bluuebunny/crossref_metadata_2025 huggingface dataset:
Leveraging Google Earth Engine (GEE) for determining land use and land cover changes around Tasik Chini Malaysia.
Authors: Akhir Nurul Syazna Mat , Salim Pauziyah Mohammad , Yusoff Zaharah Mohd
Published: September 2023

This study explores the capability of Google Earth Engine in determining land use and land cover changes around Tasik Chini Malaysia which is one of the tourism areas severely affected by landscape changes. Two Landsat satellite composite data spanning ten years of difference and Machine Learning Approach algorithm namely Random Forest (RF) and Support Vector machine (SVM) are used to create landuse land cover changes (LULCC) map of the area. GEE is capable of processing time series data as well as performing temporal aggregation. In our case median metrics is used in creating many different alternatives of image composites for creating the LULC map with ease but accurate result. It is an excellent alternative for geospatial and big data analysts for both advance and novice users in processing long term EO dataset especially in dealing with many imageries. The best classification accuracy with the highest Overall Accuracy (OA) is by using Random Forest classifier with 81.58% for the year 2010 and 83.59% for 2020. The Kappa coefficient of both years are 0.75 and 0.78. It is found using this technique, Tasik Chini lost about 6600 hectares of forest area and an increase of bareland and develop area especially around the Tasik Chini lake due to the reported increase of mining activities for the past few years.
Dielectric breakdown and sub-wavelength patterning of monolayer hexagonal boron nitride using femtosecond pulses
Authors: Ahmad Sabeeh Irfan , Dave Arpit , Sarpong Emmanuel , Yao Hsin-Yu , Solomon Joel M , Jiang Jing-Kai , Luo Chih-Wei , Chang Wen-Hao , Her Tsing-Hua
Published: September 2023

Hexagonal boron nitride (hBN) has emerged as a promising two-dimensional (2D) material for many applications in electronics and photonics. Although its linear and nonlinear optical properties have been extensively studied, the interaction of hBN with high-intensity laser pulses, which is important for realizing high-harmonic generation, creating deterministic defects as quantum emitters, and resist-free patterning in this material, has not been investigated. Here we report the first systematic study of dielectric breakdown in chemical vapor deposition (CVD)-grown hBN monolayers induced by single femtosecond laser pulses. We report a breakdown fluence of 0.7 J cm−2, which is at least 7× higher than that of other monolayer 2D materials. A clean removal of hBN without leaving traces behind or causing lateral damage is demonstrated. The ablation features exhibit excellent fidelity with very small edge roughness, which we attribute to its ultrahigh fracture toughness due to its heterogeneous nature with three-fold symmetry. Moreover, even though defects are known to be abundant in CVD-grown hBN, we show experimentally and theoretically that its nonlinear optical breakdown is nearly intrinsic as defects only marginally lower the breakdown threshold. On top of this, we observe that hBN monolayers have a 4–5× lower breakdown threshold than their bulk equivalent. The last two observations can be understood if the carrier generation in monolayers is intrinsically enhanced due to its 2D nature. Finally, we demonstrate laser patterning of array of holes and lines in hBN with sub-wavelength feature sizes. Our work advances the fundamental knowledge of light-hBN interaction in the strong field regime and firmly establishes femtosecond lasers as novel and promising tools for resist-free patterning of hBN monolayers with high fidelity.
Raman study of layered breathing kagome lattice semiconductor Nb3Cl8
Authors: Jeff Dylan A , Gonzalez Favian , Harrison Kamal , Zhao Yuzhou , Fernando Tharindu , Regmi Sabin , Liu Zhaoyu , Gutierrez Humberto R , Neupane Madhab , Yang Jihui , Chu Jiun-Haw , Xu Xiaodong , Cao Ting , Khondaker Saiful I
Published: September 2023

Niobium chloride (Nb3Cl8) is a layered two-dimensional semiconducting material with many exotic properties including a breathing kagome lattice, a topological flat band in its band structure, and a crystal structure that undergoes a structural and magnetic phase transition at temperatures below 90 K. Despite being a remarkable material with fascinating new physics, the understanding of its phonon properties is at its infancy. In this study, we investigate the phonon dynamics of Nb3Cl8 in bulk and few layer flakes using polarized Raman spectroscopy and density-functional theory (DFT) analysis to determine the material’s vibrational modes, as well as their symmetrical representations and atomic displacements. We experimentally resolved 12 phonon modes, five of which are A
1g
modes while the remaining seven are Eg
modes, which is in strong agreement with our DFT calculation. Layer-dependent results suggest that the Raman peak positions are mostly insensitive to changes in layer thickness, while peak intensity and full width at half maximum are affected. Raman measurements as a function of excitation wavelength (473–785 nm) show a significant increase of the peak intensities when using a 473 nm excitation source, suggesting a near resonant condition. Temperature-dependent Raman experiments carried out above and below the transition temperature did not show any change in the symmetries of the phonon modes, suggesting that the structural phase transition is likely from the high temperature P

3
m

ˉ

1 phase to the low-temperature R

3
m

ˉ

phase. Magneto-Raman measurements carried out at 140 and 2 K between −2 and 2 T show that the Raman modes are not magnetically coupled. Overall, our study presented here significantly advances the fundamental understanding of layered Nb3Cl8 material which can be further exploited for future applications.
Rediscovering orbital mechanics with machine learning
Authors: Lemos Pablo , Jeffrey Niall , Cranmer Miles , Ho Shirley , Battaglia Peter
Published: September 2023

We present an approach for using machine learning to automatically discover the governing equations and unknown properties (in this case, masses) of real physical systems from observations. We train a ‘graph neural network’ to simulate the dynamics of our Solar System’s Sun, planets, and large moons from 30 years of trajectory data. We then use symbolic regression to correctly infer an analytical expression for the force law implicitly learned by the neural network, which our results showed is equivalent to Newton’s law of gravitation. The key assumptions our method makes are translational and rotational equivariance, and Newton’s second and third laws of motion. It did not, however, require any assumptions about the masses of planets and moons or physical constants, but nonetheless, they, too, were accurately inferred with our method. Naturally, the classical law of gravitation has been known since Isaac Newton, but our results demonstrate that our method can discover unknown laws and hidden properties from observed data.
Double quantum dots in atomically-precise graphene nanoribbons
Authors: Zhang Jian , Qian Liu , Borin Barin Gabriela , Chen Peipei , Müllen Klaus , Ruffieux Pascal , Fasel Roman , Zhang Jin , Calame Michel , Perrin Mickael L
Published: September 2023

Bottom-up synthesized graphene nanoribbons (GNRs) are precise quantum materials, offering a high degree of tunability of their physical properties. While field-effect transistors and single quantum dot (QD) devices have been reported, the fabrication of double QD devices using GNRs remains challenging due to their nanometer-scale dimensions. In this study, we present a multi-gate double QD device based on atomically precise GNRs that are contacted by a pair of single-walled carbon nanotube electrodes. At low temperatures, the device can be tuned with multiple gates and reveals triangular features characteristic for charge transport through a double QD system. From these features, the QD level spacing, as well as the interdot tunnel coupling and lead-dot tunnel couplings are extracted. Double QD systems serve as essential building blocks for developing different types of qubits based on atomically precise GNRs.
Gut microbiome correlates with plasma lipids in amyotrophic lateral sclerosis
Authors: Guo Kai , Figueroa-Romero Claudia , Noureldein Mohamed H , Murdock Benjamin J , Savelieff Masha G , Hur Junguk , Goutman Stephen A , Feldman Eva L
Published: September 2023

Amyotrophic lateral sclerosis (ALS) is a complex, fatal neurodegenerative disease. Disease pathophysiology is incompletely understood but evidence suggests gut dysbiosis occurs in ALS, linked to impaired gastrointestinal integrity, immune system dysregulation and altered metabolism. Gut microbiome and plasma metabolome have been separately investigated in ALS, but little is known about gut microbe-plasma metabolite correlations, which could identify robust disease biomarkers and potentially shed mechanistic insight. Here, gut microbiome changes were longitudinally profiled in ALS and correlated to plasma metabolome. Gut microbial structure at the phylum level differed in ALS versus control participants, with differential abundance of several distinct genera. Unsupervised clustering of microbe and metabolite levels identified modules, which differed significantly in ALS versus control participants. Network analysis found several prominent amplicon sequence variants strongly linked to a group of metabolites, primarily lipids. Similarly, identifying the features that contributed most to case versus control separation pinpointed several bacteria correlated to metabolites, predominantly lipids. Mendelian randomization indicated possible causality from specific lipids related to fatty acid and acylcarnitine metabolism. Overall, the results suggest ALS cases and controls differ in their gut microbiome, which correlates with plasma metabolites, particularly lipids, through specific genera. These findings have the potential to identify robust disease biomarkers and shed mechanistic insight into ALS.
Description of Cryptococcosis Following SARS-CoV-2 Infection: A Disease Survey Through the Mycosis Study Group Education and Research Consortium (MSG-19)
Authors: Walker Jeremey , McCarty Todd , McGwin Gerald , Ordaya Eloy E , Vergidis Paschalis , Ostrosky-Zeichner Luis , Mammadova Mehriban , Spec Andrej , Rauseo Adriana M , Perfect John , Messina Julia , Vilchez Gabriel , McMullen Rachel , Jones Carolynn T , Pappas Peter G ,   for the Mycoses Study Group Education and Research Consortium (MSGERC) Cryptococcal Registry Cohort, Yetmar Zachary , Masayuki Nigo , Steinbrink Julie , Cahuayme-Zuniga Lizbeth , Vootukuri Shobha , Onyeaghala Chizaram , Ta Tuan V , Kale Pratibha , Franklin Alexander , Gandhi Ravi , Ostrander Darin , Miceli Marisa , Warner Nathaniel , Thomas Lora , Obeid Karam , La Hoz Ricardo M , Sochanska Ada , Klausing Benjamin , El-Herte Rima , Tirmizi Amir , Traver Edward C , Thompson George R , Gorsline Chelsea , Sivasubramanian Geetha , Osborn Rebecca , Mounajjed Mark
Published: September 2023

Background

Invasive fungal infections have been described throughout the COVID-19 pandemic. Cryptococcal disease after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported in several isolated case reports and 1 larger case series. We sought to describe cryptococcal infections following SARS-CoV-2 through establishing a database to investigate underlying risk factors, disease manifestations, and outcomes.

Methods

We created a crowdsourced call for cases solicited through the Mycoses Study Group Education and Research Consortium, the Centers for Disease Control and Prevention Emerging Infectious Diseases Network, and infectious diseases Twitter groups. Data were collected in a web-based and secure REDCap survey without personal identifiers.

Results

Sixty-nine cases were identified and submitted by 29 separate institutional sites. Cryptococcosis was diagnosed a median of 22 days (interquartile range, 9–42 days) after SARS-CoV-2 infection. Mortality among those with available follow-up was 72% (26/36) for the immunocompetent group and 48% (15/31) for the immunocompromised group (likelihood ratio, 4.01; P = .045). We observed a correlation between disease manifestation (central nervous system infection, proven/probable disseminated disease, and respiratory) and mortality (P = .002).

Conclusions

The mortality rate of 59% for patients with cryptococcosis following SARS-CoV-2 is higher than that of modern Cryptococcus cohorts. There was an association between immunocompromised status and cryptococcal disease manifestations as well as mortality. Moreover, our series emphasizes the need for clinical and laboratory assessment of opportunistic infections beyond 30 days when concerning symptoms develop.
Urinary markers of the alternative and lectin complement pathway are increased in IgA vasculitis nephritis
Authors: Marro Julien , Chetwynd Andrew J , Hawkes Jennifer , Northey Sarah J , Oni Louise
Published: September 2023

Background

IgA vasculitis (IgAV) is the most common form of childhood vasculitis. Nephritis (IgAVN) occurs in 50% of patients and 1–2% progress to chronic kidney disease stage 5. The pathophysiology of nephritis remains largely unknown, but recent evidence suggests that the complement system may be involved. The aim of this cross-sectional study was to explore whether there is evidence of alternative and/or lectin complement pathway activation in children with IgAVN.

Methods

Children with IgAV were recruited and grouped according to proteinuria: IgAVN or IgAV without nephritis (IgAVwoN). Age and sex-matched healthy controls (HCs) were also recruited. Cross-sectional urine and plasma concentrations of complement factor D (CFD), factor B (CFB), and MBL-associated protease 1 (MASP-1) were performed using commercially available enzyme-linked immunoassays.

Results

A total of 50 children were included (IgAVN, n = 15; IgAVwoN, n = 20, HCs, n = 15). The mean age was 8.5 ± 3.7 years old, male:female ratio was 1:1. Urinary CFD and CFB concentrations were statistically significantly increased in children with IgAVN (3.5 ± 5.4 μg/mmol; 25.9 ± 26.5 μg/mmol, respectively) compared to both IgAVwoN (0.4 ± 0.4 μg/mmol, P = 0.002; 9.2 ± 11.5 μg/mmol, P = 0.004) and HCs (0.3 ± 0.2 μg/mmol, P < 0.001; 5.1 ± 6.0 μg/mmol, P < 0.001). No statistically significant difference was reported for the plasma concentrations of CFD and CFB. Urinary MASP-1 concentrations were statistically significantly increased in IgAVN (116.9 ± 116.7 ng/mmol) compared to HCs (41.4 ± 56.1 ng/mmol, P = 0.006) and plasma MASP-1 concentrations were increased in IgAVwoN (254.2 ± 23.3 ng/mL) compared to HCs (233.4 ± 6.6 ng/mL, P = 0.046).

Conclusion

There is evidence of complement pathway products in the urine of children with IgAVN that warrants further investigation.
Odor cues rather than personality affect tadpole deposition in a neotropical poison frog
Authors: Peignier Mélissa , Ringler Max , Ringler Eva
Published: September 2023

Animals constantly need to evaluate available external and internal information to make appropriate decisions. Identifying, assessing, and acting on relevant cues in contexts such as mate choice, intra-sexual competition, and parental care is particularly important for optimizing individual reproductive success. Several factors can influence decision-making, such as external environmental cues and the animal’s own internal state, yet, we have limited knowledge on how animals integrate available information. Here, we used an entire island population (57 males, 53 females, and 1,109 tadpoles) of the neotropical brilliant-thighed poison frog Allobates femoralis to investigate how 2 factors (olfactory cues and personality traits) influence the ability of males to find and use new resources for tadpole deposition. We experimentally manipulated the location of tadpole deposition sites and their associated olfactory cues, and repeatedly measured exploration and boldness in adult males. We further reconstructed tadpole deposition choices via inferred parent–offspring relationships of adult frogs and tadpoles deposited in our experimental pools using molecular parentage analysis. We found that the discovery and use of new rearing sites were heavily influenced by olfactory cues; however, we did not find an effect of the measured behavioral traits on resource discovery and use. We conclude that in highly dynamic environments such as tropical rainforests, reliable external cues likely take priority over personality traits, helping individuals to discover and make use of reproductive resources.
Do Students Learn More with an Additional Teacher in the Classroom? Evidence from a Field Experiment
Authors: Haaland Venke Furre , Rege Mari , Solheim Oddny Judith
Published: September 2023

We present a field experiment investigating treatment effects of an additional teacher in the classroom on student learning. The treatment targets literacy instruction during first and second grades. Nearly 6,000 students in 300 classrooms participated in the experiment. The treatment has on average no effects on student learning. However, boys seem to benefit, with treatment impacts of about 0.12 and 0.09 standard deviations on the national literacy assessment and the reading self-concept, respectively. The effects seem to be particularly large for boys with low skills at baseline, with treatment impacts of 0.23 and 0.22 standard deviations.
Implementation and first outcomes of a novel standard operating procedure for preprocedural transoesophageal echocardiography screening in course of atrial arrhythmia ablation
Authors: Dittrich Sebastian , Kece Fehmi , Scheurlen Cornelia , van den Bruck Jan-Hendrik , Filipovic Karlo , Wörmann Jonas , Erlhöfer Susanne , Pavel Friederike , Schipper Jan-Hendrik , Sultan Arian , Lüker Jakob , Steven Daniel
Published: September 2023

Aims

Preprocedural transoesophageal echocardiography (TEE) screening for left atrial (LA) thrombi is the standard of care in many centres performing atrial fibrillation (AF) ablation. However, TEE imposes procedural risks for patients and is often challenging to implement in daily practice, besides causing patient discomfort. At our centre, a novel standard operating procedure (SOP) was implemented, aiming to identify patients that can be exempt from TEE screening. We aimed to assess whether this screening approach may reduce preprocedural TEEs without imposing patients of higher risks for cerebrovascular events (CVEs).

Methods and results

Data of 1874 consecutive patients treated by catheter ablation of LA arrhythmias between 2018 and 2022 were retrospectively analysed. A cohort of 937 patients, where decision to perform TEE screening was based on a new SOP (considering rhythm at admission, CHA2DS2-VASc score, and sufficient anticoagulation), was compared to a matched cohort receiving TEE before every procedure. Number of performed TEEs and incidences of CVEs were compared. Implementation of the new SOP led to a 67% reduction in TEEs performed (old SOP: 933 vs. new SOP: 305). No significant differences between the groups were detected regarding transitory ischaemic attack (old SOP: 5 vs. new SOP: 3; P = 0.48) and stroke (no events). No solid thrombi were detected during TEE screening.

Conclusion

The number of preprocedural screening TEEs before AF ablation procedures can be safely reduced by applying risk stratification based on rhythm at admission and CHA2DS2-VASc score, if anticoagulation was performed properly.
How to ablate the septo-pulmonary bundle: a case-based review of percutaneous ablation strategies to achieve roof line block
Authors: Tonko Johanna Bérénice , Silberbauer John , Mann Ian
Published: September 2023

Electrical conduction through cardiac muscle fibres separated from the main myocardial wall by layers of interposed adipose tissue are notoriously difficult to target by endocardial ablation alone. They are a recognised important cause for procedural failure due to the difficulties of delivering sufficient energy via the endocardial radiofrequency catheter to reach the outer epicardial layer without risking adverse events of the otherwise thin walled atria. Left atrial ablations for atrial fibrillation (AF) and tachycardia are commonly affected by the presence of several epicardial structures, with the septo-pulmonary bundle (SPB), Bachmann’s bundle, and the ligament of Marshall all posing substantial challenges for endocardial procedures. Delivery of a transmural lesion set is essential for sustained pulmonary vein isolation and for conduction block across linear atrial lines which in turn has been described to translate into a reduced AF/atrial tachycardia recurrence rate. To overcome the limitations of endocardial-only approaches, surgical ablation techniques for epicardial or combined hybrid endo-epicardial ablations have been described to successfully target these connections. Yet, these techniques confer an increase in procedure complexity, duration, cost, and morbidity. Alternatively, coronary venous system ethanol ablation has been successfully employed by sub-selecting the vein of Marshall to facilitate mitral isthmus line block, although this approach is naturally limited to this area by the coronary venous anatomy. Increased awareness of the pathophysiological relevance of these epicardial structures and their intracardiac conduction patterns in the era of high-resolution 3D electro-anatomical mapping technology has allowed greater understanding of their contribution to the persistence of AF as well as failure to achieve transmural block by traditional ablation approaches. This might translate into novel catheter ablation strategies with procedural success rates comparable to surgical ‘cut-and-sew’ techniques. This review aims to give an overview of percutaneous catheter ablation strategies to target the SPB, an important cause of failed block across the roof line and isolation of the left atrial posterior wall and/or the pulmonary veins. Existing and investigational technologies will be discussed and an outlook of future approaches provided.
Predicting Covid-19 infection and death rates among E.U. minority populations in the absence of racially disaggregated data through the use of US data comparisons
Authors: Cecchi Dimeglio Paola , Fullilove Robert E , Cecchi Catherine , Cabon Yann , Rosenberg Jessica
Published: September 2023

Background

The E.U.’s lack of racially disaggregated data impedes the formulation of effective interventions, and crises such as Covid-19 may continue to impact minorities more severely. Our predictive model offers insight into the disparate ways in which Covid-19 has likely impacted E.U. minorities and allows for the inference of differences in Covid-19 infection and death rates between E.U. minority and non-minority populations.

Methods

Data covering Covid-19, social determinants of health and minority status were included from 1 March 2020 to 28 February 2021. A systematic comparison of US and E.U. states enabled the projection of Covid-19 infection and death rates for minorities and non-minorities in E.U. states.

Results

The model predicted Covid-19 infection rates with 95–100% accuracy for 23 out of 28 E.U. states. Projections for Covid-19 infection and mortality rates among E.U. minority groups illustrate parallel trends to US rates.

Conclusions

Disparities in Covid-19 infection and death rates by minority status likely exist in patterns similar to those observed in US data. Policy Implications: Collecting data by race/ethnicity in the E.U. would help document health disparities and craft more targeted health interventions and mitigation strategies.
Identification of CryAB as a target of NUAK kinase activity in Drosophila muscle tissue
Authors: Zhao Ziwei , Brooks David , Guo Yungui , Geisbrecht Erika R
Published: September 2023

Phosphorylation reactions performed by protein kinases are one of the most studied post-translational modifications within cells. Much is understood about conserved residues within protein kinase domains that perform catalysis of the phosphotransfer reaction, yet the identity of the target substrates and downstream biological effects vary widely among cells, tissues, and organisms. Here, we characterize key residues essential for NUAK kinase activity in Drosophila melanogaster myogenesis and homeostasis. Creation of a NUAK kinase-dead mutation using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 results in lethality at the embryo to larval transition, while loss of NUAK catalytic function later in development produces aggregation of the chaperone protein αB-crystallin/CryAB in muscle tissue. Yeast 2-hybrid assays demonstrate a physical interaction between NUAK and CryAB. We further show that a phospho-mimetic version of NUAK promotes the phosphorylation of CryAB and this post-translational modification occurs at 2 previously unidentified phosphosites that are conserved in the primary sequence of human CryAB. Mutation of these serine residues in D. melanogaster NUAK abolishes CryAB phosphorylation, thus, proving their necessity at the biochemical level. These studies together highlight the importance of kinase activity regulation and provide a platform to further explore muscle tissue proteostasis.
The Impact of Hearing Impairment on Health Indicators in a Multiethnic Population of Older Adults in Singapore
Authors: Fenwick Eva K , Gupta Preeti , Chan Aurora W D , Man Ryan E K , Aravindhan Amudha , Ng Jia Hui , Cheng Ching-Yu , Wong Tien Y , Chan Angelique , Teo Neville Wei Yang , Sabanayagam Charumathi , Lamoureux Ecosse L
Published: September 2023

Background and Objectives

To determine the impact of hearing impairment (HI) on health indicators in a multiethnic Singaporean population of older adults.

Research Design and Methods

In this cross-sectional, population-based study, pure-tone averages of air-conduction thresholds at 500 Hz, 1,000 Hz, 2,000 Hz, and 4,000 Hz were calculated for each ear. Eight categories of HI were defined ranging from: 1: No HI to 8: Bilateral severe HI. Health indicators included hearing-related quality of life (H-QoL), depressive symptoms, frailty, gait speed, instrumental activities of daily living, sarcopenia, and cognitive impairment. Multivariable regression models determined the independent associations between HI and outcomes.

Results

A total of 2,503 older adults (mean age ± SD 73.4 ± 8.4; 55.2% female participants) were enrolled. Of these, 289 (11.6%), 259 (10.4%), 798 (31.9%), 303 (12.1%), 515 (20.6%), 52 (2.1%), 155 (6.2%), and 115 (4.6%) had hearing levels in Cats 1 to 8, respectively; and 20 (0.8%) used a hearing aid. Compared to those with no HI, participants with unilateral mild HI (Cat 2) had a 107% reduction in H-QoL (β: 0.63; CI: 0.18, 1.09, p = .006), increasing to a 2,816% reduction (β: 16.78; CI: 13.25, 20.31, p < .001) in those with bilateral severe HI-Cat 8 (p-trend < .001). Those with Cat 8 also had lower gait speed and we observed a nonsignificant increase in odds of frailty as HI worsened.

Discussion and Implications

H-QoL is affected across the spectrum of severity and laterality of HI. Interventions to alleviate the effects of HI and provision of QoL support are warranted. Other health indicators were only affected in late stages, suggesting that slowing disease progression is crucial in clinical management.
Tracing titanomagnetite alteration with magnetic measurements at cryogenic temperatures
Authors: Kosterov Andrei , Surovitskii Leonid , Maksimochkin Valerii , Yanson Svetlana , Smirnov Aleksey
Published: September 2023

Titanomagnetite containing up to 0.6–0.7 Ti atoms per formula unit is a primary magnetic mineral phase in submarine basalts and in some terrestrial volcanic rocks. On a geological timescale, it often undergoes alteration, forming new magnetic phases that may acquire (thermo)chemical remanent magnetization. The initial stage of this natural process can be modelled by prolonged laboratory annealing at moderately elevated temperatures. In this study, our goal is to characterize the alteration products resulting from annealing a submarine basalt containing homogeneous titanomagnetite Fe3−xTixO4 (x ≈ 0.46) at temperatures of 355, 500 and 550 °C for up to 375 hr, by examining their magnetic properties over a wide range of temperatures.

The effect of extended annealing is most apparent in the low-temperature magnetic properties. In the fresh sample, a magnetic transition is observed at 58 K. Below the transition temperature, the field-cooled (FC) and zero-field-cooled (ZFC) saturation isothermal remanent magnetization (SIRM) curves are separated by a tell-tale triangular-shaped area, characteristic for titanomagnetites of intermediate composition. The room-temperature SIRM (RT-SIRM) cycle to 1.8 K in zero field has a characteristic concave-up shape and is nearly reversible. For the annealed samples, the magnetic transition temperature shifts to lower temperatures, and the shape of the curves above the transition changes from concave-up to concave-down. The shape of the RT-SIRM cycles also progressively changes with increasing annealing time. The SIRM loss after the cycle increases up to ∼30 per cent for the samples annealed for 375 hr at 355 °C, and for 110 hr at 500 and 550 °C.

The Curie temperatures of the newly formed magnetic phases exceed the Curie temperature of the fresh sample (205 °C) by up to 350 °C. While this effect is most commonly attributed to extensive single-phase oxidation (maghemitization), the behaviour observed at cryogenic temperatures appears incompatible with the known properties of highly oxidized titanomaghemites. Therefore, we propose that, at least in the initial stage of the ‘dry’, that is, not involving hydrothermalism, alteration of titanomagnetite, temperature- and time-controlled cation reordering is the primary mechanism driving changes in both low- and high-temperature magnetic properties.
The Complement System
Authors: Juris Stephen
Published: September 2023

This chapter discusses some of the important components of the innate immune system that act to keep pathogens at bay. It highlights a key component of the innate immune system involving soluble plasma proteins: the complement system. The complement system constitutes a variety of proteins involved in recognizing and tagging foreign molecules and pathogens. The chapter points out how this family of proteins coats the surface of foreign molecules and cells, tagging them to mark them as candidates for destruction by innate immune cells. It explains how the complement system bears a remarkable similarity to the body's blood-clotting system as it involves a cascade of different proteins, each of which must be activated by cleavage via a protease to induce the next step in the process.
Overview of Adaptive Immunity
Authors: Juris Stephen
Published: September 2023

This chapter provides an overview and examines the function of the adaptive immune system, covering how adaptive immune system employs B cells and T cells that specialize in pathogen recognition and destruction. It looks at how circulating B cell and T cell expresses a specific receptor involved in pathogen recognition. Circulating T cells that are activated when their receptors recognize a pathogen function in the cellular arm of our adaptive immune system, and circulating B cells that are activated when their receptors recognize a pathogen function in the humoral arm of our adaptive immune system. The chapter describes elegant mechanisms of genetic recombination that alter the genes of these receptors in a manner that allows them to be expressed during the development of B cells and T cells. It highlights the adaptive immune response that is based on specificity and diversity, which functions by recognizing and combating specific antigens.
Mucosal Immunity
Authors: Juris Stephen
Published: September 2023

This chapter outlines the function of a mucosal tissue, including its role in detecting and combating pathogens that come into contact with mucosal surfaces. It describes the lymphoid tissue associated with mucosal surfaces and explains how it functions in a unique way to activate an immune response. It also compares the mucosal tissue with draining lymphoid tissue and examines the innate and adaptive immune responses employed at mucosal surfaces. The chapter talks about the mucosa-associated lymphoid tissue (MALT) that protects mucosal surfaces and functions as the secondary lymphoid tissue in systemic immunity that minimizes the need for inflammation for antigen delivery. It mentions plasma cells that protect mucosal surfaces and secrete isotype switched antibodies to aid in pathogen neutralization.
Allergies and Hypersensitivity Reactions
Authors: Juris Stephen
Published: September 2023

This chapter explores the various hypersensitivity reactions that can occur, which depend on the immune system's ability to recognize foreign antigens through the action of cellular receptors. It looks at the various types of hypersensitivity reactions and describes how these responses are identical to the ways in which the body reacts to foreign pathogens. It also reviews the four types of hypersensitivity reactions which differ based on the immune response: Type I, Type II, Type III, and Type IV. The chapter points out that Type I hypersensitivity reactions are driven by allergen recognition by IgE bound to granulocytes, while Type II hypersensitivity reactions are driven by the action of soluble immunoglobulins. Type III hypersensitivity reactions are caused by inefficient clearance of soluble antigens bound as small immune complexes in the bloodstream, while Type IV hypersensitivity is an induction of the cellular arm of the adaptive immune response.
Programming Basics and Applications to Bioinformatics
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter covers the fundamentals of programming using the Python programming language, a popular language for bioinformatics. With a basic understanding of biology, probability, and computer science, the chapter emphasizes that biologists become better users of bioinformatics tools and computer scientists become better developers of bioinformatics tools. The chapter then unravels how data flows through a program through variables. It also demonstrates the data types of Python including integers, floating point numbers, strings, lists, tuples and dictionaries. The chapter then shifts to unfold the creation of useful Python data structures such as a two-dimensional matrix (a list of lists in Python). It also investigates how program execution is controlled by if-tests and loops which use relational and logical operators. Finally, the chapter highlights the use of functions and modules in hierarchical design. It then studies how to develop a Kyte-Doolittle sliding window tool using Python.
Developing a Bioinformatics Tool
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter guides through the development of a pairwise sequence alignment tool that implements global, ends-free global, and local alignment. It focuses on the algorithms needed to implement the tool. However, because Python is a commonly used programming language for bioinformatics, the chapter encourages you to apply the Python concepts to implement your pairwise sequence alignment tool. The chapter begins by analysing the output report of an existing local sequence alignment tool, EMBOSS Water, to familiarize ourselves with its inputs, outputs, and functionality. It then looks at an overview of simple pairwise alignment (SPA), and introduces the concept of algorithms–taking a look at different ways to express algorithms. Towards the end, the chapter explains the longest common subsequence (LCS) algorithm and how it can be extended to implement local and global pairwise alignment. It then assesses the complexity of algorithms–that is, how much memory and time they require.
Protein Structure Prediction
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter concentrates on protein structure prediction programs. It provides strong foundational knowledge of protein structures and the Protein Data Bank. The chapter reviews how secondary and tertiary structures of proteins are experimentally determined and how bioinformatics programs can be used to visualize these structures. However, the structures of many proteins, especially those associated with membranes, are difficult to elucidate through experiments. The chapter then introduces bioinformatics software programs that predict the structures of such proteins. Such predictions can often be verified through biochemical experiments. Finally, the chapter looks at how threading is used to predict tertiary structures and how threading differs from homology modelling.
Nucleic Acids
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter analyses the nucleic acids DNA and RNA, which are polynucleotides that encode the genetic information used to construct and maintain living organisms. Double-stranded DNA is, in effect, the blueprint used to direct cell processes. The chapter highlights how cells convert DNA’s operating instructions into the nucleotide sequence of single-stranded RNA molecules. It outlines RNAs’ numerous functions, which include polypeptide synthesis, the regulation of gene expression, and protection from foreign nucleic acids introduced by viral infections. Investigations of nucleic acid structure and function, now almost 70 years old, have given humans a previously unimagined understanding of biological processes and a powerful tool used in such diverse fields as disease diagnosis and treatment and forensic investigations.
The Oceanic Environment
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter explores the oceanic environment. It explains the topography and structure of the ocean floor, and argues that its main features include the continental shelf, continental slope, deep-sea floor, and oceanic ridge systems. Many of the ocean's major features are due to the unique set of chemical and physical properties of water. The chapter also notes that seawater density is controlled mainly by salinity and temperature. It cites that the Coriolis effect increases with increasing latitude while it deflects currents to the right of the wind in the Northern Hemisphere and the left of the wind in the Southern Hemisphere.
Life in a Fluid Medium
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter considers the important properties of water which strongly affect the functioning of marine organisms. Seawater is a fluid that surrounds marine organisms so its motion can be stressful and displace an organism. The very density and other physical properties of water have profound effects on marine organisms, depending on their size and shape and the water velocity conditions. The chapter considers using water motion for biological advantage, which references how the principle of continuity allows the calculation of flow velocity in a biological circulatory system. It also considers the concepts of Reynolds number, turbulence, drag, and Bernoulli's principle.
Reproduction, Dispersal, and Migration
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter discusses the notion of reproduction, dispersal, and migration as fundamental processes that enable living populations to grow and exploit new habitats. It explains that on the one hand dispersal is the undirected movement of an individual to a new place, while on the other hand, migration involves directed movement between specific places. The adaptive value of sex is the maintenance of genetic diversity, which increases adaptability to disease and other challenges. Meanwhile, nonsexual reproduction permits the same genetic type to increase rapidly in an open environment. The chapter also explains that genetic variation can be used to identify barriers to coastal zone dispersal.
Marine Vertebrates and Other Nekton
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter looks into marine vertebrates and other nekton. It considers the classification of nekton. This ranges between fishes, cephalopods, marine mammals, birds, and reptiles. As they must overcome many ocean currents to swim, most nekton live at high Reynolds numbers, and they have momentum while moving through the water. Moreover, swimming often involves undulatory movements with the aid of paired and single fins. The chapter then discusses the features and characteristics of cephalopods, fish, pinnipeds, cetacea, seabirds, sea otters, and sea turtles. It also considers various feeding strategies that fish exhibit, such as suspension feeding and carnivory.
Polar Marine Biology
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter explores polar marine biology. Polar ecosystems are influenced by strong seasonality, especially of ice cover. Also, a diverse phytoplankton assemblage fuels the polar food webs. Carnivores exert top-down effects, so overfishing of carnivores has had strong effects on polar food webs. The chapter considers the impact of climate change and ocean warming on the organization of polar ecosystems. It examines the food webs and the impact of climate change within Arctic marine systems and Antarctic marine systems. Global climate change is decreasing summer ice cover in the Arctic, so major changes are occurring in sea temperature and the organization of benthic communities.
Fisheries and Food from the Sea
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter notes the function and characteristics of fisheries and food from the sea. It explores prehistoric fishing practices by examining the reports of anthropologists and explorers who have observed aboriginal societies. Fishery populations are renewable resources, so nutrients and energy are fueling their regrowth, despite the exploitation of humans. The life history of a fishery species and the size of the stock must be understood before sensible planning can be done regarding fishery management. The chapter introduces the general principles of mariculture, often known as aquaculture, wherein habitats of some natural populations can be simulated, changed for the convenience of harvest, or enhanced to increase yields.
Endocrine and Neuroendocrine Physiology
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter describes endocrine and neuroendocrine physiology. It highlights how hormones change an animal's physiology and its behaviour. Nerve and endocrine cells often work in tandem to help ensure that all of an animal's tissues function together in an integrated, and often mutually reinforcing, manner. The chapter then details the cellular mechanisms of synthesis, storage, and secretion of two chemical classes of hormones, which are peptides and steroids. It considers the endocrine control of nutrient metabolism in mammals. Additionally, the chapter describes the endocrine controls employed by vertebrates to maintain appropriate body fluid volume and the appropriate concentrations of salts in their body fluids.
Genomics, Proteomics, and Related Approaches to Physiology
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter covers genomics, proteomics, and related approaches to physiology. It defines genomics as the study of the genomes of an organization, which is also inextricably related to advanced methods of information processing. Genomics allows physiologists to adopt a new bottom-up approach to the study of physiological phenomena. The chapter then looks into the differences between top-down and bottom-up approaches to the study of physiology. The chapter also considers screening, profiling, and transcriptomics as research strategies. Moreover, metabolomics features the study of all organic compounds in cells and tissues other than macromolecules coded by the genome.
Introduction
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This introductory chapter provides an overview of the diversity of extant invertebrates living on Earth. It explains how classifications reflect how people view the evolutionary history of life, which consists of evolutionary relationships and phylogenetic history. Classifications are lists of species, ranked in a subordinated fashion that reflects their evolutionary relationships and phylogenetic history. Moreover, marine, freshwater, and terrestrial environments present different kinds of challenges for animals, especially in terms of water balance, excretion, reproduction, support, and locomotion. Significant changes in animal phylogeny primarily revolve around the rapidly expanding field of molecular phylogenetics, new paleontological work and new ultrastructural and embryological studies.
Introduction to the Animal Kingdom
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter looks into the development, life histories, and origin of the animal kingdom. It discusses some fundamental aspects of invertebrate development and life history and the role these fields have played in understanding animal evolution. The patterns of early development are related to the mode of reproduction, the presence or absence of larval stages in the life cycle, and the ecology of the adult. Thus, molecular biology had a massive impact on the study of development, animal phylogenetics and evolution. The chapter then expounds on the relationships between ontogeny and phylogeny and the origin of the metazoan condition, multicellularity, and bilateral condition.
Gnathifera
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter examines the spiralian protostome clade Gnathifera. Gnathifera includes the four phyla of Gnathostomulida, Rotifera, Micrognathozoa, and Chaetognatha. Despite the small size of many gnathostomulids, rotifers, and micrognathozoans, gnathiferans show a remarkable complexity of anatomy, especially in their jaw structures. Moreover, the composition of the jaws, built of translucent rods with an electron-dense core, and the jaws having pincers caudally articulating into unpaired pedicles, are unifying features of the clade. Gnathostomulids and chaetognaths are strictly marine while micrognathozoans and most rotifers inhabit fresh waters. The chapter then expounds on the differences and characteristics of gnathostomulids, chaetognaths, micrognathozoan, and rotifers.
The Lophophorates
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter covers the phyla. These possess a unique feeding structure called a lophophore, and these are Phoronida, Bryozoa, and Brachiopoda. The primary unifying feature of the Lophophorata was the lophophore itself, a ciliated tentacular feeding structure, and the associated epistome. Studies of molecular phylogenetics highlight how the three lophophorate phyla are allied with spiralian protostome, and aspects of their development have deuterostome-like characteristics that are likely secondarily derived or have been reinterpreted. The chapter then considers the long and torturous taxonomic history of the lophophorates. It looks at the lophophorate body plan, referencing how all lophophorates are built for benthic life and suspension feeding.
Introduction to Ecdysozoa
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter focuses on the large protostome clade Ecdysozoa. Unlike the Spiralia, Ecdysozoa can be defined by clear morphological synapomorphies, including their three-layered cuticle that is moulted, a process regulated by ecdysteroid hormones. Ecdysozoa contains eight phyla, which are commonly organized into three subclades: Scalidophora, Nematoida, and Panarthropoda. The chapter then discusses the characteristics of Phyla Kinorhyncha, Priapula, and Loricifera under the clade Scalidophora while also sharing visual figures to illustrate the body plans of the clade's respective members. It mentions the likely focus of embryology, genomics, and relationships among scalidophoran and the other ecdysozoan phyla for future research on Scalidophora.