seq to evaluate the significant differences in chromatin accessibility. The similarities and differences in chromatin accessibility between these related islet endocrine cells help define their fate in support of their distinct functional roles. We identify patterns that suggest that both alpha and delta cells are poised, but repressed, from becoming beta-like. We also identify patterns in differentially enriched chromatin that have transcription factor motifs preferentially associated with different regions of the genome. Finally, we not only confirm and visualize previously discovered common endocrine- and cell specific- enhancer regions across differentially enriched chromatin, but identify novel regions as well. We compiled our chromatin accessibility data in a freely accessible database of common endocrine- and cell specific-enhancer regions that can be navigated with minimal bioinformatics expertise.
Conclusions: Both alpha and delta cells appear poised, but repressed, from becoming beta cells in murine pancreatic islets. These data broadly support earlier findings on the plasticity in identity of non-beta cells under certain circumstances. Furthermore, differential chromatin accessibility shows preferentially enriched distal-intergenic regions in beta cells, when compared to either alpha or delta cells.
Lactation stage tweaks heamatological, serum biochemical, oxidative stress marker and endocrinological profiles in crossbred cows under tropical humid island ecosystem of Andaman and Nicobar Islands
Authors: Ponraj Perumal , De AK , Bhattacharya Debasis
Published: October 2022

The present study was outlined to appraise the interrelation between heamatological, blood metabolic profiles and lactation stages in crossbred (CB) dairy cows in ANI. Healthy (n = 18) CB cows with age of 5–7 years were selected from cattle breeding farm, ICAR-CIARI, Port Blair, ANI. Heamatological profiles, serum biochemical profiles, oxidative stress markers and endocrinological profiles were measured at 15-day interval from day 01 to 305 of lactation and divided into first (day 01 to 90), second (day 91 to 180) and third (day 181 to 305) stage of lactation. Average milk yield (L) was not significantly differed among the stages of lactations; however, first (8.42 ± 1.18) and second (9.67 ± 0.25) stages were had higher than third (7.82 ± 0.47) stage of lactation. Hematological profiles were not-differed significantly among the stages of lactation; however, these values were within the range of bovine species. Serum biochemical profiles such as glucose, triglyceride, total cholesterol, total protein and globulin were escalated significantly (p < 0.05) as stage of lactation advanced whereas albumin and creatinine were dwindled significantly (p < 0.05) as lactation stages progressed. Aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), calcium, phosphorous and magnesium were non-significantly differed among the stages of lactation. Similarly, serum endocrinological profiles such as Triiodo thyronine (T3), Thyroxine (T4) were surged and prolactin and cortisol were diminished significantly (p < 0.05) as stages of lactation progressed. Total antioxidant capacity (TAC) was increased and oxidative stress marker (malondialdehyde; MDA) was decreased significantly (p < 0.05) as stage progressed. It is concluded that among different stages of lactation, first and second stages are more stressful events as contrast to third stage of lactation in crossbred cattle in humid tropical island ecosystem of ANI.
Fault Diagnosis for PV System Using a Using deep learning optimized via PSO Heuristic Combination Technique
Authors: eldeghady ghada , Kamal hanan A. , Hassan Mohamed A. Mustafa
Published: October 2022

The authors have requested that this preprint be removed from Research Square.
The role of sodium fluorescein in pediatric supratentorial intra-axial tumor resection: new insights from a monocentric series of 33 consecutive patients
Authors: Falco Jacopo , Broggi Morgan , Schiariti Marco , Vetrano Ignazio Gaspare , Esposito Silvia , Ferroli Paolo , Acerbi Francesco
Published: October 2022

Surgical resection represents the mainstay of treatment, in pediatric central nervous system (CNS) tumors, and aggressive resection correlates with prognosis for several histotypes. Sodium fluorescein (SF), a green, water-soluble dye, is used as neurosurgical fluorescent tracer thanks to its property to accumulate in cerebral regions of blood-brain barrier disruption, acting as a valid tool to improve the extent of resection in tumors enhancing at preoperative MRI. Brain neoplasms represent a heterogeneous group of tumors in the pediatric age, constituting the most common solid cancers; they typically show a varying degree of contrast enhancement on MRI. In March 2016 the authors started a prospective, observational trial to evaluate intraoperative fluorescence’s characteristics of CNS tumors, the percentage of extent of resection thanks to fluorescein aid and side effects related to fluorescein administration. This report is based on a retrospective analysis of a group of 33 consecutive pediatric patients harboring a supratentorial lesion. In 17 of 33 (51.5%) procedures fluorescence was reported as intense, in 14 of 33 (42.4%) moderate and in 2 of 33 (6.1%) slight. Intraoperative fluorescence corresponds to preoperative MRI documented contrast enhancement. In 28 of 33 (84.8%) surgical procedures SF was considered useful, in 2 of 33 (6.1%) partial useful, and in 3 of 33 (9.1%) not essential because the tumor was already recognizable. No adverse effect to SF administration was registered. Fluorescein-guided surgery with a dedicated filter on the microscope is a safe and effective technique to improve visualization and resection of different pediatric brain tumors.
Heat-light soaking treatments for high-performance CIGS solar cells on flexible substrates
Authors: Carron Romain , Nishiwaki Shiro , Yang Shih-Chi , Ochoa Mario , Sun Xiaoxiao , Feurer Thomas , Tiwari Ayodhya
Published: October 2022

Cu(In,Ga)Se2 (CIGS) solar cells are sensitive to heat-light soaking (HLS) treatments performed at elevated temperatures. Such treatments often result in improved open-circuit voltage at the expense of short-circuit current and/or fill factor, and may be reversible. In this contribution, we analyze the changes brought in the devices by heat and light treatments to CIGS, to deliver hints regarding the fundamental reasons behind the observed changes and to ensure the long-term stability of the performance improvement. We apply HLS treatments to improve the performance of low-temperature grown CIGS solar cells on flexible polyimide and on glass substrates. We first investigate the treatment conditions favorable for device performances. A gain in open-circuit voltage is obtained, with no clear statistical impact on short-circuit current and fill factor. The changes are stable over periods of several months. Then we combine material analysis techniques to optoelectronic and electrical characterization on samples subject to a unique HLS treatment at the optimal conditions. The voltage gain arises from a large increase in the doping density in the absorber layer, correlated with increased concentrations of alkali elements Na and Rb. This improvement is partly offset by a reduction in minority charge carrier lifetime. The microscopic origin for the observed changes is discussed. At low temperatures, we also measure device enhancement due to the front interface behavior, however with unclear impact on standard operating conditions. The HLS treatment yielded a CIGS solar cell with certified record 21.4% power conversion efficiency on a flexible substrate.
Mild Course of COVID-19 infection in a patient with Rasmussen Encephalitis
Authors: Yıldız Sibel Öz , Günbey Ceren , Bilginer Burçak , Oguz Kader Karli , Gülhan Bora , Anlar Banu , Yalnızoğlu Dilek
Published: October 2022

Rasmussen encephalitis (RE) is a rare disease of unknown etiology that affects one hemisphere and causes refractory epilepsy, progressive neurological and cognitive dysfunction. A 17-year-old patient with RE underwent unilateral hemispheric surgery. Her seizures started at nine years old and she underwent left temporal lobectomy at 10 years old. She had been receiving intravenous immunoglobulin and tacrolimus in addition to antiseizure medications. Three weeks after hemispheric surgery, she had COVID-19 infection with mild symptoms. We suggest that light course of COVID-19 infection maybe due to exposure to long-term immunomodulatory treatment.
Investigating the impact of the transport system on the regional performance: Empirical evidence from Tunisian cities
Authors: Ghannouchi Imen , Aloulou Foued , Farhat Asma
Published: October 2022

This study aims to estimate the performance level of 24 Tunisian cities using the DEA method from 2008 to 2016. the scores were then regressed in a set of transport related factors to assess the impact of transport infrastructure on the variation of efficiency scores between the 24 cities and to interpret its contribution to their performance. Furthermore, we used multiple metrics of Total Factor Productivity (TFP) and applied \(\beta\) and \(\sigma\) convergence/divergence of productivity to detect the sense of its evolution between cities. The key findings reveal the following: (i) The majority of regions have efficiency level ranging from 50–80%. (ii) The results of the second stage reveal the motorization rate has a negative impact on efficiency because it represents a source of traffic congestion when the number of vehicles exceeds the road capacity. The population density is negatively correlated with efficiency since regions with high population density are more charged and involve more traffic problem than those with weak density. (iii) The \(\beta\) and \(\sigma\) convergence/divergence tests show that there is a convergence of TFP in the sense that the lower productive cities have a faster tendency to be more productive than the higher ones.
A New Strategy for the Synthesis of Valuable Benzenoid Aromatics from Bioderived 5-Hydroxymethylfurfural (HMF) under Mild Conditions
Authors: Zheng Shasha , Wozniak Bartosz , Kallmeier Fabian , Barath Eszter , Tin Sergey , de Vries Johannes
Published: October 2022

To mitigate the effects of global warming, synthesis of aromatic chemicals that play indispensable roles in our daily lives from renewable resources is of great importance. Herein, we present a new strategy to synthesize bio-based C6-aromatics from 5-hydroxymethylfurfural (HMF) under very mild conditions. The versatile bio-based intermediate 2,5-dioxohexanal (DOH) containing three carbonyl groups was successfully synthesized from HMF in high yield. Simple intramolecular aldol condensation of DOH and secondary amines, depending on the acid, selectively produced a range of bio-based 4-substituted phenols and 1,4-di-(dialkylamino)benzenes (Wurster’s blue analogues) in satisfactory yields. In the absence of amines, the industrially important hydroquinone was also synthesized from DOH under acidic condition. Using a similar approach, catechol was prepared from HMF via 4,5-dioxohexanal (DOA) as intermediate.
Interelectrode gas-liquid-solid three-phase flow analysis and simulation for drilling holes with high aspect ratio by micro EDM
Authors: Cao Peiyao , Tong Hao , Li Yong , Chen Jialong
Published: October 2022

In micro electrical discharge machining (micro EDM) using the non-hollow circular cross-section tool electrode with the side flushing technique, when the aspect ratio of machined micro-hole is expected to be further increased, the discharge debris expelling speed and the working fluid renewal efficiency are weakened, which hinders the improvement of machining efficiency and accuracy with increased machining depth. In order to reveal the flow behavior of the working fluid in the micro EDM gap, so as to realize the high-precision and high-efficiency machining of micro-hole with high aspect ratio, a three-phase flow simulation model of fluid, bubble and debris is established in Fluent under the ideal assumption that the spark discharges occur continuously to generate high-pressure bubbles. The simulation results show that when the boundary condition of the flushing pressure at the side gap entrance is set to 0, the pressure wave emitted when the high-pressure bubble expands, which is formed by the instantaneous gasification of the working fluid between electrodes under high temperature, is the source of pneumatic force that drives the working fluid flow at the micron scale. Affected by the gap flow channel structure and the viscous resistance from inner wall, the flow velocity direction of the fluid dragging the discharge debris to rise up and expel will change, forming a dynamic alternation process of flowing into and out of the side machining gap entry. As the machining depth increases, due to the energy attenuation of the pressure wave propagating from the bottom gap to the side gap entrance, the expelling speed of the discharge debris decreases exponentially at the side gap entrance, resulting in the reduced machining efficiency and accuracy. However, when the simulated bubble generation frequency is increased to the MHz level, the expelling efficiency of debris has a step-like improvement. The continuous and high-frequency generation of high-pressure bubbles can maintain a high pressure gradient in the bottom gap, and the discharge debris is able to continuously move upward without falling back to accumulate in the bottom gap, which is beneficial to the stable and smooth machining process, realizing the high-precision and high-efficiency machining of micro-hole with high aspect ratio.
Structural and electronic properties of neutral and anionic boron clusters doped with Rubidium atom
Authors: Gao Jia Hui , Yuan Yu Quan , Li Yuan Yuan , Zhang Xin Cheng , Wang Ying Ying , Liu Ting , Hu Yan Fei
Published: October 2022

Alkali metal-doped boron clusters have captured much attention because of their novel electronic properties and structural evolution. In the study of RbBn0/– system clusters, the minimum global search of the potential energy surface and structure optimization at the level of PBE1PBE by using the CALYPSO method and Gaussian package coupled with DFT calculation; the geometrical structures and electronic properties are systematically investigated. At n = 8, the ground-state structures are composed of an Rb atom above B atoms, forming a structurally stable pagoda cone. By stability analysis and charge transfer calculation, the RbB8– cluster shows more stability. It found that s-p hybridization between Rb atom and B atoms as well as s-p hybridization between B atoms is one of the reasons for the outstanding stability exhibited in the RbB80/– clusters by using DOS and HOMO-LUMO orbital contour maps. The chemical bonding of the RbB80/– groups was analyzed by using the AdNDP method, and B atoms with larger numbers readily form multi-center chemical bonds with the Rb atom. From the results of the bonding analysis, the interaction between the Rb atom and B atoms strengthens the stability of the RbB80/– clusters. It is hoped that this work provides a direction for experimental manipulation.
Zambian Mandarin CFL Teachers' Professional Development in the New Normal: Challenges and Innovations
Authors: Zhong Wanjuan , Muyunda Gift , Cheng Jun
Published: October 2022

Mandarin Chinese language, particularly regarding foreign language teachers' professional development, has been studied in depth. However, the Covid-19 pandemic has posed various challenges in professional development (PD) particularly in the education sector where the ‘new normal’ experience is all about online interaction and distance learning. Hence, little evidence has been conducted to examine the challenges and innovations of Mandarin CFL teachers in developing countries with regard to continuous professional development during the new normal. This research study, based on sequential explanatory mixed methods research design, is aimed at exploring the availability and provision of Mandarin CFL PD opportunities in public schools in the context of Zambia and the perception of Mandarin CFL teachers on its coherence and adequacy framed from a social cultural perspective. A total of 207 Mandarin Chinese as a Foreign Language (CFL) male and female teachers participated in a custom-designed 15-item questionnaire, as well as four school head teachers, four school coordinators, one CPD focal participated in semi-structured interviews to explore their perceptions, practices and challenges of online school based CFL PD program during the Covid-19 lockdown. The results show that Mandarin CFL teachers have a positive perception of CFL PD programs implemented during the Covid-19 pandemic despite the practice of teacher OTPD program implementation is at low level in the sampled schools. Furthermore, the results show that Mandarin CFL teachers lack support from school management and immediate supervisors and lack of collaboration between Mandarin CFL teachers and school head teachers were among the factors that affected the implementation of CFL professional development (PD) programs during the Covid-19 pandemic. Also, the study shows that Mandarin CFL teachers with more teaching experience relatively positively perceived PD programs during the Covid-19 pandemic and Mandarin CFL teachers 2nd-degree holders practice more PD activities than 1st-disagree holders in the selected secondary schools. On the basis of these results, this study recommends that teacher educators, policy-makers, and other decision-making bodies should consider long-term ongoing professional development (PD) for teachers of Mandarin Chinese language in digital literacy.
Clinical range and outcomes of cerebral cavernous malformations in pediatric patients: A single center data results
Authors: Sel Çiğdem Genç , Köken Özlem Yayıcı , Kayılıoğlu Hülya , Yüksel Deniz , Aksoy Ayşe , Öztoprak Ülkühan , Aksoy Erhan , Oğuz Kader Karlı
Published: October 2022

Purpose
Cerebral cavernous malformations (CCMs) are vascular abnormalities that have been reported in the literature to cause seizures, headaches, intracerebral hemorrhages, gait ataxia, and focal neurological deficits. This study aims to review pediatric cases of CCMs in a single reference center.
Materials and methods
The retrospective data files of 6 Turkish CCM patients were evaluated. All the patients underwent magnetic resonance imaging (MRI) studies that included diffusion-weighted imaging, and susceptibility-weighted imaging (SWI). During a detailed neurological examination, the clinical and family history, age at the onset of symptoms, detailed neuroimaging findings, electroencephalogram (EEG) records, and outcomes of the patients were documented.
Results
The female to male ratio was 3/3. The age at the onset of symptoms was between 2.25 and 11 years (mean: 17.37 ± 3.26 years). The neurological manifestations on admission were: intracranial hypertension and cerebral hemorrhages (n: 1), seizures (n: 2), speech delays and articulation phonation problems (n: 2), and specific learning disability disorders (n: 1). The common neuroimaging findings of all the patients were that all of them had CCMs on their SWI sequences and were type 4 on the Zambramski classification of cerebral cavernomas.
Conclusions
Specific learning disabilities, speech delays and phonation problems, and focal and multifocal epileptic EEG discharges, with or without clinical seizures, can be indicators of underlying pediatric CCMs. The sensitivity of SWI in detecting CCMs was very high in children, as all the patients’ lesions in this study were type 4 on the Zambramski classification of cerebral cavernomas.
Characterization of A Reassortant H11N9 Subtype Avian Influenza Virus Isolated from Spot-billed Duck in China
Authors: Wang Bo , Han Shuyi , Yang Ziwen , Su Qianqian , He Hongxuan
Published: October 2022

H11N9 viruses in wild birds might have provided the NA gene of human H7N9 virus in early 2013 in China, which evolved with highly pathogenic strains in 2017 and caused severe fatalities. To investigate the prevalence and evolution of the H11N9 influenza viruses, 16781 samples were collected and analyzed during 2016–2020. As a result, a novel strain of influenza A (H11N9) virus with several characteristics that increase virulence was isolated. Phylogenetic analyses showed that it was a sextuple-reassortant virus of H11N9, H3N8, H3N6, H7N9, H9N2, and H6N8 viruses present in China, similar to the H11N9 strains in Japan and Korea during the same period. This was the H11N9 strain isolated from China most recently, which add a record to viruses in wild birds. Therefore, comprehensive surveillance and enhanced biosecurity precautions are particularly important for the prediction and prevention of potential pandemics resulting from reassortant viruses with continuous evolution and expanding geographic distributions.
LEVYEFO-WTMTOA: The hybrid of the multi-tracker optimization algorithm and the electromagnetic field optimization
Authors: Safi-Esfahani Faramarz , Mirjalili Seyedali , mohammadhoseini Leili
Published: October 2022

Many engineering optimization problems can be solved using meta-heuristics. Despite their merits, such algorithms face common challenges of early convergence rate and the imbalance between the exploitation and exploration phases. These algorithms have strengths and weaknesses considering the convergence rate, local search, and global search criteria. This study presents the new algorithm called the LEVYEFO-WTMTOA that combines the Modified Multi-Tracker Optimization Algorithm (MTOA) and the electromagnetic field optimization (EFO) approach. The LEVYEFO-WTMTOA applies the following proposals to escape from local optima: 1) the Morlet wavelet transform is used to determine the Radius of Search (RS) of the MTOA; 2) a mutation phase based on the combination of the best global position in the electromagnetic field optimization algorithm and the levy law is used in the exploration phase to update the new position 3) it has focused on balancing local and global search and escaping from the local optima trap of the MTOA. To evaluate the proposed LEVYEFO-WTMTOA algorithm, the CEC2018 benchmark suite is used, and the results are compared with the original MTOA, EFO, MEFO, MVO Levy, GSA, and COA algorithms in terms of mean error. The results demonstrate that the proposed algorithm performs better than the baseline algorithms. The applications of LEVYEFO-WTMTOA on several classical engineering problems are included as well.
Perceptions and acceptability of the Controlled Human Malaria Infection (CHMI) model in The Gambia: a qualitative study
Authors: Dabira Edgard Diniba , Fehr Alexandra , Beloum Nathalie ,   Jean-Pierre Van geertruyden2, Achan Jane , Erhart Annette , Martinez-Alvarez Melisa , Alessandro Umberto D'
Published: October 2022

Controlled human malaria infection (CHMI) studies, i.e. the deliberate infection of healthy volunteers with malaria parasites to study immune response and/or test drug or vaccine efficacy, are increasingly being conducted in malaria endemic countries, including in sub-Saharan Africa. However, there have been few studies on the perceptions and acceptability of CHMI by the local communities. This qualitative study assessed the perception and acceptability of such studies in The Gambia following the first CHMI study conducted in the country in March-May 2018. Data were collected through non-participant observation, in-depth interviews and focus group discussions and analyzed using NVivo 12 software with an inductive-deductive approach. Sixty-seven participants were involved, including volunteers enrolled in the CHMI, community stakeholders and members of the Gambian Ethics Committee. Respondents expressed a positive view about CHMI. Key motivating factors for participation were the financial compensation, comprehensive health checks, and willingness to support malaria research. Risks associated with participation were considered low. Concerns raised included the frequency of bleeding and the blood volume collected.
Hybrid projection methods for solving pseudo-monotone variationalinequalities in Banach spaces
Authors: Eskandani G. Zamani Eskandani , Lotfikar R. Lotfikar , Raeisi M. Raeisi
Published: October 2022

The authors have requested that this preprint be removed from Research Square.
Assessment of indigenous knowledge of fisheries and fish processing at Lake Ziway, Oromia Regional State, Ethiopia
Authors: Legesse Aklilu , Wakjira Mulugeta , Jimma Worku , Bayissa Tokuma Negisho
Published: October 2022

The present study aimed to assess the ecological, historical and cultural value of the traditional knowledge of fisheries by local people around Lake Ziway for better management and sustainable use of the lake resources and to sustain their livelihood. Field observations and questionnaires were used to collect data on the ecological, historical and cultural value of the traditional knowledge of fisheries from April to October 2020. The study revealed that careful consideration of ecological, historical, and socio-cultural aspects of fish and fisheries exists, and the value of this ecological and cultural knowledge provides a necessary base for the sustainable use of resources in the area. In the study area, there are traditional fishing methods such as hand kicking, pool-trapping, handpicking and others developed by the fishermen. The tools used to catch fish were made manually from locally available materials such as ‘gubo’ tree, ‘balsa’ wood, cotton thread, and others. From this point of view, it can be said that indigenous knowledge plays a vital role in the survival of poor fishermen. Therefore, this knowledge should be upgraded and documented for further usage by the coming generations. On the other hand, some fish species available in the lake are very scarce in the present studies. Therefore, detailed studies and investigations are required to take management measures for these species.
Early Postnatal Care Attendance among Postnatal Women in Ubungo Municipal Council, Dar es Salaam, Tanzania: a qualitative study
Authors: Panga Rehema , Mosha Idda H.
Published: October 2022

Adequate utilization of postnatal care services is associated with improved maternal and neonatal health outcomes.The World Health Organization recommends postnatal women to attend postnatal care as early as seven days after delivery because most maternal deaths occur within 7 days of the postnatal period. However, many postnatal women who deliver in health facilities attend postnatal care very late during 42 days for child immunization. Little information is known as to why postnatal women who deliver in health facilities delay initiating postnatal care clinics for seven days post-delivery. This study aimed at exploring reasons as to why women who deliver in health facilities delay attending early postnatal care services.
Methods
A cross-sectional design using a qualitative approach was used to explore factors associated with early postnatal care attendance among postnatal women in Ubungo Municipal, Dar es Salaam, Tanzania. Study participants were purposively selected. In-depth interviews were used to collect data. Audio recorded interviews were transcribed verbatim and translated into English. Thematic analysis approach was used to excerpt reasons for the delay in seeking early postnatal care services in Ubungo Municipality.
Findings
The finding of this study revealed lack of awareness on the appropriate time to start early postnatal care visits and the recommended number of postnatal visits, perception of postnatal women that the postnatal period is a normal condition that does not require health personnel’s attention,thus the perception that no need to initiate early postnatal care clinics (PNC) if they were not sick.
Similarly, long waiting time,transport costs, and health care providers’ attitudes were major reasons reported by postnatal women to contribute to late postnatal care attendance.
Therefore, health care providers should continue providing education to pregnant women and postnatal women on when to attend and the importance of attending early postnatal care.
Determination of feeding rate ratio in coupled fed-batch fermentation with pH feedback considering limited number of switches
Authors: Chen Chihua , Wang Juan , Zhao Feiyan , Wang Jichao
Published: October 2022

This paper focuses on binary optimal control of fed-batch fermentation of glycerol by Klebsiella pneumoniae with pH feedback considering limited number of switches. To maximize the concentration of 1,3-propanediol at terminal time, we propose a binary optimal control problem subjected to time-coupled combinatorial constraint with the ratio of feeding rate of glycerol to that of NaOH as control variables. Based on time-scaling transformation and discretization, the binary optimal control problem is first transformed into a mixed binary parameter optimization problem consisting not only continuous variables but also binary variables, which is then divided into two subproblems via combinatorial integral approximation decomposition. Finally, a novel fruit fly optimizer with modified sine cosine algorithm and adaptive maximum dwell rounding are applied to solve the obtained subproblems numerically. Numerical results show the rationality and feasibility of the proposed method.
Stability analysis of chaotic systems from data
Authors: Margazoglou Georgios , Magri Luca
Published: October 2022

The prediction of the temporal dynamics of chaotic systems is challenging because infinitesimal perturbations grow exponentially. The analysis of the dynamics of infinitesimal perturbations is the subject of stability analysis. In stability analysis, we linearize the equations of the dynamical system around a reference point, and compute the properties of the tangent space (i.e., the Jacobian). The main goal of this paper is to propose a method that learns the Jacobian, thus, the stability properties, from observables (data). First, we propose the Echo State Network (ESN) with the Recycle Validation as a tool to accurately infer the chaotic dynamics from data. Second, we mathematically derive the Jacobian of the Echo State Network, which provides the evolution of infinitesimal perturbations. Third, we analyse the stability properties of the Jacobian inferred from the ESN, and compare them with the benchmark results obtained by linearizing the equations. The ESN correctly infers the nonlinear solution, and its tangent space with negligible numerical errors. In detail, (i) the long-term statistics of the chaotic state; (ii) the covariant Lyapunov vectors; (ii) the Lyapunov spectrum; (iii) the finite-time Lyapunov exponents; (iv) and the angles between the stable, neutral, and unstable splittings of the tangent space (the degree of hyperbolicity of the attractor). This work opens up new opportunities for the computation of stability properties of nonlinear systems from data, instead of equations.
Mathematics Subject Classification (2020) 68T07 · 34D08 · 37D45 · 37M22
Inhibition of DYRK1B suppresses inflammation in allergic contact dermatitis model and Th1/Th17 immune response
Authors: Wongchang Thamrong , Pluangnooch Panwadee , Hongeng Suradej , Wongkajornsilp Adisak , Thumkeo Dean , Soontrapa Kitipong
Published: October 2022

Allergic contact dermatitis (ACD) is a type IV hypersensitivity mainly mediated by Th1/Th17 immune response. Topical corticosteroid is currently the first-line treatment for allergic contact dermatitis (ACD) and systemic administration of immunosuppressive drugs are used in patients with severe disseminated cases. However, increased risk of adverse effects has limited their use. Thus, the development of a novel immunosuppressant for ACD with low toxicity is a challenging issue. In this study, we began our study by using a murine contact hypersensitivity (CHS) model of ACD to examine the immunosuppressive effects of DYRK1B inhibition. We found that mice treated with a selective DYRK1B inhibitor show reduced ear inflammation. In addition, a significant reduction of Th1 and Th17 cells in the regional lymph node upon DYRK1B inhibition was observed by FACS analysis. Studies in vitro further revealed that DYRK1B inhibitor does not only suppressed Th1 and Th17 differentiation, but also promotes regulatory T cells (Treg) differentiation. Mechanistically, FOXO1 signaling was enhanced due to the suppression of FOXO1Ser329 phosphorylation in the presence of DYRK1B inhibitor. Therefore, these findings suggest that DYRK1B regulates CD4 T cell differentiation through FOXO1 phosphorylation and DYRK1B inhibitor has a potential as a novel agent for treatment of ACD.
Perinatal factors influencing mortality and morbidity two years after esophageal atresia primary repair: a single center retrospective study
Authors: Lefèvre Noémie Capucine , Gouez Morgane Le , Lesage Fabrice , Rousseau Véronique , Giuseppi Agnès , Abadie Véronique , Lapillonne Alexandre , Kermorvant-Duchemin Elsa
Published: October 2022

Purpose: Long-term digestive, respiratory and neurological morbidity is significant in children who have undergone surgery for esophageal atresia (EA), especially after staged repair for long-gap EA. Risk factors for morbidity after primary repair (non-long-gap populations) have been less documented. We investigated perinatal factors associated with unfavourable outcome in children two years after a primary esophageal anastomosis.
Methods: Single-center retrospective study, based on neonatal, surgical, and paediatric records of children born between December 1, 2002, and December 31, 2018, and followed up to age 2 years. The primary endpoint was unfavourable outcome at 2-years of age, defined by death or survival with severe respiratory, digestive, or neurologic morbidity. Univariate analyses followed by logistic regression analyses were performed to identify perinatal risk factors of unfavourable outcome among survivors at discharge.
Results: 150 neonates were included (mean birth weight 2520±718 g, associated malformations 61%); at age two, 45 (30%) had one or more severe morbidities, 11 had died during the neonatal stay and 2 after discharge (8.7% deaths). In multivariate analyses in the 139 survivors at discharge, duration of ventilatory support (invasive and non-invasive) for more than 8 days (OR 3.74; CI95%[1.68-8.60]; p=0.001) and achievement of full oral feeding before hospital discharge (OR 0.20; CI95%[0.06-0.56]; p=0.003) were independently associated with adverse outcome after adjustment for sex, preterm birth, associated heart defect, any surgical complication and the occurrence of more than one nosocomial infections during the neonatal stay.
Conclusions: Potentially modifiable neonatal factors are associated with 2-year unfavourable outcome after primary repair of EA.
A Hierarchical Porous towards High Performance CO2 capture and Congo Red Adsorption
Authors: Zhang Tingting , Li Jiaxin , Hua Yumeng , Dou Jiali , Wang Song , Chen Xuecheng , Li Sanxi
Published: October 2022

To achieve the goal of carbon neutrality, controlling CO2 emissions is a primary problem to be solved in the current environmental protection field. Eliminating the environmental pollution of dyes in industrial wastewater is also an urgent problem to be solved in the field of environmental protection. The adsorption technique is an effective way to deal with these two issues. Developing high-efficiency adsorbents to work in the adsorption field. In this work, a two steps carbonization method has been developed to prepare porous carbon by a carbonization procedure. The morphology and structure of the prepared porous carbon were investigated by SEM, XPS, XRD, and BET techniques. Selectively optimization, the as-prepared porous carbon materials exhibit a high specific surface area of 1476 m2 g− 1 and a high total pore volume of 0.951 cm3 g− 1. The PCMCA-900 shows the highest CO2 uptake of 7.67 mmol g− 1 at 0 ºC, stable cycling stability. Moreover, when PCMCA-900 was used as an adsorbent to remove Congo red in water, an adsorption capacity of 652.3 mg g− 1 was achieved. The above-mentioned results prove that potassium citrate derived porous carbon is a desirable candidate for excellent CO2 adsorption and Congo red in industrial wastewater.
Variability in and Formation of Homogeneous Regions of Precipitation Trends Across the Amazon River Basin, Determined From the Global Precipitation Climatology Centre - Gpcc
Authors: Filho David Figueiredo Ferreira , Pessoa Francisco Carlos Lira
Published: October 2022

Spatiotemporal patterns of precipitation are influenced by complex interactions between climate and land cover changes, such as deforestation, fires and droughts. The Amazon River Basin has local and global impacts in regard to the hydrological cycle; therefore, it is fundamental to understand how precipitation patterns and intensity are changing. The aim of this study was to analyze precipitation trends and form homogeneous regions of precipitation trends in the Amazon River Basin using data from the meteorological satellite Global Precipitation Climatology Centre (GPCC), applying nonparametric methods (Mann-Kendall, Spearman and Sen's slope) and fuzzy C-means to identify specific regions that are undergoing changes in hydrological patterns. The results show changes in the behavior of rainfall over time and in the intensity of the events. The statistics applied to form clusters resulted in 6 well-divided homogeneous groups, each with unique characteristics. Specifically, the central-southern areas of the basin showed negative precipitation trends (-1.17 mm/year) forming a homogeneous region (RH 1), while in the northern region, there was an increasing trend in precipitation (2.73 mm/year). In general, over the 37 years studied, the wet areas have tended to become wetter and the dry areas drier. Other homogeneous regions had their own results and unique characteristics, which are in agreement with other studies, such as those in Porto Velho, Rondônia, where this area had a diagonal pattern of precipitation decrease.
Complete genome sequence of mimosa mosaic virus, a new sobemovirus infecting Mimosa sensitiva L.
Authors: Kauffmann Caterynne Melo , Boari Alessandra de Jesus , Silva João Marcos Fagundes , Blawid Rosana , Nagata Tatsuya
Published: October 2022

A sobemovirus, tentatively named “mimosa mosaic virus” (MimMV), was found by high-throughput sequencing and isolated from the mimosa (Mimosa sensitiva L.) plant. The genome sequence was also confirmed by Sanger sequencing and comprises 4595 nucleotides. Phylogenetic analysis of the amino acid (aa) sequences of the P2b (from ORF2b) and the coat protein showed 52.7% and 31.8% aa sequence identities with those of blueberry shoestring virus, respectively. The complete genome sequence identity to MimMV with other sobemoviruses was less than 47%. These analyses suggest that MimMV is considered a new species of the genus Sobemovirus.
A single-institution retrospective series of SARs-Cov-2 infection in adult glioma patients
Authors: Lanman Tyler , Ruiz Amber N. , Nagpal Seema
Published: October 2022

Background
A subset of cancer patients is particularly vulnerable to SARS-Cov-2 infection; however, real-world outcomes-based data on primary central nervous system tumor patients is sparse. This retrospective series describes a cohort of adult glioma patients seen at Stanford Cancer Center between 1/1/2020 through 6/30/2022 who contracted SARS-Cov-2, which, to our knowledge, currently represents the largest single-institution comprehensive analysis of this patient population.
Methods
We performed a retrospective search of patients seen in the Stanford Neuro-Oncology clinic, identifying 29 cases of COVID-19 amongst glioma patients and extracted clinical data via individual chart review.
Results
Out of the 29 cases, 14 had high-grade glioma (grades 3 and 4) and 15 had low-grade (grades 1 and 2). At the time of COVID-19 diagnosis, 15 patients had been vaccinated against SARS-Cov-2, 8 patients were taking dexamethasone, and 8 were undergoing cancer-specific treatment. Obesity, prior tobacco use, and diabetes were the most common comorbidities. Cough, sore throat, and congestion were the most common symptoms. Five patients were admitted to the hospital and two received COVID-19-specific treatment. None of the patients died from Covid-related causes or complications.
Conclusion
Our data suggest that glioma patients seen at Stanford Cancer Center do not experience an exceptionally high COVID-19 infectivity, hospitalization, or mortality rate, especially when compared to other vulnerable populations such as lung cancer patients. High vaccination rates, adherence to COVID-19 guidelines, and low prevalence of comorbidities may have contributed to these results.
Multi-region sequencing depicts intratumor heterogeneity and clonal evolution in cervical cancer
Authors: Wang Chen , Bai Rui , Liu Yu , Wang Kun , Wang Yu , Yang Jian , Cai Haoyang , Yang Ping
Published: October 2022

Cervical cancer is a heterogeneous malignancy mainly caused by human papillomavirus (HPV). While a few studies have revealed heterogeneity of cervical cancer in chromosome levels, the correlation between genetic heterogeneity and HPV integration in cervical cancer remains unknown. Here, we applied multi-region whole-exome sequencing (WES) and HPV integration analysis to explore intratumor heterogeneity (ITH) in cervical cancer. We sequenced 20 tumor regions and 5 adjacent normal tissues from 5 cervical cancer patients, analysis based on somatic mutations and somatic copy number alterations (SCNAs) levels were performed. Variable heterogeneity was observed between the five patients with different tumor stages and HPV infection statuses. We found HPV integration has a positive effect on somatic mutation burden, but the relation to SCNAs remains unclear. Frequently mutated genes in cervical cancer were identified as trunk events, such as FBXW7, PIK3CA, FAT1 in somatic mutations and TP63, MECOM, PIK3CA, TBL1XR1 in SCNAs. New potential driver genes in cervical cancer were summarized including POU2F2, TCF7 and UBE2A. The SCNAs level has potential relation with tumor stage, and Signature 3 related to homologous recombination deficiency (HRD) may be the appropriate biomarker in advanced cervical cancer. Mutation signature analysis also revealed a potential pattern that APOBEC-associated signature occurs in early-stage and signatures associated with DNA damage repair arise at the later stage of cervical cancer evolution. In a conclusion, our study provides insights into the potential relationship between HPV infection and tumor heterogeneity. Those results enhanced our understanding of tumorigenesis and progression in cervical cancer.
Comprehensive Evaluation of Artifact Reduction and Tissue Recovery Effects of Metal Artifact Reduction Function Based on Full-Reference Metric
Authors: Jung Yunsub , Song You Seon , Lee In Sook , Rhee Seung Joon
Published: October 2022

For the comprehensive evaluation of metal artifact reduction (MAR) function, which is a post-processing technique that artifacts reduction caused by metal implants, not only the removal of metal artifacts but also the evaluation of the area restored by MAR is required. In this study, we have conducted the computed tomography (CT) scan both the evaluation image and the reference image at the same location of phantom for the full-reference based evaluation. The evaluation image and reference image were reconstructed into 24 image sets according to the tube potentials, image reconstruction method, and use of the MAR function. Images of two different positions were selected according to the distance from metal and material (bone, tissue) distribution, and bone and tissue were automatically segmented in all images. After Gaussian modeling of each segmented area, FWHM and centroid metrics were extracted. These two metrics were used to compare non-MAR image and MAR image compared to non-metal image. In addition, FWHMNM, FWHMM, CENTNM, and CENTM were calculated using the ratio of the evaluation image and the reference image, then MAR image and non-MAR image were compared. The occurrence of metal artifacts differed according to the distance from the metal and the tube potential. The effect of artifact reduction by the MAR function was confirmed in most regions except for some regions very close to the metal (p < .05). The tissue recovery effect through the application of the MAR function was different depending on the distance from the metal and the material, but the distribution of pixel values was maintained well even after the MAR function was applied (p < .05). Overall, the MAR function restored the original image information while reduction metal artifacts. However, in the regions of severe metal artifacts that are very close to the metal, the MAR function was limited.