bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Snow Cover on Spring Vegetation Phenology Vary With Temperature Gradient Across the Pan‐Arctic
Authors: Wu Youlv , Xiao Pengfeng , Zhang Xueliang , Liu Hao , Dong Yuanbiao , Feng Lian
Published: March 2023

Extensive and complex changes in spring vegetation phenology have occurred in the Pan‐Arctic over the last several decades. However, the role of snow cover at the start of the growing season (SOS) under different climatic conditions remains unclear. Therefore, we compare the effects of four snow indicators on SOS from 1982 to 2015 based on long‐term remote sensing data and found that snow cover end date (SCED) is the main snow indicator affecting SOS, with SOS advancing 0.56 days for each 1‐day advance in SCED, explaining 12%–90% of SOS variability in 63% of the Pan‐Arctic region. The results also demonstrate that SCED is the dominant factor on SOS in 13% of the Pan‐Arctic region and the effects of SCED on SOS vary with temperature gradient rather than precipitation gradient. In cold areas, the positive effect of SCED on SOS diminished with increasing temperature, while in warm areas, the positive effect of SCED on SOS increased with increasing temperature. As the climate warms, the impact of SCED on SOS is expected to weaken in cold areas and increase in warm areas. The findings have crucial implications for understanding future vegetation phenological responses to climate change across the Pan‐Arctic.
Theoretical insights into the defect performance of the wide bandgap semiconductor BaS
Authors: Chen Yu , Fan S. W. , Gao G. Y.
Published: March 2023

In WBGSM BaS, the high density of electrons can be obtained by means of the Liint defects.
In situ and real-time vibrational spectroscopic characterizations of the photodegradation of nitrite in the presence of methanediol
Authors: Cheng Chiao-Mi , Lu Cheng-Zong , Hou Chun-Yao , Jhao Yuan-Jyun , Lai Yi-Fen , Chen I-Chia , Chuang Yi-Hsueh , Chu Li-Kang
Published: March 2023

Nitric oxide (NO) and hydroxyl radical (OH), which are the photolytic products of nitrite, have potential for use in the oxidation of the dissolved formaldehyde, methanediol (CH2(OH)2), which is regarded as the precursor of atmospheric formic acid.
Ergodesign and composite materials
Authors: Terekhova N. , Kumashkova A. , Dyukov M.
Published: March 2023

This article is devoted to the study of the relationship between materials and ergodesign with various attributes. Examples of experimental research demonstrating the possibilities of using materials, along with other design and ergonomics tools, are given. The article describes the history of the development of Russian design and ergonomics as stages of the creation of the theory and methodology of ergodesign. The trends of formation and new developments in this area are considered. It is concluded that the creation of new objects of the subject world and systems cannot be carried out without integrated design activities with the introduction of the achievements of ergodesign, which is an innovative technology of integrated design. The article also responds to the problem, because of which the concept of ergodesign was adopted, namely the rapid development of technology without taking into account the needs and characteristics of a person. The urgency of the research is due to the rapid development of technologies that impose new requirements on various design products. This also applies to materials that are the basis of any material form, and from the point of view of innovative design, they must have unique properties, ensuring high-quality human activity at a new higher level.
Simulation of energetic composite materials combustion
Authors: Dimitrienko Yu. , Zakharov A. , Koryakov M.
Published: March 2023

A numerical approach to simulate the evolution of the combustion surface of an energetic composite materials is described. Cubic spline interpolation is used to describe the dynamically changing shape of the combustion surface. The statement of the interpolation problem for the parametric description of the geometry and the problem of choosing the method for parameterizing the control points are given. The direct step-bystep method is used to calculate the combustion front. The normal velocity of the combustion surface is variable and is determined from the solution of an additional gas dynamics problem. The basic formulae for calculating the combustion rate of a solid propellant that consists of a particle-reinforced energetic composition are given. Examples of combustion simulation of a laboratory-scale structure for three values of the initial geometry parameters are presented.
Detection of fault zone head waves and the fault interface imaging in the Xianshuihe–Anninghe Fault zone (Eastern Tibetan Plateau)
Authors: Wang Longtan , Zhou Yijian , Zhou Shiyong , Zhang Hao
Published: March 2023

Fault zone head waves (FZHWs) are an essential diagnostic signal that provides high-resolution imaging of fault interface properties at seismogenic depth. In this study, we validate the existence of a bi-material interface in the Xianshuihe–Anninghe Fault (XAF) zone around their intersection and determine the cross-fault velocity contrast. We employ a semi-automatic workflow to detect and pick FZHWs and direct P waves. In addition, to improve the identification ability of potential FZHWs in the automatic picking process, we adopt a ‘forward-detecting and backward-picking’ strategy combining the short-term average/long-term average (STA/LTA) algorithm with a kurtosis detector. The polarization and characteristic periods of the waveforms are then used to manually refine the picks and evaluate the quality. The results indicate that the average velocity contrast along the southern Xianshuihe Fault is 3–5 per cent, with the northeast side characterizing a faster P-wave velocity, in agreement with tomographic results. A systematic moveout between FZHWs and the direct P waves over a 100 km long fault segment reveals a single continuous interface in the seismogenic zone. The single bi-material fault structure might be conducive to the preparation of large earthquakes and further influences the corresponding dynamic rupture processes.
Tilting and Silting Theory of Noetherian Algebras
Authors: Kimura Yuta
Published: March 2023

We develop silting theory of a Noetherian algebra $\Lambda $ over a commutative Noetherian ring $R$. We study mutation theory of $2$-term silting complexes of $\Lambda $, and as a consequence, we see that mutation exists. As in the case of finite-dimensional algebras, functorially finite torsion classes of $\Lambda $ bijectively correspond to silting $\Lambda $-modules, if $R$ is complete local. We show a reduction theorem of $2$-term silting complexes of $\Lambda $, and by using this theorem, we study torsion classes of the module category of $\Lambda $. When $R$ has Krull dimension one, we describe the set of torsion classes of $\Lambda $ explicitly by using the set of torsion classes of finite-dimensional algebras.
Estimated mortality with early empirical antibiotic coverage of methicillin-resistant Staphylococcus aureus in hospitalized patients with bacterial infections: a systematic review and meta-analysis
Authors: Carey George B , Holleck Jürgen L , Ein Alshaeba Samer , Jayakrishnan Ritujith , Gordon Kirsha S , Grimshaw Alyssa A , Gunderson Craig G
Published: March 2023

Objectives

We performed a systematic review and meta-analysis to estimate the effect of early active empirical antibiotics for MRSA on mortality, both in patients admitted with MRSA infections and in patients admitted with common infectious syndromes, for whom the causative pathogen may not have been MRSA.

Methods

A systematic literature search was conducted using Embase, MEDLINE, PubMed, Web of Science, Cochrane, Scopus and Google Scholar from the earliest entry through to 26 April 2022. We included studies of patients hospitalized with culture-proven MRSA infections that compared mortality rates depending on whether patients received active empirical antibiotics. The primary outcome was the adjusted OR for mortality with early active empirical antibiotics. After performing random-effects meta-analysis, we estimated the absolute risk reduction in mortality with initial empirical MRSA coverage for common infectious syndromes based on the prevalence of MRSA and baseline mortality rate for each syndrome, as reported in the medical literature.

Results

Of an initial 2136 unique manuscripts, 37 studies (11 661 participants) met our inclusion criteria. Fifteen studies (6066 participants) reported adjusted OR of mortality. The pooled adjusted OR for mortality was 0.64 (95% CI, 0.48–0.84), favouring active empirical antibiotics. The estimated absolute mortality benefit was 0% for patients with pneumonia, 0.1% (95% CI, 0.04–0.2) for non-critically ill patients with soft tissue infections, 0.04% (95% CI, 0.01–0.05) for non-critically ill patients with urinary tract infections, 0.6% (95% CI, 0.2–1.0) for patients with septic shock, and 1.0% (95% CI, 0.3–1.4) for patients with catheter-related infections admitted to ICUs.

Conclusions

For the three most common infections in the hospital, the absolute benefit on mortality of empirical antibiotics against MRSA is 0.1% or less. Meaningful benefit of empirical antimicrobials against MRSA is limited to patients with approximately 30% mortality and 10% prevalence of MRSA. Avoiding empirical antibiotics against MRSA for low-risk infections would substantially reduce the use of anti-MRSA therapy.
I’m Suffocating
Authors: Bell Daniel
Published: March 2023

Dyspnea is an uncomfortable abnormal awareness of breathing and hails as one of the most frightening sensations for patients to experience and one that is distressing to not only the patient but families, lay caregivers and professional caregivers. Whether in the context of known life-threatening illness, benign illness, or undifferentiated illness, dyspnea has a significant impact on well-being and deserves prompt efforts at alleviation. Dyspnea may be acute or chronic and can have a significant negative impact on quality of life and well-being in serious illness. Given the many mechanisms of dyspnea, applying a multimodal approach involving pharmacological, nonpharmacological, and mechanical therapeutic options can prove synergistic to both disease-modifying care and symptomatic relief.
All Stopped Up
Authors: Brachman Laura
Published: March 2023

There are a number of palliative devices and therapies employed in advanced illness to alleviate symptoms and improve quality of life. The decision to use these devices is inextricably related to goals of care (GOC). These goals are usually met when the devices work well. However, if a complication arises, the patient may present to the emergency department. While a simple intervention may allow the patient to return home with the device intact, on occasion a revisiting of GOC and whether they are being met may be indicated. This chapter will present a road map for evaluating how to proceed in the face of malfunction of a number of devices commonly used in palliative care. Sometimes a straightforward intervention will allow the patient to return home on the same path, while other times, particularly if goals are not being met, a different way forward must be considered.
Endotracheal Tube Selection
Authors: Horvath Balazs , Kloesel Benjamin
Published: March 2023

Endotracheal tube selection not only is determined by several factors that are related to the developmental stage of the pediatric patient, but also is influenced by both coexisting pathology and the type of the planned intervention. As the understanding of the pediatric airway anatomy changed, cuffed endotracheal tubes were introduced to a much younger patient population, including neonates. However, it has remained important to select the right size tube for age and airway anatomy, and specialized high-volume/low-pressure cuffed endotracheal tubes must be considered for pediatric patients. This chapter reviews the fundamentals of proper endotracheal tube selection for neonates, infants, and children.
Warming Devices
Authors: Brzozowski Eric , Ohliger Shelley
Published: March 2023

Temperature monitoring and regulation are necessary for any general or regional anesthetic lasting longer than 30 minutes to avoid perioperative hypothermia. This chapter discusses methods of heat transfer and warming devices that are frequently used by anesthesia providers to improve temperature control, specifically in the pediatric patient. Commonly used methods of temperature regulation include insulation, forced air warmers, radiant warmers, intravenous fluid warmers, water mattresses, airway heating and humidification, and cardiopulmonary bypass. The risks, benefits, and efficiency of various warming devices are discussed. By the end of this chapter, anesthesia providers will have a better understanding of mechanisms used to regulate temperature in the perioperative setting.
Agents, Techniques, and Mapleson Circuits
Authors: Sinton Jamie W.
Published: March 2023

Children have very elastic blood vessels, higher body water content, shorter stature, and therefore lower blood pressure due to the effects of scaling. The hemodynamic effects of inhaled, intravenous, and awake spinal anesthetics are examined. Children often undergo induction of general anesthesia via inhalation with sevoflurane. However, some populations of children either require or benefit from total intravenous anesthesia (TIVA), either entirely or thereafter. This chapter explains some details regarding differences in hemodynamic effect and the side-effect profile for inhaled anesthetic versus TIVA. Next, anesthetic drug effects are discussed in the context of how they differ from effects in adults.
Otolaryngology
Authors: Ford Timothy , Abd-Elsayed Alaa
Published: March 2023

Pediatric otolaryngology procedures constitute a diverse set of procedures, each with different degrees of invasiveness and special anesthetic considerations. Patients undergoing otolaryngologic surgery can have potentially life-threatening upper airway obstruction or have severe pulmonary insufficiency requiring diagnostic or therapeutic procedures. Even in patients without life-threatening pathology, common to the majority of these surgical procedures is their proximity to the airway, requiring the pediatric anesthesiologist to develop strategic approaches to mitigate the risk of perioperative airway complications.
Neurosurgery
Authors: Latin Itamar , Rubin Kasia
Published: March 2023

Children undergoing pediatric neurosurgical procedures require specific evaluation of the complex disease pathologies leading up to the procedure in addition to the standard process utilized for any complex surgery, including airway evaluation, laboratory panels, birth history, family history, and NPO (nothing by mouth, fasting) status. The preoperative evaluation for a craniotomy must bear in mind why the cranial vault needs entering. The acuity of symptom onset and extent of symptoms is of primary concern. Both craniotomy and hydrocephaly assessment include the need for examination of the intracranial pressure. Intraoperative management for pediatric neurosurgical cases is based on the underlying pathology and understanding of these processes. Postoperative care goals are similar to the adult population, maintaining neurologic stability as much as possible while providing appropriate analgesia and hemodynamic stability.
Thoracic Surgery
Authors: Lazar Alina
Published: March 2023

Lung isolation is challenging in children. It is usually accomplished by advancing the endotracheal tube into the nonsurgical mainstem bronchus or using a bronchial blocker or double-lumen tumen, the latter being reserved for older children. Common complications of single-lung ventilation are hypoxia, hypercarbia, loss of lung isolation, and airway obstruction. The management of postoperative pain in patients with pectus excavatum undergoing a Nuss procedure is difficult. Various anesthetic techniques have been used, including multimodal analgesia and regional blocks. Anterior mediastinal tumors can cause severe airway and vascular compression, which are exacerbated by general anesthesia, particularly in children. Tumor biopsy using a local anesthetic technique is preferable, if possible. General anesthesia should be undertaken only after a thorough preoperative assessment. Maintenance of spontaneous respiration during anesthesia, airway stenting with a rigid bronchoscope, and changing the patient’s position in case of cardiopulmonary decompensation are important elements of anesthesia planning.
Pediatric Sedation
Authors: Rubin Kasia
Published: March 2023

Sedation allows a child to be more relaxed during a medical procedure and will likely not have any memories of the procedure. Painful procedures require analgesia as well. Common procedures for which pediatric patients request sedation include cardiac catheterization, interventional or diagnostic radiology, dental procedures, gastroendoscopy, and short painful procedures, including dressing changes or other wound care. There are different levels of sedation that may allow a child to be conscious and relaxed or asleep, but maintain a patent airway. Sedation of children is often different from that of adults, as a child’s ability to control his or her own behavior is very different from of an adult, and an increased depth of sedation is necessary to complete a procedure. Most critically, children quickly pass from an intended level of sedation to a deeper level, increasing the possibility of oversedation.
Dystocia, Malposition, and Malpresentation
Authors: Feinstein Diana , Miele Daniella
Published: March 2023

Malposition, malpresentation, and shoulder dystocia are complications affecting the delivery of a fetus. A spontaneous vaginal delivery ideally occurs with the fetus in a head-down and flexed position and the occiput anterior. This position is beneficial as it minimizes the fetal head diameter and puts the body in an optimal position to pass through the maternal pelvis. Deviation from this positioning complicates the delivery. Fetal malposition describes a rotated fetus and increases maternal and fetal complications. Malpresentation is a noncephalic or nonvertex fetal position. Breech position is the most common malpresentation, and most often leads to a cesarean section delivery. A shoulder dystocia is an obstetrical emergency and increases the risk of fetal and maternal morbidity.
Trial of Labor After Cesarean Delivery
Authors: Al-Jindi Piotr , Hussain Nasir
Published: March 2023

Trial of labor after a previous cesarean (TOLAC) delivery is proposed to meet patients’ needs and decrease maternal mortality compared with repeated cesarean section. TOLAC provides an option for the delivering mother to experience a vaginal delivery. However, this risk is higher if the TOLAC fails, and cesarean section is required after the TOLAC. TOLAC carries around a 1% risk of uterine rupture. The most sensitive sign of uterine rupture is fetal bradycardia, detected by fetal heart tone monitoring. Epidural analgesia does not delay the diagnosis of uterine rupture. Uterine rupture is an obstetric emergency, and efforts should concentrate on resuscitation while the patient is prepared for emergency laparotomy.
Chemical and Biological Warfare
Authors: Horoszczak Cassian , Watt Stacey
Published: March 2023

Chemical and biological warfare agents pose as major health threats in not only modern warfare, but also their potential use in domestic terrorism. Chemical warfare agents can be categorized into toxic agents (which includes nerve agents and cyanide salts), incapacitating agents, and incendiary/burn-causing agents. Nerve agents function as anticholinesterase inhibitors, causing a cholinergic toxidrome, which is treated with atropine and pralidoxime following exposure. Cyanide inactivates cytochrome oxidase, resulting in cellular anoxia and is treated with a first-line combination of sodium thiosulfate and hydroxocobalamin. The Centers for Disease Control and Prevention categorizes bioagents with the potential for bioterrorism use into three categories. Category A includes high-priority agents that pose a risk to national security; these include anthrax, botulism, plague, smallpox, tularemia, and viral hemorrhagic fever. Categories B and C include mid-to-lower priority agents with potential for major health impacts.
Organ Donors and Procurement
Authors: Gyorfi Michael J. , Abd-Elsayed Alaa
Published: March 2023

Organ donation can be broken down by the type of donor. The majority of organs are procured after neurologic death (brain death). Organs can also be donated after circulatory death and even from living donors. Each method of donation has various physiologic derangements and challenges that must be overcome to preserve the organ for a successful donation. The need for organs vastly outnumbers the available organs for donation. Standardized criteria for donation and management have been shown to increase the quality and the number of suitable grafts. Communication between the surgical team and anesthesiologist is paramount for optimizing organ survival.
Medication Errors
Authors: Hanna Joseph Salama , Saad Ramsey
Published: March 2023

Adverse drug events (ADEs) comprise the largest single category of adverse events experienced by hospitalized patients, accounting for about 19% of all injuries. At least a quarter of all medication-related injuries are preventable. Preventable ADEs include errors made by the clinician and systematic errors. The occurrence of ADEs is associated with increased morbidity and mortality, prolonged hospitalizations, and higher costs of care. A medication error is any mistake in the intended use of a medication (e.g., wrong medication, wrong dose, or infusion of the wrong medication into the wrong place, as with a connection error). The perioperative period is a high-risk setting for such errors. This chapter reviews the basic definitions of medication errors as well as methods used for detection and prevention.
Crisis Management and Teamwork
Authors: Lagrew Mollie K. , Giordano Christopher
Published: March 2023

Anesthesiology was the first medical specialty to adopt and apply the concept of crisis resource management (CRM), modeled after the aviation industry, with the goal of increasing patient safety by reducing human error. A paradigm shift in education from a focus on technical skills toward incorporating what are now known as nontechnical skills (NTSs) occurred over 30 years ago, equipping anesthesiologists with the necessary tools to handle complex situations. Much of the groundbreaking work for CRM and NTSs in anesthesia was introduced by Gaba and colleagues and further developed by Salas, who explored team cognition and team training requirements that could also be extended to improve healthcare systems. This chapter focuses on some of those foundational tools that can be implemented to improve crisis management and teamwork.
Six Sigma and Lean Operations for the Anesthesiologist
Authors: Curcuru Caitlin N. , Kurian Dinesh J.
Published: March 2023

As specialists in perioperative management, anesthesiologists have a unique set of skills to drive quality improvement in healthcare. Two complementary methods that have been used to improve many aspects of healthcare are Six Sigma and Lean. Using a five-phase approach to identify and control sources of variation, Six Sigma operates on the principle that inadequacies in system processes stem from undesirable variation. Six Sigma aims to identify and correct undesired process variation. Lean methodology’s operating principle is that waste is commonly used to cover up process problems. By focusing on eliminating waste, problems can be uncovered and corrected. Lean focuses on eight such sources of waste. Each methodology has a slightly different focus on how to achieve quality improvement. Lean and Six Sigma can be used to direct interventions to improve healthcare delivery, quality, and efficiency.
Barriers to Quality Improvement
Authors: Saad Ramsey , Hanna Joseph Salama
Published: March 2023

Quality improvement has contributed to safety in the operating room over the past few decades. Changes to safety have come from developing fail-safe equipment, advances in engineering, process improvement to minimize the chance of human error, and improvement in communication. Change is not an easy process. This applies to quality improvement as well. Change is a process that involves a change in the culture and team effort on behalf of the entire institution. Barriers may be related to provider, patient, or institutional factors. Quality improvement is a continuous process, and there yet remains to be room for improvement. This chapter outlines the most common challenges to improvement and suggestions to overcome these challenges.
Federal Regulatory Requirements and Quality Payment Programs
Authors: Saad Ramsey , Hanna Joseph Salama
Published: March 2023

The field of anesthesiology has advanced significantly over the past few decades. This has been partly due to various quality improvement measures adopted by various institutions and on a national level as well. There has been a nationwide trend to adjust payments based on quality metrics. This applies to anesthesia as well. The two most common quality payment programs are the Merit-Based Incentive Payment System (MIPS) and an alternative payment model (APM). The anesthesiologist ideally should be familiar with the different payment programs as there may be a direct financial impact related to the metrics. This chapter outlines the different quality payment programs and how these can affect providers in the field of anesthesiology.
Skin cancers
Authors: Ajithkumar Thankamma
Published: March 2023

Radiotherapy has an established role in the management of non-melanoma skin cancers. Radiotherapy alone is curative in early-stage disease basal cell and squamous cell carcinoma, whereas it is used in combination with surgery in patients with advanced disease. In early-stage disease, the choice between radiotherapy and surgery depends on careful consideration of cosmetic and functional outcomes and patient preference. This chapter discusses the features of different types of skin cancers, the role of radiotherapy, and practical details on radiotherapy planning. It also summarizes the evidence underpinning current clinical practice. The radiotherapeutic management of Kaposi’s sarcoma, cutaneous angiosarcoma, and keloid is also discussed.
Gynaecological cancers
Authors: Ajithkumar Thankamma
Published: March 2023

Radiotherapy has an established role in the curative, adjuvant, and palliative treatment of cervical cancer. Definitive chemo-radiotherapy is curative in 70-75% of patients with stage IIB and 30-50% of patients with stage III cervical cancer. While surgery is the primary treatment of choice for endometrial cancer, selected patients are considered for adjuvant radiotherapy and a group of patients with medically inoperable early-stage disease are considered for primary radiotherapy. This chapter discusses the clinical and imaging features of different gynaecological cancers, the role of radiotherapy for tumours arising in different sites, and practical details on radiotherapy planning. It also summarizes the evidence underpinning current clinical practice.
Sarcomas
Authors: Ajithkumar Thankamma
Published: March 2023

Sarcomas, which comprise less than 1% of malignant tumours, are heterogeneous cancers with different biology and characteristic genetic abnormalities. The common subtypes of soft tissue sarcoma are leiomyosarcoma, liposarcoma, synovial sarcoma, rhabdomyosarcoma, fibrosarcoma, and malignant peripheral nerve sheath tumours whereas the common types bone sarcomas are Ewing’s sarcoma, osteosarcoma and chondrosarcoma. Radiotherapy has an established role in the management of adult soft-tissue sarcomas, and Ewing’s sarcoma. In other histological subtypes, the role of radiotherapy is individualized. This chapter discusses the clinical and imaging features of different sarcomas, the role of radiotherapy, and practical details on radiotherapy planning. It also summarizes the evidence underpinning current clinical practice.
Neural and behavioural dynamics of the individual and collective self(s)
Authors: Huepe David , Canales-Johnson Andrés , Rivera-Rei Álvaro , Ibanez Agustín , Bekinschtein Tristan A.
Published: March 2023

Usually considered as internal representations of self-concepts, the individual-self and the collective-self have been primarily studied in social and personality psychology while the experimental and theoretical advances of the cognitive and neurophysiological mechanisms of these self-representations are poorly understood. Two competing hypotheses emerge to understand their structure: first, each self-representation corresponds to a specific and independent dimension of self-concept and is therefore conceptualized as separate cognitive components and different brain networks are predicted; and second, both “selfs”, collective and individual, are part of the same structure and interdependent, sharing similar networks and showing a hierarchical organization from a core-self. Both perspectives have some support from current theories in social psychology but are still speculative and faintly supported by empirical evidence. To test this, we designed an experiment using sentences that would activate the individual or collective-self representations in 80 healthy right-handed participants. We use reaction times during a decision-making task, in combination with individualism/collectivism scales and characterize the neural dynamics throughout the experiment using event-related potentials and fronto-parietal informational connectivity networks. Participants reacted slower to the collective than individual self conditions and showed differences in neural activity and information Integration level that distinguished between each type of self. More importantly, the neural integration measure representing the core-self (subtraction between individual and collective wSMI) was only associated with the individualism scores but not collectivism, lending further support for the core-self perspective. We interpret that the collective self, in the broader sense, is a part of the self-concept and therefore probably assembled from the core-self.
An integrative framework for circular RNA quantitative trait locus discovery with application in human T cells
Authors: Nguyen Dat Thanh
Published: March 2023

Molecular quantitative trait locus (QTL) mapping of genetic variants with intermediate molecular phenotypes has proven to be a powerful approach for prioritizing genetic regulatory variants and causal genes identified by Genome-wide association studies (GWAS). Recently, this success has been extended to circular RNA (circRNA), a potential group of RNAs that can serve as markers for the diagnosis, prognosis, or therapeutic targets of cancer, cardiovascular, and autoimmune diseases. However, the detection of circRNA QTL (circQTL) currently is heavily reliant on a single circRNA detection algorithm for circRNA annotation and quantification which implies limitations in both sensitivity and specificity. In this study, we show that circQTL results produced by different circRNA calling tools are extremely divergent, making difficulties in interpretation. To resolve this issue, we develop an integrative method for circQTL mapping and implement it as an automated, reproducible, and scalable, and easy-to-use framework based on Nextflow, named cscQTL. Compared to the existing approach, the new method effectively identify circQTLs with an increase of 20-100% circQTLs detected and recovered all circQTLs that are highly supported by the single method approach. We apply the new method to a dataset of human T cells and discover genetic variants that control the expression of 55 circRNAs. By collocation analysis, we further identify circBACH2 and circYY1AP1 as potential candidates for immune disease regulation. cscQTL is freely available at:https://github.com/datngu/cscQTL.
Atmospheric transport of particulate matter and particulate-bound agrochemicals from beef cattle feedlots: human health implications for downwind agricultural communities
Authors: Emert Amanda D. , Green Frank B. , Griffis-Kyle Kerry , Smith Philip N.
Published: March 2023

Background

Beef cattle feedlot-derived particulate matter (PM) is a complex mixture of dust, animal waste, agrochemicals, and bioaerosols. No empirical data currently exists quantifying human exposure of PM-bound agrochemicals downwind of feedlots.

Objectives

There were three objectives of the current study: 1) to determine spatial extent and magnitude of PM transport downwind of large beef cattle feedlot facilities, 2) to quantify occurrence of pyrethroid insecticides and anthelmintics in feedlot-derived PM, and 3) to assess cumulative human health risk of agrochemicals in agriculture-adjacent communities downwind of feedlots.

Methods

Authors investigated downwind transport (<1 to >12 km) of total suspended particulates (TSP) from three feedlots in the Southern Great Plains (SGP) of North America. PM collected on TSP filters was analyzed via UHPLC-MS/MS for six pyrethroids (bifenthrin, λ-cyhalothrin, cypermethrin, esfenvalerate, fenvalerate, and permethrin) and five macrocyclic lactones (MLs; abamectin, doramectin, eprinomectin, ivermectin, and moxidectin). An empirical distance decay model was used to determine probabilistic PM concentrations in downwind ambient air.

Results

Downwind TSP concentrations exhibited rapid decline from 0.01 - ≤1.6 km (Monte Carlo-simulated mean ± SEM; 5,049 ± 96.1 µg/m3) and subsequent stabilization >1.6 – 12.4 km (1,791 ± 9.9; µg/m3). TSP concentrations did not converge to background levels within the spatial extent of the study (12.4 km). Agrochemicals were detected downwind >LOQ at greater overall frequency (40.6%) than upwind locations (26.8%). Two pyrethroids were detected at the highest overall downwind concentrations (mean ± SEM; fenvalerate = 5.9 ± 0.8, permethrin = 1.1 ± 0.3 ng/m3), and screening-level cumulative exposure estimates indicate elevated pyrethroid risk (LOC = 1; RI = 0.173) in children (1-2 yrs) living near commercial agricultural operations in the SGP.

Discussion

Results significantly expand the known distribution of feedlot-derived PM and agrochemicals, and consequently highlight exposure pathways unrecognized in residential human health assessments and feedlot risk evaluations.
Home-Cage Sipper Devices Reveal Age and Sex Differences in Ethanol Consumption Patterns
Authors: Rice RC , Baratta AM , Farris SP
Published: March 2023

Free-choice paradigms such as two-bottle choice (2BC) are commonly used to characterize ethanol consumption and preference of rodent models used to study alcohol use disorder (AUD). However, these assays are limited by low temporal resolution that misses finer patterns of drinking behavior, including circadian drinking patterns that are known to vary with age and sex and are affected in AUD pathogenesis. Modern, cost-effective tools are becoming widely available that could elucidate these patterns, including open-source, Arduino-based home-cage sipper devices. We hypothesized that adaptation of these home-cage sipper devices would uncover distinct age- and sex-related differences in temporal drinking patterns. To test this hypothesis, we used the sipper devices in a continuous 2BC paradigm using water and ethanol (10%; v/v) for 14 days to measure drinking patterns of male and female adolescent (3-week), young adult (6-week), and mature adult (18-week) C57BL/6J mice. Daily grams of fluid consumption were manually recorded at the beginning of the dark cycle, while home-cage sipper devices continuously recorded the number of sips. Consistent with prior studies, females consumed more ethanol than males, and adolescent mice consumed the most out of any age group. Correlation analyses of manually recorded fluid consumption versus home-cage sipper activity revealed a statistically significant prediction of fluid consumption across all experimental groups. Sipper activity was able to capture subtle circadian differences between experimental groups, as well as distinct individual variation in drinking behavior among animals. Blood ethanol concentrations were significantly correlated with sipper data, suggesting that home-cage sipper devices can accurately determine individual timing of ethanol consumption. Overall, our studies show that augmenting the 2BC drinking paradigm with automated home-cage sipper devices can accurately measure ethanol consumption across sexes and age groups, revealing individual differences and temporal patterns of ethanol drinking behavior. Future studies utilizing these home-cage sipper devices will further dissect circadian patterns for age and sex relevant to the pathogenesis of AUD, as well as underlying molecular mechanisms for patterns in ethanol consumption.

Highlights

Female mice consume more ethanol than males in a continuous access paradigm

Adolescent male and female mice consume more ethanol than young or mature adult mice

Automated home-cage sipper devices accurately measure ethanol consumption

Devices reveal sex- and age-dependent differences in circadian drinking patterns

Devices reveal distinct individual variation in circadian drinking patterns
The immune receptor SNC1 monitors helper NLRs targeted by a bacterial effector
Authors: Wang Ming-Yu , Chen Jun-Bin , Wu Rui , Guo Hai-Long , Chen Yan , Li Zhen-Ju , Wei Lu-Yang , Liu Chuang , He Sheng-Feng , Du Mei-Da , Guo Ya-long , Peng You-Liang , Jones Jonathan DG , Weigel Detlef , Huang Jian-Hua , Zhu Wang-Sheng
Published: March 2023

Plants deploy intracellular receptors to counteract pathogen effectors that suppress cell-surface receptor-mediated immunity. To what extent pathogens manipulate also immunity mediated by intracellular receptors, and how plants tackle such manipulation, remains unknown.Arabidopsis thalianaencodes three very similar ADR1 class helper NLRs (ADR1, ADR1-L1 and ADR1-L2), which play key roles in plant immunity initiated by intracellular receptors. Here, we report thatPseudomonas syringaeAvrPtoB, an effector with E3 ligase activity, can suppress ADR1-L1- and ADR1-L2-mediated cell death. ADR1, however, evades such suppression by diversification of two ubiquitination sites targeted by AvrPtoB. The intracellular sensor NLR SNC1 interacts with and guards the CCRdomains of ADR1-L1 and ADR-L2. Removal of ADR1-L1 and ADR1-L2 or delivery of AvrPtoB activates SNC1, which then signals through ADR1 to trigger immunity. Our work not only uncovers the long sought-after physiological function of SNC1 in pathogen defense, but also that reveals how plants can use dual strategies, sequence diversification and a multiple layered guard-guardee system, to counteract pathogen attack on core immunity functions.
Past, present and future in the geographical distribution of Mexican tepezmaite cycads: genusCeratozamia
Authors: Gómez-Díaz Jorge Antonio , Carvajal-Hernández César Isidro , Dáttilo Wesley
Published: March 2023

Ceratozamia morettii,C. brevifronsandC. tenuisare cycads considered endangered in montane forests in the center of Veracruz state. However, the amount of theoretical and empirical information available on the historical distribution of these species and how they could be affected in the future by the effects of climate change is still limited. Our objective was to generate information on the spatial distribution of the species since the last glacial maximum, present and future. To map the spatial distribution of species, we created a potential distribution model for each species. The spatial data used for the models included 19 bioclimatic data variables in the present, at the last glacial maximum using two models (CCSM4 and MIROC), and in the future (2080) using two models of the RCP 8.5 scenario of climate change (HadGEM2-CC and MIROC5). We found that each species occupies a unique ecoregion and climatic niche.Ceratozamia morettiiandC.tenuishave a similar pattern with an expansion of their distribution area since the last glacial maximum with the larger distribution area in the present, and with a projected reduction in their distribution under future climatic conditions. ForC. brevifrons,we also showed an increase in their distributional area since the last glacial maximum and we showed that this expansion will continue under future climatic conditions when the species will reach its maximum distributional area. Projections about the future of these endemic cycad species show changes in their habitat highlighting that temperate zone species will face imminent extinction if no effort is made to protect them. On the other hand, the tropical climate species will apparently be favored.
Egr-2 coordinates intestinal remodeling by promoting midline patterning and pharynx regeneration in planarians
Authors: Morkotinis Vasileios , Forsthoefel David J.
Published: March 2023

Regeneration requires remodeling of pre-existing structures and their integration with new cells and tissue. Identification of injury-induced regulators of these processes is central to regenerative biology. In planarian flatworms, the intestine remodels after amputation to re-establish normal morphology and integrate with the regenerating pharynx, the centrally located feeding organ. How these events are initiated and coordinated is currently unclear. In a candidate screen for injury-induced regulators of intestinal regeneration, we found that the transcription factor Early growth response protein 2 (Egr-2) was required for collective migration and fusion of intestinal branches at the anterior midline. Even though inhibition ofegr-2by RNA interference increased dorsoventral (DV) muscle fibers at the midline between intestinal branches, bulk RNA sequencing of regenerating tissue revealed negligible dysregulation of DV-, body wall-, or intestinal-muscle-associated transcripts. Instead, the midline polarity cueslit-1and subsets of pharynx-associated transcripts were dysregulated. Bothegr-2andslit-1RNAi delayed early pharynx regeneration, consistent with reducedslit-1expression inegr-2(RNAi)regenerates in the region of pharynx specification. Furthermore, inhibition of pharynx regeneration regulatorsfoxF-1andfoxAdelayed integration with the intestine and disrupted formation of the intestine’s midline anterior branch.Our findings suggest that the pharynx plays an inductive role in initiation of intestinal remodeling, and demonstrate how injury-induced reprogramming influences subsequent tissue assembly and integration during regeneration.
Identifying environmental factors affecting the production of pea aphid dispersal morphs in field populations
Authors: Bosch Michael J , Ives Anthony R
Published: March 2023

Many species of insects show phenotypically plastic dispersal traits in response to suboptimal environmental conditions. These polyphenetic traits can have large impacts on the population dynamics of the dispersing insects. Therefore, it is important to understand what environmental factors affect the development of dispersal traits and how these factors affect population dynamics via immigration/emigration.

Pea aphids (Acyrthosiphon pisum) exhibit a polyphenetic wing dimorphism in which individuals are either winged (alate) or not (apterous). The production of alate offspring is determined by environmental cues experienced by the mother. Environmental factors associated with these cues have been intensively studied, with crowding, host plant quality, natural enemies, and fungal infection being shown to affect the production of pea aphid alates under controlled laboratory conditions. Nonetheless, environmental factors affecting alate production have rarely been studied in field populations of pea aphids.

Using data from a three-year study of alate production in 5-9 alfalfa (lucerne) fields, we examined the effects of (i) pea aphid abundance, (ii) host plant maturity, (iii) temperature, (iv) predator and herbivore abundance, (v) parasitism, and (vi) entomopathic fungal incidence. In twice-weekly samples taken over the growing season, alate production ranged from 0 to 83% of the nymphal population.

Pea aphid abundance, temperature, and alfalfa maturity together explained 67% of the variation in alate production. The other factors we investigated explained little variation. These results suggest there is a limited number of key environmental factors that consistently predict changes in alate production in field populations, while many factors identified in lab studies may be unimportant. Our results highlight the value of investigating factors affecting the expression of plastic traits in insect species at a broad spatiotemporal scale and under natural conditions.
Epitranscriptome analysis of NAD-capped RNA by spike-in-based normalization
Authors: Li Dean , Ge Shuwen , Liu Yandong , Pan Miaomiao , Wang Xueting , Han Guojing , Zou Sili , Liu Rui , Niu Kongyan , Zhao Chao , Liu Nan , Qu Lefeng
Published: March 2023

The hub metabolite, nicotinamide adenine dinucleotide (NAD), can be used as an initiating nucleotide in RNA transcription to result in NAD-capped RNA (NAD-RNA). NAD-RNA that intimately connects metabolite with gene expression can be developed as novel biomarkers for aging and disease. Epitranscriptome-wide profiling of NAD-RNAs involves chemo-enzymatic labeling and affinity-based enrichment; yet currently available computational analysis cannot adequately remove variations associated with capture procedures. Here, we propose a spike-in-based normalization and data-driven evaluation framework, enONE, for the omic-level analysis of NAD-capped RNAs. We demonstrate that carefully designed spike-in RNAs, together with modular normalization procedures and evaluation metrics, can lead to the optimal normalization that maximally removes unwanted variations, empowering quantitative and comparative assessment of NAD-RNAs from different datasets. Using enONE and a human aging cohort, we reveal critical features of NAD-capped RNAs that occur with normal age. enONE facilitates the discovery of NAD-capped RNAs that are responsive to physiological changes, laying a critical foundation for functional investigations into this modification.
Model-based concept to extract heart beat-to-beat variations beyond respiratory arrhythmia and baroreflex
Authors: Baranauskas Mindaugas , Stanikūnas Rytis , Kaniušas Eugenijus , Lukoševičius Arūnas
Published: March 2023

Heart rate (HR) and its variability (HRV) reflect the autonomous nervous system (ANS) modulation, especially sympathovagal balance. This work aims to present concept of a personalizable HR model and an in silico system to identify the HR regulation parameters and subsequently capture residual heart beat-to-beat variations from individual psychophysiological recordings in humans. The model encompasses respiratory sinus arrhythmia (RSA) and baroreflex mechanisms, and uses respiration and blood pressure signals and the time instances of R peaks from an electrocardiogram as inputs. The system extracts the residual displacements of the modeled R peaks relative to the real R peaks. Three components – tonic, spontaneous, and 0.1 Hz changes – can be derived from these R peak residual displacements and can, therefore, enhance HRV analysis beyond RSA and baroreflex. Our model-based concept suggests that these residuals are not merely modeling errors. The proposed method could help to investigate additional neural regulation impulses from the higher-order brain and other influences.