bluuebunny/crossref_metadata_2025 huggingface dataset:
The roles of high conservation value area to support biodiversity conservation in Indonesia
Authors: Mijiarto Joko , Arief Harnios , Purnamasari Intan
Published: September 2023

Oil palm plantations are often considered as one of the causes of the decline in biodiversity. Conversion of forest land to oil palm is the main factor. However, legally, land conversion can be carried out and oil palm plantation companies have also protected areas that have high conservation value, including important animal habitats. The purpose of this study is to assess the role of high conservation value areas in the conservation of biodiversity. The study was conducted on several oil palm plantations in Indonesia by conducting a literature review of high conservation value documents on several oil palm plantation companies. High conservation value areas in oil palm plantations are determined based on the presence of endangered and protected animals such as proboscis monkeys and orangutans. With the stipulation of the area as a HCV area, the presence of these animals becomes more concerned because the company has the responsibility to monitor the presence of these animals. In addition, the company also conducts socialization to the community and workers to take care of these animals. The existence of the HCV area also indirectly supports the government’s program in this case is the establishment of an Essential Ecosystem Area that functions to protect important animals outside the conservation area.
Mycorrhizae utilization in palm oil nurseries to reduce inorganic fertilizer dose
Authors: Sakiah  , Yosephine I O , Sukariawan A , Naibaho T , Guntoro  , Saragih A P
Published: September 2023

Fertilization in palm oil nurseries is an invaluable tending activity to obtain healthy and robust seedlings. This research aims is to identify the dose percentage level of the inorganic fertilizer which can be reduced by applying mycorrhizae in oil palm nurseries. The research design used a non-factorial completely randomized design, as the treatment factor was the dose of fertilizer in oil palm nurseries. There are 5 levels of treatment, namely P0 (100% of the standard dose + 50 g mycorrhizae), P1 (75% of the standard dose + 50 g mycorrhizae), P2 (50% of the standard dose + 50 g mycorrhizae), P3 (25% of the standard dose + 50 g mycorrhizae), and P4 (0 inorganic fertilizer + 50 g Mycorrhizae). Each treatment was arranged in four replications. The data were analyzed using ANOVA, if F-count > F-table then it is continued with Duncan Multiple Range Test. The observation variables included plant height, number of leaves and stem diameter, root length, canopy dry weight, roots dry weight, and P uptake. The results showed that there were significant differences in plant height, number of leaves, stem diameter, roots dry weight, canopy dry weight and P uptake in leaves as well as, while the observations of root length showed no significant difference. The application of 50 grams of mycorrhizae with a 50-75% standard dose of fertilization resulted in optimal seedling growth. Mycorrhizae utilization can reduce the application of inorganic fertilizers up to 25-50%.
Double pulse gas metal arc welding process parameter optimization and weld performance analysis based on response surface method
Authors: Bin Kun , Yao Ping , Xu Min , Lin Qian , Gu Yuqing
Published: September 2023

Double pulse gas metal arc welding (DP-GMAW) is a low-frequency modulated high-frequency pulse welding, which can fully stir the molten pool, and improve the forming and performance of the weld. In this study, a mathematical model was developed using the response surface method (RSM) with three main process parameters (welding current, peak-to-base ratio, welding speed) as input values with three key geometric characteristics parameters, and the mechanical properties of the resulting welds were investigated. The results showed that the parameter model developed in this study had less error and could optimize the process parameters better; the optimal process parameters (welding current, peak-to-base ratio, welding speed) were 160 A, 39.93%, and 83.11 cm min−1, respectively. The improved welding parameters result in better mechanical properties and better weld profile, and more stable welding process. As a result, this experiment provides a new perspective for process parameter optimization and mechanical properties research for weld manufacturing.
Low-temperature giant coercivity in Co6.2Ga3.8−x
Ge
x
(x = 2.4 to 3.2)
Authors: Kitagawa Jiro , Nomura Himawari , Nishizaki Terukazu
Published: September 2023

The observation of giant coercivity exceeding 20 kOe at low temperatures in several transition-metal-based compounds has attracted significant attention from a fundamental perspective. This research is also relevant to developing rare-earth-free permanent magnets, wherein cobalt is one of the primary elements used. To facilitate easy fabrication, rare-earth-free and Co-based inorganic bulk magnets that exhibit giant coercivity are highly demanded but rarely reported. Herein, we report the observation of low-temperature giant coercivity in polycrystalline metallic Co6.2Ga3.8−x
Ge
x
(x = 2.4 to 3.2) with the hexagonal Fe13Ge8-type structure composed of Kagome and triangular lattices. As the Ge content x decreases from 3.2, the magnetic ground state changes from ferrimagnetism to ferromagnetism at x = 2.6. In the ferrimagnetic state, we observed a signature of spin frustration arising from the Kagome and/or triangular lattices of Co atoms. The ferromagnetic ordering temperatures for the x = 2.6 and 2.4 samples are 46 K and 60 K, respectively. The coercive fields rapidly increase upon cooling and reach values of 26 kOe and 44 kOe in the x = 2.6 and 2.4 samples, respectively, at 2 K.
Trace formula of the differential operator with delays on a quantum graph
Authors: Yang Chuan-Fu , Wei Li-Xiao , Xu Xin-Jian
Published: September 2023

In this paper a class of differential operators with retarded arguments on a lasso graph is studied. We derive the asymptotic expressions of its large eigenvalues and obtain a new regularized trace formula for this class of differential operators.
13. Contagion and connections: Applying network thinking to violence and organized crime
Authors: Campana Paolo
Published: September 2023

This chapter looks into the application of network thinking to violence and organized crime. The COVID-19 global pandemic showcased how connections matter and far-reaching consequences for the life and well-being of individuals and communities. Infectious pathogens exploit the web of social relations to increase their spread across individuals and places, which then results in the emergence of epidemics. Criminology has been slow to adopt social network analysis, but it does elucidate the mechanisms concerning violence and co-offending that involve gangs and organized crime. The chapter explains that relations and individual characteristics do not need to be treated in opposition to each other, but can be modelled and explored jointly.
24. Green criminology
Authors: Brisman Avi , South Nigel
Published: September 2023

Criminology must maintain relevance in a changing world and engage with new challenges. Perhaps pre-eminent among those facing the planet today are threats to the natural environment and, by extension, to human health and rights and to other species. A green criminology has emerged as a (now well-established) criminological perspective that addresses a wide range of crimes, harms and offences related to the environment and environmental victims. This chapter provides a review of green criminological work on climate change, consumption and waste, state-corporate and organized crimes, animal abuse, and wildlife trafficking. It also considers the strengths and weaknesses of current approaches to regulation, enforcement and control.
31. Understanding penal decision-making: Courts, sentencing, and parole
Authors: Padfield Nicola , Tata Cyrus
Published: September 2023

This chapter expounds on the understanding of penal decision-making under the critical perspective that understands the interplay between courts, sentencing, and parole. It examines key issues in the daily realities of the work of sentencing and parole and their implications for research and policy. Conventional wisdom and popular assumptions about criminal justice have been led by a preoccupation with the most serious, glamorous cases. The chapter highlights the significance of the presumption of innocence, citing that cases are judged as unique and criminal justice agencies work autonomously in penal decision-making. It considers several strategies to reduce the use of imprisonment by promoting community alternatives
Extraordinarily high serum CA 19-9 in setting of pancreatic necrosis and underlying pancreatic adenocarcinoma: a case report
Authors: McConnell Ashlyn , Stoneman Tyler , Hewlett Stanley
Published: September 2023

Carbohydrate antigen (CA 19-9) is the most validated marker for both sensitivity and specificity of pancreatic adenocarcinoma used to aid diagnosis of symptomatic patients as well as to evaluate the progression or treatment of disease. Though higher levels of CA 19-9 tend to correlate with neoplastic disease, elevated levels are also often seen in patients with benign gastrointestinal diseases, such as obstructive jaundice and pancreatitis. We present a case of a 74-year-old male who was admitted for abdominal pain and worsening jaundice who was diagnosed with extensive pancreatic necrosis and an underlying invasive pancreatic adenocarcinoma whose serum level of CA 19-9 was found to be extraordinarily high.
Organizational Structure and Pricing: Evidence from a Large U.S. Airline
Authors: Hortaçsu Ali , Natan Olivia R , Parsley Hayden , Schwieg Timothy , Williams Kevin R
Published: September 2023

Firms facing complex objectives often decompose the problems they face, delegating different parts of the decision to distinct subunits. Using comprehensive data and internal models from a large U.S. airline, we establish that airline pricing is not well approximated by a model of the firm as a unitary decision maker. We show that observed prices, however, can be rationalized by accounting for organizational structure and for the decisions by departments that are tasked with supplying inputs to the observed pricing heuristic. Simulating the prices the firm would charge if it were a rational, unitary decision maker results in lower welfare than we estimate under observed practices. Finally, we discuss why counterfactual estimates of welfare and market power may be biased if prices are set through decomposition, but we instead assume that they are set by unitary decision makers.
Targeting enhanced neutralizing antibody responses via increased germinal center activity: early-phase vaccine trials with novel clinical designs
Authors: Hahn William O. , Hill Joshua A. , Kublin James G.
Published: September 2023

Purpose of review

Recent advances in the understanding of the difficult immunologic requirements for the induction of broadly neutralizing antibodies for HIV have spurred interest in optimizing vaccine approaches intended to stimulate a robust germinal center reaction. In preclinical models, techniques to optimize the germinal center response have included alterations in the timing, dose, and delivery method of immunogens and have resulted in substantially enhanced germinal center responses in lymph nodes and neutralizing antibodies in serum. One of the most promising approaches involves splitting the initial dose of vaccine into a series of gradual escalating doses administration (“fractional escalating doses”). In principle, these techniques may have broad implications for vaccines targeting a robust antibody response.

Recent findings

We review the upcoming vaccine trials that will test these concepts in clinical practice. The trials include both HIV and non-HIV immunogens, and will involve testing these concepts in both healthy adults and immunocompromised persons.

There are multiple trials that will test whether techniques to alter vaccine delivery such as fractional escalating doses enhances immunologic outcomes.
Advances in Cardiac Workup for Transient Ischemic Attack: Improving Diagnostic Yield and Reducing Recurrent Stroke Risk
Authors: Al-sabbagh Mohammed Q. , Thirunavukkarasu Sibi , Eswaradass Prasanna
Published: September 2023

Transient ischemic attack (TIA) is a warning sign for an impending stroke, with a 10–20% chance of a stroke occurring within 90 days of the initial event. Current clinical practice for cardiac workup in TIA includes cardiac enzymes, with 12-lead electrocardiogram, transthoracic echocardiography, and 24-hour Holter monitoring. However, the diagnostic yield of these investigations is variable, and there is a need for better diagnostic approaches to increase the detection of cardiac abnormalities in a cost-effective way. This review article examines the latest research on emerging diagnostic tools and strategies and discusses the potential benefits and challenges of using these advanced diagnostic approaches in clinical practice. Novel biomarkers, imaging techniques, and prolonged rhythm monitoring devices have shown great promise in enhancing the diagnostic yield of cardiac workup in TIA patients. Echocardiography, Transcranial Doppler ultrasound, cardiac MRI, and cardiac CT are among the promising diagnostic tools being studied. We conclude the article with a suggested diagnostic algorithm for cardiac workup in TIA. Further research is necessary to enhance their usefulness and to outline future directions for research and clinical practice in this field.
Designing the coronary artery bypass surgery operation of the future
Authors: Ruel Marc
Published: September 2023

Purpose of review

This article discusses current shortcomings in coronary artery bypass surgery and ways to overcome them.

Recent findings

Minimally invasive coronary bypass surgery, robotic coronary bypass, and hybrid approaches aim to avoid sternotomy, employ arterial grafts, and minimize the use of cardiopulmonary bypass. Other considerations such as bypass graft validation, the optimization of guideline-directed medical therapy, and the development of coronary surgery specialists are also crucial to further the benefits of coronary artery bypass grafting on future patients.

Coronary artery bypass grafting must become less invasive, be better validated, and be carried out with an even higher emphasis on quality, including graft validation and preoperative/postoperative optimization, if it is to remain the best treatment for advanced, severe coronary artery disease.
Advances in cardiac pacing with leadless pacemakers and conduction system pacing
Authors: Somani Sulaiman , Rogers Albert J.
Published: September 2023

Purpose of review

The field of cardiac pacing has undergone significant evolution with the introduction and adoption of conduction system pacing (CSP) and leadless pacemakers (LLPMs). These innovations provide benefits over conventional pacing methods including avoiding lead related complications and achieving more physiological cardiac activation. This review critically assesses the latest advancements in CSP and LLPMs, including their benefits, challenges, and potential for future growth.

Recent findings

CSP, especially of the left bundle branch area, enhances ventricular depolarization and cardiac mechanics. Recent studies show CSP to be favorable over traditional pacing in various patient populations, with an increase in its global adoption. Nevertheless, challenges related to lead placement and long-term maintenance persist. Meanwhile, LLPMs have emerged in response to complications from conventional pacemaker leads. Two main types, Aveir and Micra, have demonstrated improved outcomes and adoption over time. The incorporation of new technologies allows LLPMs to cater to broader patient groups, and their integration with CSP techniques offers exciting potential.

The advancements in CSP and LLPMs present a transformative shift in cardiac pacing, with evidence pointing towards enhanced clinical outcomes and reduced complications. Future innovations and research are likely to further elevate the clinical impact of these technologies, ensuring improved patient care for those with conduction system disorders.
Perinatal and Other Risk Factors for Common Infections in Infancy: A Prospective Cohort Study
Authors: Hyvönen Sanni , Tapiainen Terhi , Pokka Tytti , Solasaari Terhi , Korpela Katri , de Vos Willem M. , Salonen Anne , Kolho Kaija-Leena
Published: September 2023

Objective:

Limited data from prospective cohort studies in high-income countries are available on the perinatal risk factors for common infections in children. Our hypothesis was that perinatal factors may be risk factors for infectious episodes during the first year of life.

Methods:

In this prospective Health and Early Life Microbiota birth cohort study of full-term infants (n = 1052) born in 2016–2018, the number and duration of infection episodes were collected online at weekly to monthly intervals. In a multivariate regression model, the main exposures were perinatal factors such as mode of delivery and intrapartum antibiotics. Environmental factors were additional exposures. The outcomes were the number and duration of infectious episodes in the first year of life.

Results:

The mean number of infection episodes was 4.2 (2.9 SD). The mean duration of infection symptoms was 44 days (40 SD). Upper respiratory infections accounted for 83% of the episodes (3674/4455). Perinatal factors were not associated with the number nor the duration of infection episodes, but cesarean section was associated with an increased occurrence of urinary tract infections in infancy [adjusted odds ratio (aOR): 3.6; 95% confidence interval (CI): 1.13–11.1]. Of the additional exposures male sex (aOR: 1.1; 95% CI: 1.0–1.2) and the presence of siblings (aOR: 1.3; 95% CI: 1.2–1.4) were associated with the number of infection episodes.

Conclusions:

This prospective cohort study showed that perinatal factors, mode of delivery and intrapartum antibiotics were not associated with the risk of common infections in infancy, but cesarean delivery was associated with a risk of urinary tract infections.
Large-scale momentary brain co-activation patterns are associated with hyperalgesia and mediate focal neurochemistry and cross-network functional connectivity in fibromyalgia
Authors: Mawla Ishtiaq , Huang Zirui , Kaplan Chelsea M. , Ichesco Eric , Waller Noah , Larkin Tony E. , Zöllner Helge J. , Edden Richard A.E. , Harte Steven E. , Clauw Daniel J. , Mashour George A. , Napadow Vitaly , Harris Richard E.
Published: September 2023

Fibromyalgia has been characterized by augmented cross-network functional communication between the brain's sensorimotor, default mode, and attentional (salience/ventral and dorsal) networks. However, the underlying mechanisms of these aberrant communication patterns are unknown. In this study, we sought to understand large-scale topographic patterns at instantaneous timepoints, known as co-activation patterns (CAPs). We found that a sustained pressure pain challenge temporally modulated the occurrence of CAPs. Using proton magnetic resonance spectroscopy, we found that greater basal excitatory over inhibitory neurotransmitter levels within the anterior insula orchestrated higher cross-network connectivity between the anterior insula and the default mode network through lower occurrence of a CAP encompassing the attentional networks during sustained pain. Moreover, we found that hyperalgesia in fibromyalgia was mediated through increased occurrence of a CAP encompassing the sensorimotor network during sustained pain. In conclusion, this study elucidates the role of momentary large-scale topographic brain patterns in shaping noxious information in patients with fibromyalgia, while laying the groundwork for using precise spatiotemporal dynamics of the brain for the potential development of therapeutics.
Small intestinal bacterial overgrowth: current update
Authors: Zafar Hammad , Jimenez Brenda , Schneider Alison
Published: September 2023

Purpose of review

This article aims to provide an up-to-date review of small intestinal bacterial overgrowth (SIBO), including etiology and risk factors, clinical manifestations, diagnostic evaluation for suspected SIBO, and therapeutic options.

Recent findings

Recent advances in breath testing, capsule and urine-based testing have opened new avenues and improved diagnostic yield of SIBO. Nonantibiotic-based treatment strategies have shown promising results in initial trials.

Small intestinal bacterial overgrowth (SIBO) is a condition defined by the excess bacteria or changes in bacterial composition of the small intestine. These are associated with various gastrointestinal (GI) symptoms such as bloating, abdominal distension, diarrhea, nutrient deficiencies, and even frank weight loss. Small bowel jejunal aspirate of >105CFU/ml has traditionally been considered the gold standard for diagnosis. Glucose and lactulose breath testing have become more common in clinical practice as they are noninvasive, easily accessible, and have lower cost. Treatment focuses on the eradication of excess bacteria in the small bowel and is traditionally done with the use of oral antibiotics. Other emerging therapies may include probiotics, diet manipulation, and prokinetic agents.
Pediatric tracheostomy decannulation: what's the evidence?
Authors: Raynor Tiffany , Bedwell Joshua
Published: September 2023

Purpose of review

Pediatric decannulation failure can be associated with large morbidity and mortality, yet there are no published evidence-based guidelines for pediatric tracheostomy decannulation. Tracheostomy is frequently performed in medically complex children in whom it can be difficult to predict when and how to safely decannulate.

Recent findings

Published studies regarding pediatric decannulation are limited to reviews and case series from single institutions, with varying populations, indications for tracheostomy, and institutional resources. This article will provide a review of published decannulation protocols over the past 10 years. Endoscopic airway evaluation is required to assess the patency of the airway and address any airway obstruction prior to decannulation. There is considerable variability in tracheostomy tube modification between published protocols, though the majority support a capping trial and downsizing of the tracheostomy tube to facilitate capping. Most protocols include overnight capping in a monitored setting prior to decannulation with observation ranging from 24 to 48 h after decannulation. There is debate regarding which patients should have capped polysomnography (PSG) prior to decannulation, as this exam is resource-intensive and may not be widely available. Persistent tracheocutaneous fistulae are common following decannulation. Excision of the fistula tract with healing by secondary intention has a lower reported operative time, overall complication rate, and postoperative length of stay.

Pediatric decannulation should occur in a stepwise process. The ideal decannulation protocol should be safe and expedient, without utilizing excessive healthcare resources. There may be variability in protocols based on patient population or institutional resources, but an explicitly described protocol within each institution is critical to consistent care and quality improvement over time. Further research is needed to identify selection criteria for who would most benefit from PSG prior to decannulation to guide allocation of this limited resource.
Circulating Tumor DNA Is an Accurate Diagnostic Tool and Strong Prognostic Marker in Pancreatic Cancer
Authors: Sellahewa Rav , Moghaddam Samar Masoumi , Lundy Joanne , Jenkins Brendan J. , Croagh Daniel
Published: September 2023

Objective

The objectives of the study are to investigate the sensitivity and specificity of circulating tumor DNA (ctDNA) for the diagnosis of pancreatic cancer and to assess the utility of ctDNA as a prognostic marker in this disease.

Methods

Cell-free DNA was extracted from plasma of patients who underwent endoscopic ultrasound fine-needle aspiration or surgical resections for pancreatic cancer. The cell-free DNA was then analyzed using droplet digital polymerase chain reaction for KRAS G12/13 mutations. Eighty-one patients with pancreatic cancer and 30 patients with benign pancreatic disease were analyzed.

Results

ctDNA KRAS G12/13 mutations were detected in 63% of all patients with pancreatic cancer and in 76% of those patients who also had KRAS G12/13 mutations detected in the pancreatic primary. Specificity and tissue concordance were both 100%. Circulating tumor DNA corresponded with tumor size and stage, and high ctDNA was associated with significantly worse prognosis on both univariate and multivariate testing.

Conclusion

Our study shows that ctDNA is an accurate diagnostic tool and strong prognostic marker in patients with pancreatic cancer. The continued investigation of ctDNA will enable its implementation in clinical practice to optimize the care and survival outcomes of patients with pancreatic cancer.
Nonossifying Fibroma Involving Epiphysis of Long Bone—Case Report and Review of the Literature
Authors: Serinelli Serenella , Enniss Brent A. , Damron Timothy A. , Stock Harlan , de la Roza Gustavo L.
Published: September 2023

Nonossifying fibroma (NOF) is a common benign bone neoplasm and is usually observed in the first 2 decades of life. Most NOFs occur in the metaphysis of long bones of the lower extremities and migrate toward the diaphysis during skeletal maturation. Epiphyseal involvement by NOF has been rarely reported, with only one case found in the English literature. The authors report the second case of NOF involving the epiphysis of a long bone, the proximal tibia of a 21-year-old woman. Clinicians and pathologists should be aware of the rare possibility of epiphyseal involvement of long bones by this condition. Pathologists should select appropriate immunohistochemistry markers to rule out alternative diagnoses.
The Role of Morphology in Predicting Fumarate Hydratase–deficient Uterine Leiomyomas in Young Women
Authors: Bayram Aysel , Bagbudar Sidar , Sozen Hamdullah , Onder Semen , Yavuz Ekrem
Published: September 2023

Hereditary leiomyomatosis and renal cell carcinoma is caused by germline mutations in the fumarate hydratase (FH) gene and is associated with an increased incidence of leiomyomas and a potentially aggressive variant of renal cell carcinoma. Pathologic evaluation of uterine leiomyoma can provide an opportunity for early recognition of the syndrome. We reviewed all archived slides of the cases to identify the characteristic morphologic features described for FH-deficient leiomyomas. We performed immunohistochemistry on whole sections of patients with uterine leiomyoma to evaluate for both FH and 2-succinocysteine (2SC) expression. Of the 106 cases, 19 showed the characteristic eosinophilic nucleoli with perinuclear halos, and 24 revealed a characteristic eosinophilic cytoplasmic inclusion consisting of pink globules present within the cytoplasm. Both of these morphologic findings were present together in 15 cases, and hemangiopericytomatous vessels were detected in 23 cases. The loss of FH protein expression was detected in 14 out of 106 cases (13%), and 13 out of 106 cases (12%) were positive for 2SC. We detected 10 cases with both 2SC-positive and FH expression loss. The presence of eosinophilic nucleoli with perinuclear halos and eosinophilic cytoplasmic inclusion was associated with both loss of FH protein expression and 2SC positivity (P < 0.001). These findings underscore the importance of hematoxylin and eosin–based predictive morphology in FH-deficient uterine leiomyomas. Therefore, morphologic assessment of uterine leiomyomas for features of FH deficiency can serve as a screening tool for hereditary leiomyomatosis and renal cell carcinoma syndrome, allowing patients to be divided according to their hereditary risk assessment.
Sports Nutrition Knowledge and Breakfast Beliefs and Habits in Regularly Exercising Adults
Authors: Hillman Angela R. , Green Rachel
Published: September 2023

This study investigated the sports nutrition knowledge and breakfast consumption habits and beliefs in adults who regularly exercise. Participants (N = 404) identifying as athletes (n = 47), former athletes (n = 65), and nonathletes (n = 292) completed a survey. Sports nutrition knowledge was inadequate (52% correct); former athletes scored better than nonathletes (62% vs 49%). The Internet was the primary source of information (35%); 4% of participants consulted registered dietitians. Approximately 40% of participants do not eat before exercise and those who do consume fruit/fruit juice or meal replacement bars. This study indicates a need for more accessible and reliable nutrition information for exercisers.
A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes
Authors: Kleijn Istvan T. , Marguerat Samuel , Shahrezaei Vahid
Published: September 2023

Coarse-grained resource allocation models (C-GRAMs) are simple mathematical models of cell physiology, where large components of the macromolecular composition are abstracted into single entities. The dynamics and steady-state behaviour of such models provides insights on optimal allocation of cellular resources and have explained experimentally observed cellular growth laws, but current models do not account for the uptake of compound sources of carbon and nitrogen. Here, we formulate a C-GRAM with nitrogen and carbon pathways converging on biomass production, with parametrizations accounting for respirofermentative and purely respiratory growth. The model describes the effects of the uptake of sugars, ammonium and/or compound nutrients such as amino acids on the translational resource allocation towards proteome sectors that maximized the growth rate. It robustly recovers cellular growth laws including the Monod law and the ribosomal growth law. Furthermore, we show how the growth-maximizing balance between carbon uptake, recycling, and excretion depends on the nutrient environment. Lastly, we find a robust linear correlation between the ribosome fraction and the abundance of amino acid equivalents in the optimal cell, which supports the view that simple regulation of translational gene expression can enable cells to achieve an approximately optimal growth state.
Impact of misinformation in the evolution of collective cooperation on networks
Authors: Meng Yao , Broom Mark , Li Aming
Published: September 2023

Human societies are organized and developed through collective cooperative behaviours. Based on the information in their environment, individuals can form collective cooperation by strategically changing unfavourable surroundings and imitating superior behaviours. However, facing the rampant proliferation and spreading of misinformation, we still lack systematic investigations into the impact of misinformation on the evolution of collective cooperation. Here, we study this problem by classical evolutionary game theory. We find that the existence of misinformation generally impedes the emergence of collective cooperation on networks, although the level of cooperation is slightly higher for weak social cooperative dilemma below a proven threshold. We further show that this possible advantage diminishes as social connections become denser, suggesting that the detrimental effect of misinformation further increases when ‘social viscosity’ is low. Our results uncover the quantitative effect of misinformation on suppressing collective cooperation, and pave the way for designing possible mechanisms to improve collective cooperation.
Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment
Authors: Yue Yu-Yan , Ye Yu-Qi , Zhou Zi-Yang , Zhang Meng-Di , Jia Ya-Wei , Du Zong-Jun
Published: September 2023

Two novel Gram-stain-negative, facultative anaerobic, chemoheterotrophic, non-motile and rod-shaped strains were isolated from intertidal sediment sampled at Xiaoshi Island, Weihai, PR China. Full sequence analysis of the 16S rRNA genes showed that the two strains were closely related to members of the genus

Winogradskyella

and the phylogenetic similarities to their closest relative,

Winogradskyella aquimaris

, were 96.7 and 95.8 %, respectively. The DNA G+C contents of strains 2Y89T and D23T were 33.3 and 35.1 mol%, respectively. The respiratory quinone detected in both strains was MK-6. The major fatty acids detected in strain 2Y89T were iso-C15 : 0 and iso-C15 : 1G, and in strain D23T they were iso-C15 : 1G, iso-C15 : 0 and iso-C17 : 03–OH. The principal polar lipids of strain 2Y89T mainly included phosphatidylethanolamine, aminoglycolipids, unidentified aminolipids, unidentified glycolipids and unidentified lipids; strain D23T was the same as strain 2Y89T except that it did not contain aminoglycolipids. Based on the phenotypic, chemical taxonomic, genotypic and phylogenetic features established in this study, we suggest that the new strains represent two novel species of the genus

Winogradskyella

, for which the names Winogradskyella vincentii sp. nov. (type strain 2Y89T=MCCC 1H00477T=KCTC 92034T) and Winogradskyella alexanderae sp. nov. (type strain D23T=MCCC 1H00462T=KCTC 92023T) are proposed.
Somatic mutations reveal hyperactive Notch signaling and racial disparities in prurigo nodularis
Authors: Rajeh Ahmad , Cornman Hannah L. , Gupta Anuj , Szeto Mindy D. , Kambala Anusha , Oladipo Olusola , Parthasarathy Varsha , Deng Junwen , Wheelan Sarah , Pritchard Thomas , Kwatra Madan M. , Semenov Yevgeniy R. , Gusev Alexander , Yegnasubramanian Srinivasan , Kwatra Shawn G.
Published: September 2023

Prurigo nodularis (PN) is a chronic inflammatory skin disease that disproportionately affects African Americans and is characterized by pruritic skin nodules of unknown etiology. Little is known about genetic alterations in PN pathogenesis, especially relating to somatic events which are often implicated in inflammatory conditions. We thus performed whole-exome sequencing on 54 lesional and nonlesional skin biopsies from 17 PN patients and 10 atopic dermatitis (AD) patients for comparison. Somatic mutational analysis revealed that PN lesional skin harbors pervasive somatic mutations in fibrotic, neurotropic, and cancer-associated genes. Nonsynonymous mutations were most frequent inNOTCH1and the Notch signaling pathway, a regulator of cellular proliferation and tissue fibrosis, andNOTCH1mutations were absent in AD. Somatic copy-number analysis, combined with expression data, showed that recurrently deleted and downregulated genes in PN lesional skin are associated with axonal guidance and extension. Follow-up immunofluorescence validation demonstrated increasedNOTCH1expression in PN lesional skin fibroblasts and increased Notch signaling in PN lesional dermis. Finally, multi-center data revealed a significantly increased risk ofNOTCH1-associated diseases in PN patients. In characterizing the somatic landscape of PN, we uncover novel insights into its pathophysiology and identify a role for dysregulated Notch signaling in PN.
Separate and overlapping mechanisms of statistical regularities and salience processing in the occipital cortex and dorsal attention network
Authors: Beffara Bertrand , Hadj-Bouziane Fadila , Ben Hamed Suliann , Boehler C. Nico , Chelazzi Leonardo , Santandrea Elisa , Macaluso Emiliano
Published: September 2023

Attention selects behaviorally relevant inputs for in-depth processing. Beside the role of traditional signals related to goal-directed and stimulus-driven control, a debate exists regarding the mechanisms governing the effect of statistical regularities on attentional selection, and how these are integrated with other control signals. Using a visuo-spatial search task under fMRI, we tested the joint effects of statistical regularities and stimulus-driven salience. We found that both types of signals modulated occipital activity in a spatially-specific manner. Salience acted primarily by reducing the attention bias towards the target location when associated with irrelevant distractors, while statistical regularities reduced this attention bias when the target was presented at a low probability location, particularly at the lower levels of the visual hierarchy. In addition, we found that both statistical regularities and salience activated the dorsal frontoparietal network. Additional exploratory analyses of functional connectivity revealed that only statistical regularities modulated the inter-regional coupling between the posterior parietal cortex and the occipital cortex. These results show that statistical regularities and salience signals are both spatially represented at the occipital level, but that their integration into attentional processing priorities relies on dissociable brain mechanisms.
Scalable joint non-negative matrix factorisation for paired single cell gene expression and chromatin accessibility data
Authors: Morgans William , Sharrocks Andrew D. , Iqbal Mudassar
Published: September 2023

Single cell multi-modal technologies provide powerful means to simultaneously profile components of the gene regulatory path-ways of individual cells. These are now being employed to study gene regulatory mechanisms in a variety of biological systems. Tailored computational methods for integration and analysis of these data are much-needed with desirable properties in terms of efficiency -to cope with high dimensionality of the data, inter-pretability -for downstream biological discovery and hypothesis generation, and flexibility -to be able to easily incorporate future modalities. Existing methods cover some but not all of the desirable properties for effective integration of these data.

Here we present a highly efficient method, intNMF, for representation and integration of single cell multi-modal data using joint non-negative matrix factorisation which can facilitate discovery of linked regulatory topics in each modality. We provide thorough benchmarking using large publicly available datasets against five popular existing methods. intNMF performs comparably against the current state-of-the-art, and provides advantages in terms of computational efficiency and interpretability of discovered regulatory topics in the original feature space. We illustrate this enhanced interpretability in providing insights into cell state changes associated with Alzheimer’s disease. int-NMF is available as a Python package with extensive documentation and use-cases athttps://github.com/wmorgans/quick_intNMF
Glacier extinction homogenizes functional diversity
Authors: Khelidj Nora , Caccianiga Marco , Cerabolini Bruno E.L. , Tampucci Duccio , Losapio Gianalberto
Published: September 2023

Questions

The disappearance of glaciers threatens biodiversity and the functioning of ecosystems. To date, questions remain about the response of functional diversity to glacier extinction and its potential for adaptation to climate change. How does glacier retreat and extinction affect plant functional diversity? How do mean and variation of plant traits change with glacier retreat and extinction?

Location

Four glacier ecosystems in Italian Alps. Plant communities spanning 0 to ca 5,000 years on average after glacier retreat.

Methods

We quantify how glacier retreat affects functional diversity of plant communities analysing twelve functional traits of 117 plant species across 170 plots. First, we addressed the impact of glacier retreat on functional divergence and functional homogeneity, analysing both trait average and trait variation. Next, we explored how biodiversity (i.e., plant species richness) influenced functional diversity and how glacier retreat affected such relationship. Finally, we explored the effects of glacier retreat on mean and variation of single traits associated to carbon and nitrogen cycling and resource allocation.

Results

Glacier retreat homogenizes functional diversity by reducing trait variation and making communities more functionally similar. While biodiversity positively contributes to trait heterogeneity, glacier retreat erodes the support of species richness to functional diversity. We also show how glacier extinction has medium to large negative effects on the average and variation of key functional traits associated to carbon economy, but small positive effects on leaf nitrogen content.

Conclusions

Our results demonstrate the pervasive impact of glacier extinction on the functioning of plant communities. We stress that functional diversity and trait variation should be the focus of adaptation and mitigation actions.
Context-aware single-cell multiome approach identified cell-type specific lung cancer susceptibility genes
Authors: Long Erping , Yin Jinhu , Shin Ju Hye , Li Yuyan , Kane Alexander , Patel Harsh , Luong Thong , Xia Jun , Han Younghun , Byun Jinyoung , Zhang Tongwu , Zhao Wei , Landi Maria Teresa , Rothman Nathaniel , Lan Qing , Chang Yoon Soo , Yu Fulong , Amos Christopher , Shi Jianxin , Lee Jin Gu , Kim Eun Young , Choi Jiyeon
Published: September 2023

Genome-wide association studies (GWAS) identified over fifty loci associated with lung cancer risk. However, the genetic mechanisms and target genes underlying these loci are largely unknown, as most risk-associated-variants might regulate gene expression in a context-specific manner. Here, we generated a barcode-shared transcriptome and chromatin accessibility map of 117,911 human lung cells from age/sex-matched ever- and never-smokers to profile context-specific gene regulation. Accessible chromatin peak detection identified cell-type-specific candidatecis-regulatory elements (cCREs) from each lung cell type. Colocalization of lung cancer candidate causal variants (CCVs) with these cCREs prioritized the variants for 68% of the GWAS loci, a subset of which was also supported by transcription factor abundance and footprinting. cCRE colocalization and single-cell based trait relevance score nominated epithelial and immune cells as the main cell groups contributing to lung cancer susceptibility. Notably, cCREs of rare proliferating epithelial cell types, such as AT2-proliferating (0.13%) and basal cells (1.8%), overlapped with CCVs, including those inTERT. A multi-level cCRE-gene linking system identified candidate susceptibility genes from 57% of lung cancer loci, including those not detected in tissue- or cell-line-based approaches. cCRE-gene linkage uncovered that adjacent genes expressed in different cell types are correlated with distinct subsets of coinherited CCVs, includingJAMLandMPZL3at the 11q23.3 locus. Our data revealed the cell types and contexts where the lung cancer susceptibility genes are functional.
The impact of size on middle-ear sound transmission in elephants, the largest terrestrial mammal
Authors: O’Connell-Rodwell Caitlin E. , Berezin Jodie L. , Dharmarajan Anbuselvan , Ravicz Michael E. , Hu Yihan , Guan Xiying , O’Connor Kevin N. , Puria Sunil
Published: September 2023

Elephants have a unique auditory system that is larger than any other terrestrial mammal. To quantify the impact of larger middle ear (ME) structures, we measured 3D ossicular motion and ME sound transmission in cadaveric temporal bones from both African and Asian elephants in response to air-conducted (AC) tonal pressure stimuli presented in the ear canal (PEC). Results were compared to similar measurements in humans. Velocities of the umbo (VU) and stapes (VST) were measured using a 3D laser Doppler vibrometer in the 7–13,000 Hz frequency range, stapes velocity serving as a measure of energy entering the cochlea—a proxy for hearing sensitivity. Below the elephant ME resonance frequency of about 300 Hz, the magnitude of VU/PECwas an order of magnitude greater than in human, and the magnitude of VST/PECwas 5x greater. Phase of VST/PECabove ME resonance indicated that the group delay in elephant was approximately double that of human, which may be related to the unexpectedly high magnitudes at high frequencies. A boost in sound transmission across the incus long process and stapes near 9 kHz was also observed. We discuss factors that contribute to differences in sound transmission between these two large mammals.
ProteinFlow: a Python Library to Pre-Process Protein Structure Data for Deep Learning Applications
Authors: Kozlova Elizaveta , Valentin Arthur , Khadhraoui Aous , Nakhaee-Zadeh Gutierrez Daniel
Published: September 2023

Over the past few years, deep learning tools for protein design have made significant advances in the field of bioengineering, opening up new opportunities for drug discovery, disease prevention or industrial biotechnology. However, despite the growing interest and excitement surrounding these tools, progress in the field is hindered by a lack of standardized datasets for benchmarking. Most models are trained on data from the Protein Data Bank (PDB), the largest repository of experimentally determined biological macromolecular structures. But filtering and processing this data involves many hyperparameter choices that are often not harmonized across the research community. Moreover, the task of splitting protein data into training and validation subsets with minimal data leakage is not trivial and often overlooked. Here we present ProteinFlow, a computational pipeline to pre-process protein sequence and structural data for deep learning applications. The pipeline is fully configurable and allows the extraction of all levels of protein organization (primary to quaternary), allowing end-users to cater the dataset for a multitude of downstream tasks, such as protein sequence design, protein folding modeling or protein-protein interaction prediction. In addition, we curate a feature-rich benchmarking dataset based on the latest annual release of the PDB and a selection of preprocessing parameters that are widely used across the research community. We showcase its utility by benchmarking a state-of-the-art (SOTA) deep learning model for protein sequence design. The open source code is packaged as a python library and can be accessed onhttps://github.com/adaptyvbio/ProteinFlow.
Calorimetric analysis using DNA thermal stability to determine protein concentration
Authors: Eskew Matthew W. , Reardon Patrick W. , Benight Albert S.
Published: September 2023

It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities,Cp,DNAandCp,PROfor equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm’s. For the molecules, in NaCl and CsCl buffer the evaluatedCp,PROandCp,DNAwere equivalent. Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. In all cases, evaluated protein concentrations determined from the DNA standard curve agreed with the UV-Vis concentration for monomeric proteins. For samples of multimeric proteins, streptavidin (tetramer), Herpes Simplex Virus glycoprotein D (trimer/dimer), and a 16 base pair DNA duplex (dimer), evaluated concentrations were greater than determined by UV-Vis by factors of 3.94, 2.65, and 2.15, respectively.