bluuebunny/crossref_metadata_2025 huggingface dataset:
A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia
Authors: Scott William T. , Benito-Vaquerizo Sara , Zimmermann Johannes , Bajić Djordje , Heinken Almut , Suarez-Diez Maria , Schaap Peter J.
Published: August 2023

Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.
Impact of the COVID-19 pandemic on the provision and uptake of services for the prevention of mother-to-child transmission of HIV in Zimbabwe
Authors: Chappell Elizabeth , Chimwaza Anesu , Manika Ngoni , Wedderburn Catherine J. , Mupambireyi Nenguke Zivai , Gannon Hannah , Cowan Frances , Gibb Tom , Heys Michelle , Fitzgerald Felicity , Phillips Andrew , Chimhuya Simbarashe , Gibb Diana M. , Ford Deborah , Mushavi Angela , Bwakura-Dangarembizi Mutsa
Published: August 2023

Zimbabwe is targeting elimination of mother-to-child transmission of HIV by December 2025, however the COVID-19 pandemic challenged health service delivery globally. Monthly aggregated data were extracted from DHIS-2 for all facilities delivering antenatal care (ANC). ZIMSTAT and Spectrum demographic estimates were used for population-level denominators. Programme indicators are among those in HIV care and population indicators reflect the total population. The mean estimated proportion of pregnant women booking for ANC per month did not change (91% pre-pandemic vs 91% during pandemic, p = 0.95), despite dropping to 47% in April 2020. At a programme-level, the estimated proportion of women who received at least one HIV test fell in April 2020 (3.6% relative reduction vs March (95% CI 2.2–5.1), p<0.001) with gradual recovery towards pre-pandemic levels. The estimated proportion of women who were retested among those initially negative in pregnancy fell markedly in April 2020 (39% reduction (32–45%), p<0.001) and the subsequent increase was much slower, only reaching 39% by September 2021 compared to average 53% pre-pandemic. The mean estimated proportion of pregnant women with HIV on ART was unchanged at programme-level (98% vs 98%, p = 0.26), but decreased at population-level (86% vs 80%, p = 0.049). Antiretroviral prophylaxis coverage decreased among HIV-exposed infants, at programme- (94% vs 87%, p = 0.001) and population-levels (76% vs 68%, p<0.001). There was no significant change in HIV-exposed infants receiving EID (programme: 107% vs 103%, p = 0.52; population: 87% vs 79%, p = 0.081). The estimated proportion of infants with HIV diagnosed fell from 27% to 18%, (p<0.001), while the estimated proportion on ART was stable at a programme (88% vs 90%, p = 0.82) but not population (22% vs 16%, p = 0.004) level. Despite a drop at the start of the pandemic most programme indicators rapidly recovered. At a population-level indicators were slower to return, suggesting less women with HIV identified in care.
Empathy training for service employees: A mixed-methods systematic review
Authors: Lajante Mathieu , Del Prete Marzia , Sasseville Beatrice , Rouleau Geneviève , Gagnon Marie-Pierre , Pelletier Normand
Published: August 2023

Following the surge for empathy training in service literature and its increasing demand in service industries, this study systematically reviews empirical papers implementing and testing empathy training programs in various service domains. A mixed-methods systematic review was performed to identify and describe empathy training programs and discuss their effectiveness in service quality, service employees’ well-being, and service users’ satisfaction. Included papers met those eligibility criteria: qualitative, quantitative, or mixed-methods study; one training in empathy is identifiable; described training(s) developed for or tested with service employees dealing with service users. We searched health, business, education, and psychology databases, such as CINAHL, Medline ABI/Inform Global, Business Source Premier, PsycINFO, and ERIC. We used the Mixed-Method Assessment Tool to appraise the quality of included papers. A data-based convergent synthesis design allowed for the analysis of the data. A total of 44 studies published between 2009 to 2022 were included. The narrative presentation of findings was regrouped into these six dimensions of empathy training programs: 1) why, 2) who, 3) what, 4) how, 5) where, and 6) when and how much. Close to 50% of studies did not include a definition of empathy. Four main empathic competencies developed through the training programs were identified: communication, relationship building, emotional resilience, and counseling skills. Face-to-face and group-setting interventions are widespread. Our systematic review shows that the 44 papers identified come only from health services with a predominant population of physicians and nurses. However, we show that the four empathic skills identified could be trained and developed in other sectors, such as business. This is the first mixed-methods, multi-disciplinary systematic review of empathy training programs in service research. The review integrates insights from health services, identifies research limitations and gaps in existing empirical research, and outlines a research agenda for future research and implications for service research.
Differential effect of heteronymous feedback from femoral nerve and quadriceps muscle stimulation onto soleus H-reflex
Authors: Cuadra Cristian , Wolf Steven L. , Lyle Mark A.
Published: August 2023

Excitatory feedback from muscle spindles, and inhibitory feedback from Golgi tendon organs and recurrent inhibitory circuits are widely distributed within the spinal cord to modulate activity between human lower limb muscles. Heteronymous feedback is most commonly studied in humans by stimulating peripheral nerves, but the unique effect of non-spindle heteronymous feedback is difficult to determine due to the lower threshold of excitatory spindle axons. A few studies suggest stimulation of the muscle belly preferentially elicits non-spindle heteronymous feedback. However, there remains a lack of consensus on the differential effect of nerve and muscle stimulation onto the H-reflex, and the relation of the heteronymous effects onto H-reflex compared to that onto ongoing EMG has not been determined. In this cross-sectional study, we compared excitatory and inhibitory effects from femoral nerve and quadriceps muscle belly stimulation onto soleus H-reflex size in 15 able-bodied participants and in a subset also compared heteronymous effects onto ongoing soleus EMG at 10% and 20% max. Femoral nerve stimulation elicited greater excitation of the H-reflex compared to quadriceps stimulation. The differential effect was also observed onto ongoing soleus EMG at 20% max but not 10%. Femoral nerve and quadriceps stimulation elicited similar inhibition of the soleus H-reflexes, and these results were better associated with soleus EMG at 20%. The results support surface quadriceps muscles stimulation as a method to preferentially study heteronymous inhibition at least in healthy adults. The primary benefit of using muscle stimulation is expected to be in persons with abnormal, prolonged heteronymous excitation. These data further suggest heteronymous feedback should be evaluated with H-reflex or onto ongoing EMG of at least 20% max to identify group differences or modulation of heteronymous feedback in response to treatment or task.
A conserved microtubule-binding region in Xanthomonas XopL is indispensable for induced plant cell death reactions
Authors: Ortmann Simon , Marx Jolina , Lampe Christina , Handrick Vinzenz , Ehnert Tim-Martin , Zinecker Sarah , Reimers Matthias , Bonas Ulla , Erickson Jessica Lee
Published: August 2023

Pathogenic Xanthomonas bacteria cause disease on more than 400 plant species. These Gram-negative bacteria utilize the type III secretion system to inject type III effector proteins (T3Es) directly into the plant cell cytosol where they can manipulate plant pathways to promote virulence. The host range of a given Xanthomonas species is limited, and T3E repertoires are specialized during interactions with specific plant species. Some effectors, however, are retained across most strains, such as Xanthomonas Outer Protein L (XopL). As an ‘ancestral’ effector, XopL contributes to the virulence of multiple xanthomonads, infecting diverse plant species. XopL homologs harbor a combination of a leucine-rich-repeat (LRR) domain and an XL-box which has E3 ligase activity. Despite similar domain structure there is evidence to suggest that XopL function has diverged, exemplified by the finding that XopLs expressed in plants often display bacterial species-dependent differences in their sub-cellular localization and plant cell death reactions. We found that XopL from X. euvesicatoria (XopLXe) directly associates with plant microtubules (MTs) and causes strong cell death in agroinfection assays in N. benthamiana. Localization of XopLXe homologs from three additional Xanthomonas species, of diverse infection strategy and plant host, revealed that the distantly related X. campestris pv. campestris harbors a XopL (XopLXcc) that fails to localize to MTs and to cause plant cell death. Comparative sequence analyses of MT-binding XopLs and XopLXcc identified a proline-rich-region (PRR)/α-helical region important for MT localization. Functional analyses of XopLXe truncations and amino acid exchanges within the PRR suggest that MT-localized XopL activity is required for plant cell death reactions. This study exemplifies how the study of a T3E within the context of a genus rather than a single species can shed light on how effector localization is linked to biochemical activity.
Das letras e telas às ruas
Authors: Santos Gustavo Souza
Published: August 2023

As mobilizações sociais, protestos, movimentos e manifestações políticas são frequentemente lidas por meio de uma visão utilitarista de seu conteúdo, forma e resultados. O sujeito que produz e se produz nestas mobilizações constitui um elemento direcional para se compreender os sentidos políticos que se plasmam nas ruas, nas reivindicações e em toda sorte de sinais simbólico-paradigmáticos da pólis e da política. Convém escapar à redução material e utilitária da insurgência revisitando as origens da emergência dos sujeitos para ampliar o repertório dos sentidos que denotam a realidade sociopolítica e frequentemente a interpela sob os signos da subjetividade e da política. Este texto apresenta uma reflexão sobre a produção do sujeito na mobilização social, a partir da tessitura alegórica, plástica e literária de duas obras referenciais: a peça Hamlet (1587) de do poeta e dramaturgo inglês William Shakespeare, e a obra Operários (1933) da artista visual Tarsila do Amaral.
Submundo, violência e publicidade
Authors: Magossi Priscila
Published: August 2023

O presente artigo dedica-se a apreensão sobre o modo pelo qual o submundo da cibercultura (o oligopólio de sites de pornografia, webcamming e packs eróticos) encobre a violência contra a mulher por meio do simulacro publicitário nas redes interativas. A argumentação contempla a reflexão crítica sobre o contrassenso estabelecido entre a publicidade empresarial (que anuncia a vítima como protagonista do empoderamento feminino) e o contrato de prestação de serviços (que aprisiona a mulher ao proprietário invisível por meio da autorização vitalícia da sua imagem para circulação em qualquer site erótico da rede, bem como a impede de denunciar qualquer tipificação de violência sofrida nas plataformas). Este estudo justifica a sua contribuição para a área de comunicação, cibercultura e imaginário pelo uso predatório e ideológico do imaginário pela publicidade do mencionado submundo.
Coming of Age: Antibody-drug Conjugates, Highly Targeted Anti-cancer Agents
Authors:   Sunvalley Communication, LLC, Hofland Peter
Published: August 2023

Cancer remains a major public health problem. With 1 in 6 deaths attributed to cancer, the disease is the second leading cause of death in the United States and around the world. In 2020, it is estimated that 9.6 million died of the disease.
Analysis of Biological Activities of Two Novel Metal (II) Complexes of Andrographis Paniculata Crude Extract
Authors: Oladipo Mary Adelaide , Ojo Ayodele Oluwabunmi , Ishola Kayode Taiwo
Published: August 2023

Many diseases in nature have led to the death of many young and old. Many bacteria have developed resistance to the available antibiotics on the market. And many drugs employed in treating many diseases such as diabetes mellitus are expensive and are not locally available. Therefore, in order to search for more effective, inexpensive, and locally available drugs, this study synthesized and investigated the biological activities of Andrographis paniculata crude extract and its Co (II) and Ni (II) complexes. The crude extract and synthesized complexes were characterized using a solubility test, Infrared, and Ultraviolet-Visible spectroscopic analysis. Their antibacterial potentials were investigated against two gram-negative bacteria (Escherichia coli,Staphylococcus aureus) and three gram-negative bacteria (Proteus, Klebsiella, Pseudomonas) while their antidiabetic activities were examined against ?-amylase and ?-glucosidase enzymes. Acarbose was employed as a standard drug. The crude extract and its metal complexes showed different degrees of solubility in the employed solvents. Infrared analysis suggested coordination of the crude extract to the metal ions through the oxygen donor atom while the formation of the complexes was affirmed through the occurrence of d-d transitions in the visible region of the metal complexes. The metal complexes were found to display more antibacterial activity than the crude extract. Co (II) and Ni (II) complexes of the crude extract were found to exhibit better activities against ?-amylase and ?-glucosidase enzymes, respectively than the crude extract and acarbose. It is concluded that the metal complexes could be considered potential antibacterial and antidiabetic agents.
Weed Community Structure in Patia Village Rice Fields Patia Sub-District, Pandeglang Regency
Authors: Widiyawati Ai , Susilo Hadi , Mu'jijah Mu'jijah , Suyamto Suyamto , Abdilah Nurullah Asep
Published: August 2023

Rice is a very important type of food crop because it is a staple food source. Crop losses at the farmer level due to competition with weeds reach 10-1.5%. This study aims to determine the structure of rice weed communities in rice fields in Patia Village, Patia District, and Pandeglang Regency. The research method uses an observation method with the sampling technique used as a random method. The plot used was 2 m x 2 m. Weed sampling was carried out by recording the types of weed types and counting the number of individuals of each species. Measurements of environmental factors such as temperature, humidity, pH, and light intensity were measured. The data parameters measured include the Shannon-Wiener diversity index (H'), evenness index (J'), dominance index (D), wealth index (S), and abundance of rice weed species. The results of the study were that the types of rice weeds found in the rice fields of Patia Village, District, and Patia, Pandeglang Regency, namely Ludwigia octovalvis (Jacq) Raven, Commanded cylindricaL. Beauv, Spigelia anthelmia, Ageratum conyzoides, Spihemoclea zeylanica, Altemanthera sessillis, Eclipta prostate, Cypress deformed L., Digitaria sp. and Mimosa chaste L. The structure of the weed community in the rice fields of Patia Village, Patia District, Pandeglang Regency is the Shannon-Wiener Diversity Index (H') of 1.94; Evenness Index (J') of 0.884; Dominance Index (D) of 0.15.
Legal Problems in Determining Factual Actions as Dispute Object of the State Administrative Court in Indonesia
Authors: Fadillah Nor , Hariyanto Hariyanto , Mourtadhoi Abdallah
Published: August 2023

This study’s aim is to analyze how the concept development of State Administrative Decision (KTUN) in Indonesia. It is also to analyze the legal problems of determining factual actions as the dispute object in the Administrative Court because, after the promulgation of Law Number 30 of 2014 concerning Government Administration, there are some legal effects, especially after the emergence of factual action term as renewal. This study is normative research on the rules or the Law itself and the principle of positive Law by making legal materials the object of study. The approach used in the study is the approach of legislation and conceptual approach. The research data needed in this study is through the method of literature or documents and analyzed in a descriptive-qualitative way. The results showed that the KTUN before the Law Number 30 of 2014 is a written determination issued by a state administrative body or official containing administrative legal acts based on applicable laws and regulations, which are concrete, individual and final, giving rise to legal consequences for a person or civil legal entity. While the KTUN after the renewal is a written determination that includes factual actions, decisions of bodies and/or state administration officials in the executive, legislative, judicial, and other state administrations, based on the provisions of legislation and the General Principles of Good Government (AUPB), and final in a broader sense give decisions could have the potential to cause legal consequences, and/or could apply to citizens. The renewal is to cause problems such as chaos from the meaning of terminology, for example, the use of the term decision and or action. In addition, there is no specific explanation, so it is feared that legal norms are ambiguous, especially for judges in examining cases related to factual actions.
The Effects of Different Storage Conditions and Repeated Freeze/Thaw Cycles on the Concentration, Purity and Integrity of Genomic DNA
Authors: Safarikova M. , Kubena A. A. , Frankova V. , Zima T. , Kalousova Marta
Published: August 2023

The crucial requirement of molecular genetic methods is high-quality input material. The key question is “how to preserve DNA during long-term storage.” Biobanks are recommended to aliquot isolated DNA into provided volumes. The aim of this study was to analyse the effect of repeated freezing and thawing on the genomic DNA integrity, quality and concentration. The aliquoted DNA isolated from blood cells using the automatic MagNA system and manual salting out method underwent freeze/thaw cycles at different storage conditions (−20 °C, −80 °C and liquid nitrogen). The average initial concentrations were 270.6 ng/μl (salting out method) and 125.0 ng/μl (MagNA). All concentration deviations relative to the concentration after the first freeze/ thaw cycle were less than 5 % for −20 °C and −80 °C cycling with both isolation methods. The average percentage differences of liquid nitrogen samples were higher, and the MagNA isolation method showed significant differences. There were no significant changes in the DNA purity or quality. The repeating freeze/ thaw up to 100 cycles (through −20 °C and −80 °C, respectively) did not significantly influence the integrity, concentration, or purity of genomic DNA, suggesting that storage of samples in high-volume pools without multiple aliquoting is possible. Storage in a freezer seems to be the most suitable way of long-term DNA preservation, because liquid nitrogen storage leads to formation of DNA clumps.
Investigation of the Inhibitory Effect of Platycodin D in Human Transitional Cell Carcinoma Cell Line 5637
Authors: Li X. G. , Gao S. , Yang W .S. , Sun Shu
Published: August 2023

Platycodin D is an active component isolated from Chinese herbPlatycodonis radixwith various pharmacological activities, such as antitussive, expectorant, anti-inflammatory, and analgesic effects. Interestingly, platycodin D also exerts anticancer effects against several types of cancer. However, few studies on the anti-tumour effects of platycodin against urinary bladder cancer have been reported. In this study, we explored the anti-tumour effect of platycodin D against human bladder cancer and its mechanismsin vitroandin vivo. We found that platycodin D had significant anti-proliferative effects on four types of cancer cells, especially the 5637 bladder cancer cell line, and exerted these effects by preventing cell cycle progression from G0/G1to S phase, down-regulating Ki-67 and cyclin D1 protein expression and up-regulating P21 protein expression. Furthermore, platycodin D inhibited 5637 cell migration by decreasing twist-related protein 1 (Twist1) and matrix metallopeptidase 2 (MMP2) expression and exerted significant tumour-suppressive effects in tumour-bearing nude mice. Platycodin D also increased caspase-9, caspase-8, caspase-3, and p53 expression and decreased Bcl-2 expression in tumour tissues. Taken together, our results provide a theoretical basis for application of platycodin D in treating urinary bladder cancer.
Biogenesis of nanoparticles using microorganisms: A Review
Authors: Singhal Anjum , Baweja Pooja , Gupta Sandhya , Chopra Haritma , Gandhi Pinkey Bajaj
Published: August 2023

Bionanoparticles are synthesized using novel strategies through environmentally benign approaches. Emphasis is on synthesizing nanoparticles using green chemistry principles to reduce the burden of pollution on the environment. The biological approach for the synthesis of metallic nanoparticles is also described as green synthesis (bioprocess) of nanoparticles, is now being looked at as an alternative to physio-chemical approaches and generally uses biological components like plants and microbes (bacteria, fungi, algae and yeast) and cause minimal harm to the nature. The naturally occurring potential biodegradable agents like enzymes (secreted by microbes) act as reducing agents and play a very distinct role in the synthesis of nanoparticles. Most bioprocesses occur under normal air pressure and temperature, resulting in vast energy savings and reducing the use of expensive chemicals making the green approach less costly. This process of synthesis of nanoparticles using biological systems is referred to as nanobiotechnology. Nanobiotechnology has emerged as an integration between biotechnology and nanotechnology for developing biosynthetic and environmentally friendly technology for nanoparticle synthesis. This review is mainly focused on the microbial synthesis of nanoparticles utilizing the extract of bacteria and algae. In the present review, the bio-reduction capacity of various bacteria and algae is highlighted in detail, which has yet to be discussed earlier. This is a comprehensive work underlining the synthesis of nanoparticles, their bio-reduction ability, and application of nanoparticles.
Efficacy of biofertilizers in different stress management of fruit crops- A Review
Authors: Reddy Gundu Boina Gopichand , Rajan Rajni , Chundurwar Keerthana , Kumar Akshay , Singh Tanya , Vamshi Thammali
Published: August 2023

Biofertilizers are gaining widespread acceptance in agriculture due to their numerous advantages over chemical fertilizers. These environmentally friendly alternatives play a crucial role in enhancing soil health and fertility through various mechanisms. Biofertilizers consist of diverse microorganisms that can effectively promote plant growth and development, even under abiotic stress conditions. As a result, the utilization of biofertilizers is steadily increasing, especially with the escalating costs of chemical fertilizers and their adverse effects on soil health and crop yields. Certain microorganisms, such as Azotobacter, Azospirillum, Arbuscular Mycorrhizal Fungi (AMF) Gigaspora rosea, Pseudomonas, and Funneliformis geosporus, hold substantial potential for commercial use as biofertilizers to improve the growth and development of fruit crops. In-depth research has demonstrated that biofertilizers can significantly augment the biomass and productivity of various fruit crops. Their application in fruit crop production is particularly beneficial as they not only enhance growth but also confer improved resistance to abiotic stress factors like high temperatures, drought, salinity, and metal toxicity. This comprehensive review highlights the substantial promise of biofertilizers in mitigating abiotic stress and fostering sustainable practices in fruit crop cultivation.
Responsible Chemistry
Authors: Mehlich Jan
Published: August 2023

Responsible Research and Innovation (RRI) is a concept that describes approaches and strategies to addressing and tackling risks and dual use potentials of research and development (R&D) activities that have significant societal and environmental impact [1]. Built on a scientifically rigorous foundation of RRI knowledge and expertise, the translation into applied and practical contexts such as chemical R&D is underway [2]. Here, a framework for integrating environmental and ecological ethics dimensions into chemists’ scientific integrity and good scientific practice guidelines is suggested under the umbrella of RRI.
Location of faults based on deep learning with feature selection for meter placement in distribution power grids
Authors: Degano Iván L. , Fiaschetti Leandro , Lotito Pablo A.
Published: August 2023

A problem of great interest for power distribution companies is ensuring uninterrupted service in extensive power distribution systems. Thus, the monitoring of networks and identification of system faults become essential. This work focuses on identifying a fault’s occurrence from a small number of low-cost measurements in a power distribution system. The determination of sensor locations is based on the recent feature selection approach LassoNet, where the measurement locations are ranked. It provides the most informative measures during a fault resulting in a shortening data set. It is used as input to a deep neural network without a significant loss in accuracy. We validate our method on the IEEE 13 and 34 node test feeders for distribution systems to conduct the suggested approach’s experimental studies.
Comparative analysis of fuel burnup calculations of fourth-generation European fast reactors
Authors: Ibrahim Amr
Published: August 2023

The sustainability of nuclear energy implies the continuous research and development of fast reactor technology. This work represents a comparative analysis of fuel burnup calculations of three commercial-level fast spectrum concepts which are under research and development in Europe. The investigated designs are the European Sodium-cooled Fast Reactor, the European Lead-cooled Fast Reactor, and the European Gas-cooled Fast Reactor. MCNPX transport code was used to design three representative fuel assemblies of these fourth-generation concepts to analyze and compare their neutronic and safety parameters. The neutronic and safety analysis in this work includes the evolution of infinite multiplication factor and fissile inventory, neutron yield, the average energy of neutrons causing fission, neutron energy spectrum, neutron generation time, Doppler reactivity effect, effective delayed neutron fraction, and coolant void reactivity coefficient. The fuel burnup results showed that the ESFR is superior regarding the reactivity swing and breeding of fissile 239Pu. On the other hand, analysis of safety parameters results showed that they depend mainly on fuel composition rather than on other design specifications.
Round bar notch shape optimization for tensile stress concentration testing
Authors: Ozsoy Murat , Akşen Toros Arda , Ekşi Seçil , Ozsoy Neslihan , Firat Mehmet
Published: August 2023

Notched structures in machine parts for several reasons cause discontinuity and stress concentration. It is essential to optimize these stress concentrations in notched parts. This study determined the best notch shape by creating different notch shapes by keeping two key points fixed on the spline curve in the notched region. This paper involves optimizing the shape of a fillet in a notched tension bar. An optimal shape was aimed to minimize the notch factor without causing yield anywhere in the bar by parametrically controlling the spline of the fillet via ANSYS parametric design language code. Optimal shapes of B-spline curves were obtained for round bars subject to axial tension loadings. Changing the code can also be used for bending or combined loading conditions other than tensile loading.
Simulation of Size Effect and Strength Prediction in Normal to Ultra High Strength Concrete Shear Deficient RC Beams
Authors: Fareed Shamsoon , Ayub Laiba , Khan Asad-ur-Rehman
Published: August 2023

The high rise building construction using normal strength concrete results in larger cross sections, which results in enhanced flexural behavior. Along with the improved flexural behavior, shear characteristics are also increased, which is often overshadowed. Impact of the increasing size on the behavior of reinforced concrete (RC) beams was investigated in this study. The experimental investigation was executed to evaluate the behavior of natural aggregate concrete (NAC), and recycled aggregate concrete (RAC) RC beams under four-point bending. To explicitly study the behavior of RC beams in shear, the beams were kept independent of any shear reinforcement and an shear span to effective depth of 2.68 was kept constant. Numerical simulation was then conducted to replicate the experimental program followed by the investigation of concrete compressive strength and the size effect on the shear behavior of the RC beams. Beams with varying depths of 203 mm, 400 mm, and 600 mm, and widths of 152 mm, 300 mm, and 400 mm, having compressive strength varying from 20 MPa to 150 MPa were investigated. Results were compared in terms of load-displacement relationship and cracking patterns. Furthermore, existing equations for the shear strength prediction of concrete, proposed by different codes, were also studied and compared with the numerical investigations. Based on the investigation, it was observed that the role of size effect in defining the overall shear behavior of RC beams cannot be neglected and the available equations need to be updated to account for size effect.
A New Experimental Technique to Investigate the Load-Bearing Mechanisms of Smeared Rock-Socketed Piles Using In Situ X-ray CT Imaging
Authors: Murali Arun Kumar , Haque Asadul , Bui Ha Hong
Published: August 2023

The design of rock-socketed piles at the serviceability state primarily depends on the shaft resistance (skin friction) at the interface, which may be influenced by the presence of weak smear (e.g., bentonite filter cake, soil, and remolded weak rock). To date, two-dimensional direct shear interface testing has been utilized to interpret the effect of smear on the shaft response of bored piles. However, without the nondestructive testing and three-dimensional (3D) visualization of smeared interfaces, the effect of smear at the pile-rock interface cannot be accurately assessed. This study presents a novel methodology to cast and test small-scale rock-socketed piles with 3D smeared pile-rock interfaces using in situ X-ray computed tomography (CT) imaging. A new smear casting apparatus has been designed to incorporate desired smear fabrics distribution around the model piles comprising idealized saw-tooth asperities. Different materials were trialed to represent the smeared interfaces and the most suitable one for this study was chosen to be a mixture of petroleum jelly and kaolin through the evaluation of the load-displacement behavior and the X-ray CT images. Various smear configurations were cast on the leading faces of the pile asperities (smear-dominant, balanced rock-smear, and rock-dominant) and their placement and volume were compared with the design values to provide confidence in the proposed experimental methodology. Moreover, the micromechanics evolving at the fully smeared leading-faced interface were assessed in detail using the vertical load-displacement behavior and the corresponding X-ray CT images acquired during multi-stage in situ loading. Based on the observations, the interface mechanics for the smeared shafts were classified into smear compression, subsequent smear compression with shearing, and rock shearing. The proposed experimental methodology opens new avenues for studying the smear fabric effect on the load-bearing mechanisms of smeared piles socketed in soft rock.
Equivalence of Bilinear Hysteresis and Viscous Damping Energy Dissipation
Authors: Wei Biao , Chen Mingyu , Jiang Lizhong , Yu Yujie , Min Haozheng
Published: August 2023

To evaluate the energy dissipation differences between metal dampers and viscous dampers and to gauge the degree of equivalence between bilinear hysteresis and viscous damping, we studied the equivalence of bilinear hysteresis and viscous damping. Using a MATLAB program and the principle of equal energy dissipation, the energy dissipation effect of bilinear hysteresis was equated based on the effect of viscous damping. Under a state of sinusoidal excitation, the displacement response of the numerical method, which strictly considers the bilinear hysteresis, was compared with the displacement response of the equivalent viscous damping calculation method. The results show that the oscillation periods for the two models demonstrate high consistency, with the displacement curves in the steady-state response stage nearly identical. Because of the lag in hysteresis energy dissipation, the bilinear hysteresis system always reaches the steady-state stage slower than the equivalent viscous damping system, implying that the metal damper responds more slowly to transient energy. In the free vibration stage, the bilinear hysteresis system cannot return to the initial position, while the displacement of the equivalent viscous damping system approaches zero, suggesting that the self-resetting effect of the viscous damper is better.
ZEYTİN PİRİNASININ MİKRODALGA KURUTULMASINDA ULTRASES ÖN İŞLEMİNİN ÜRÜNÜN BAZI FİZİKSEL VE KİMYASAL ÖZELLİKLERİ ÜZERİNE ETKİSİ
Authors: ALTAY Kadriye , ÇALIŞKAN KOÇ Gülşah , AKDOĞAN Arda
Published: August 2023

Bu çalışmada, mikrodalga kurutma öncesi zeytin pirinasına uygulanan ultrases ön işleminin kurutulmuş pirinanın fizikokimyasal kompozisyonu (nem, su aktivitesi ve renk), toz ürün özellikleri üzerine biyoaktif bileşenleri (toplam flavonoid, fenolik madde içeriği), antioksidan aktivitesi ve mineral madde içeriği özelliklerine etkisinin araştırılması hedeflenmiştir. Bu amaç doğrultusunda, pirina örneklerine 10 dakika ultrases ön işlemi uygulanmış ve örnekler 460W güçte 8 dakika süre ile mikrodalga fırında kurutulmuştur. Kurutma sonrası örneklerin nem içerikleri %5 (yaş bazda)’in altına düşmüştür. Ultrases ön işleminin kurutulmuş pirinanın b*, kroma ve esmerleşme indeksi değerlerini azalttığı gözlenmiştir. Toz formdaki kurutulmuş pirina örneklerinin iyi akabilirlik ve düşük yapışkanlık özelliğinde olduğu belirlenmiştir. Ultrases ön işleminin pirinaların flavonoid ve fenolik madde miktarı ve antioksidan aktivite özelliklerini azalttığı tespit edilmiştir. Ultrases ön işleminin örneklerin demir, nikel, alüminyum, mangan, kurşun ve potasyum içeriklerinde artış meydana getirdiği sonucuna varılmıştır.
DÜŞÜK ŞEKERLİ TURUNÇ MARMELATI ÜRETİMİNDE REBAUDİOSİDE A KULLANIMININ ARAŞTIRILMASI
Authors: YILDIZ TURGUT Demet , TANRİSEVEN Muslime , BAYIR YEĞİN Arzu , GÖLÜKLÜ Muharrem , TOKGÖZ Haluk , KOLA Osman
Published: August 2023

Bu çalışmada düşük şekerli turunç marmelatı üretiminde doğal tatlandırıcı olarak steviol glikozit Rebaudioside A (Reb A)’ nın kullanılabilirliğini ortaya koymak ve farklı formülasyonlarda üretilen marmelatların bazı kalite özelliklerini incelemek amaçlanmıştır. Bu kapsamda standart turunç marmelatı (kontrol) ve 15 farklı formülasyonda düşük şekerli turunç marmelatı üretilmiş ve bu ürünlerde fizikokimyasal ve duyusal analizler gerçekleştirilmiştir. Turunç marmelatlarının toplam kuru madde, suda çözünür kuru madde, pH ve titrasyon asitliği değerleri sırasıyla %44.11-78.30, 38.63-70.08 °Bx, 3.15-3.67 ve %0.09-0.28 olarak belirlenmiştir. Marmelat örneklerinde glikoz, fruktoz, sakkaroz, toplam şeker ve HMF içerikleri 20.35-20.61 g/100 g, 28.54-28.56 g/100 g, 20.70-20.75 g/100 g, 69.64-69.87 g/100 g ve 0.22-11.80 mg/kg aralığında bulunmuştur. Marmelat örneklerinin renk, lezzet, kıvam ve genel kabul edilebilirlik özelliklerini içeren duyusal analizleri hedonik test yöntemi ile gerçekleştirilmiştir. Genel kabul edilebilirlik açısından en fazla tercih edilen örneklerin suda çözünür kuru madde (SÇKM) içeriği % 25 azaltılmış 100 mg Reb A içeren marmelat, SÇKM’si %25 azaltılmış 150 mg Reb A içeren marmelat ve SÇKM’si %30 azaltılmış 100 mg Reb A içeren marmelat örnekleri olduğu tespit edilmiştir. Sonuç olarak SÇKM içeriği %25 ve 30 oranında azaltılmış, tatlandırıcı olarak 100 ve 150 mg Reb A içeren marmelat örneklerinin gerek fizikokimyasal gerekse duyusal özellikler bakımından üstün özellikler gösterdiği belirlenmiştir.
Group Active Engagements for Facilitating Principles-Based Learning in Introductory Organismal Biology
Authors: Cooke Todd J. , Jensen Jeffrey S. , Carleton Karen L. , Hall Kristi L. , Jardine Hannah E. , Kent Bretton W. , Redish Edward F. , Shultz Jeffrey W.
Published: August 2023

Organismal biology (OrgBio) comprises the diversity, structures, and functions of all organisms from bacteria to humans. Arguably, OrgBio is often the most poorly taught and least conceptually rigorous section of the introductory biology sequence offered at most U.S. institutions of higher education. This article reports on the successful implementation of conceptual and pedagogical reforms in an introductory OrgBio course offered at a large public university. Conceptual reforms were based on a theoretical framework consisting of universal physical and chemical laws, deep molecular homologies, and diverse structure–function relationships. Pedagogical reforms involved the development of group active engagements (GAEs) that were designed to encourage students to develop their abilities to engage in principles-based reasoning. A new model for characterizing different approaches toward principles-based reasoning in biology was developed to analyze these GAEs. Two surveys indicated that OrgBio students developed more favorable perceptions about the effectiveness of GAE-based course offerings, as compared to similar lecture-based versions.
Evaluation of Cost-Conscious Course-Embedded Research Projects in a Freshman Biochemistry and Molecular Biology Course
Authors: Stewart John F. , Gustafson John E. , Moore Michael E. , Forshee J. Lance , Canaan Patricia , French Donald P.
Published: August 2023

Students who experience research as undergraduates tend to remain in science, technology, engineering, and mathematics fields. Since course-based undergraduate research experiences (CUREs) are often expensive to implement, we developed a relatively inexpensive first-semester research course for majors entitled “Freshman Research in Biochemistry,” in which approximately 100 students participated in an ongoing research project each year. During this course, students conducted laboratory work related to multiple research veins, and graduate teaching assistants (TAs) and the instructor ensured that sufficient data from the laboratory were made available to the students to analyze. During three unique course iterations, students worked on faculty research projects that included connecting contigs of the draft genome of a native Oklahoma bacterial Arhodomonas isolate capable of degrading petroleum hydrocarbons, cloning antibiotic resistance genes from the genus Elizabethkingia, and analyzing RNAseq data from Elizabethkingia anopheles challenged with cell wall-active antibiotics to determine gene function, gene differential expression, and relative gene genome location. During the course, students scored results, analyzed data, maintained laboratory notebooks, and presented posters in a symposium to faculty and graduate TAs. To determine positive impacts of the course on students, they completed the Laboratory Course Assessment Survey in two course sections. Survey data indicated/students agreed that the course included elements of Iteration, Collaboration, and Discovery and Relevance. Students also reported that they gained scientific skills but were ambivalent about whether instructor feedback was harsh. Examination of Student Survey of Instruction responses showed students thought positively about the course, but some considered it too difficult. Biochemistry and Molecular Biology and Biochemistry major cohort tracking revealed no effect of Freshman Research in Biochemistry on student persistence in the major or institution. Nonetheless, we consider the course a cost-conscious model for biochemistry and molecular biology departments for introducing research to first-year students.
Authentic Scientific Research through an Undergraduate Ecology Course
Authors: Burgin Stephen R. , Siepielski Adam M.
Published: August 2023

Undergraduate science students who volunteer within a research laboratory group, or participate in funded research opportunities, in general are those who have the opportunity to engage in authentic research. In this article, we report the findings from two different iterations of a semester-long collaboration between a biology faculty member and a science education faculty member at a major research institution in the Southeastern United States. Specifically, the faculty members designed an ecology laboratory course for upper-level undergraduate students (primarily biology majors) where they would engage in an original and highly authentic ecological research project. The goal of this course was to have students explicitly learn about the nature of science (NOS), and authentic scientific practices such as inquiry and experimentation in the context of their own research. In the second year of the course, the global COVID-19 pandemic forced us to modify our approach to accomplish the same goals, but now in a remote and online format. Using questionnaires, concept inventories, and semi-structured interviews, the impact of the course on students’ understandings of NOS, inquiry, and experimentation, in addition to their perspectives on the experience within the course compared to prior laboratory coursework, was investigated. We found that students showed modest gains in each of the aforementioned desirable outcomes. These gains were generally comparable in both face-to-face and remote course settings. Additionally, students shared with us their preference for authentic laboratory work as compared with the typical laboratory work with its given research question and step-by-step instructions. Our research demonstrates what is possible in both face-to-face and remote undergraduate laboratory courses in biology and the positive impact that was observed in our students. We hope it serves as a model for other scientists and science educators as they collaborate to design authentic research-based coursework for undergraduate biology students.
Assignment Choices in an Upper Level Biology Course Increase Engagement and Course Satisfaction
Authors: Nichols Gena
Published: August 2023

Pedagogical practices such as active learning and group-based exercises are increasingly being used to engage students in course content during class meetings. However, techniques employed in class may not always contribute to engagement outside of the class meetings, or to student satisfaction with the course itself. Previous reports have shown that student autonomy and initial perceptions of the course setup influence their engagement and satisfaction, independent of the course context. To address engagement in an upper level collegiate biology class, students were allowed to choose their own assignments accounting for 50% of their total grade and also choose the due dates for those assignments; the remaining 50% came from exam scores. The goal was to allow students the option to pick assignments that best reflected their perceived strengths and preferences in order to determine whether these options increased students’ satisfaction and engagement with the course content. Students were surveyed with questionnaires at the beginning and end of the semester to monitor their perception of the course setup, their interest in the course content, and their satisfaction with the course. Comparing initial perception of the course layout with final experiences, students reported that assignment choice did increase interest in the course and resulted in a student-reported increase in personal responsibility within the course.
Radicle emergence test for cabbage can be assessed using multispectral imaging
Authors: Wagner Marie-Hélène , Powell Alison A. , Dupont Audrey , Shinohara Takashi , Ducournau Sylvie
Published: August 2023

The potential of multispectral imaging (MSI, using a VideometerLab©) to achieve automation of the assessment of radicle emergence (RE) in the RE vigour test and thereby increase the throughput of vigour testing, was examined using 12 commercial seed lots from three varieties
of cabbage (Brassica oleracea L. var capitata). The RE of the 12 lots was assessed after 48 hours germination at 20°C using both MSI (MSI RE48) and a manual count. The RE counts made using MSI were highly correlated to manual counts taken by eye at the same time (r
= 0.97, p < 0.001) and to RE assessments taken using RGB imaging (r = 0.84, p < 0.01). MSI RE48 was significantly related to field emergence after seven days (r = 0.87, p < 0.01) and glasshouse emergence after six days (r = 0.86, p
< 0.01); similar relationships with emergence were found for the RE assessments taken using RGB imaging. Our data indicate that an automated count of RE is possible in the RE test using MSI imaging and relates to seed vigour in cabbage.