bluuebunny/crossref_metadata_2025 huggingface dataset:
Beach erosion: Threat and adaptation measures of communities in the Tun Mustapha Park (TMP), Sabah, Malaysia
Authors: Saleh E , Jolis G , Osman N F , Sentian J , Joseph J , Jomitol J , Adin N
Published: November 2022

Beach erosion is among the main phenomena affecting small islands in the Coral Triangle region, particularly in the Tun Mustapha Park (TMP), Malaysia. This study was done to investigate the level of beach erosion and to determine the adaptation measures for the coastal communities to beach erosion. Field trips were carried out in May and July 2017 at seven islands (Banggi, Tiga, Balambangan, Malawali, Molleangan, Tigabu and Mandidarah) of TMP. Semi-structured interviews were conducted with 50 respondents who were the coastal inhabitants of the islands, to gain local knowledge about island beach erosion. Results indicate that beach erosion occurred during the peak of monsoon seasons and extreme events. Wind-induced high waves during the end of the year (northeast monsoon) eroded beaches, damaged houses, fishing structures and uprooted trees. Six of the islands are affected by beach erosion, whereas Mandarah island is experiencing accretion. Karakit beach is the only study site protected by seawall and beach revetment. The identified coastal adaptations to beach erosion were traditional shoreline protection by piling dead corals, sand sacks and woods on the beaches, modification and improvement to damaged building structures. Some local communities opted to move further inland and relocate to other islands or mainland Sabah to avoid the impacts of erosion. This study emphasizes the value of local knowledge shared by the coastal communities which can be incorporated with scientific baseline data for improved sustainable coastal development, protection, and management of the marine protected area.
Debris flow susceptibility analysis using a bivariate statistical analysis in the Panataran River, Kg Melangkap, Sabah, Malaysia
Authors: Sharir Kamilia , Lai Goh Thian , Simon Norbert , Ern Lee Khai , Madran Eldawaty , Roslee Rodeano
Published: November 2022

This study area is part of the Kadamaian watershed and is located on the North-West flank of Mount Kinabalu, composed of sedimentary rock from the Crocker Formation and the Mt. Kinabalu granitic pluton. Many loose seismic materials were found on the slopes during the 2015 Sabah Earthquake with a moment magnitude of 6.0. These materials later served as the source material for rainfall-induced debris flows or shallow landslides. The community closest to the Panataran river in the Kg Melangkap area is the most affected. Therefore, the objective of this study is to study the debris flow susceptibility analysis using a bivariate statistical analysis approach, namely the Frequency Ratio (FR) model. Forty-eight landslides were identified using remote sensing interpretation. Characteristics of the research area, such as slope gradient, elevation, slope aspect, lithology, slope curvature, and topographic wetness index, were selected as the factors to evaluate the debris flow susceptibility analysis. The correlations between these factors and the occurrence of landslides were established, and the results were assessed and validated based on those results. Validation findings demonstrate that this technique provides high accuracy, with an AUC of 81.8 for success rate. As a result, it can be stated that this model accurately predicted landslide susceptibility in the research area, and that it can help local authority with future land-use planning, as well as give tools for hazard mitigation.
Development of an additive fabricated biped mechanical system
Authors: Dugăeşescu Ileana , Pârvu Gabriela-Marina , Enache Vlad-Cristian
Published: November 2022

The use of mechatronic components and the incorporation of additive manufacturing into the process of product development have grown in popularity over the past several years. The goal of the research conducted in this paper is to develop a prototype of a monomobile biped mechanical system and to optimize the printing parameters for the additive manufacturing stage. This paper presents the modelling of the components of a biped mechanical system and the simulation of their operation. The modelling step is followed by setting the printing parameters in the dedicated Z-Suite software and creating the G-code for the Zortrax M300 Plus additive manufacturing equipment. Lastly, the paper presents the connection of the sensors to the Plusivo board, the mounting procedure to the 3D printed parts that make up the biped mechanical system as well as the operation methodology of the sensors. The resulting prototype is then used to monitor parameters specific to the sensors used.
Simulation of the hydraulic steering device, for a nose landing gear
Authors: Nicolin B. A. , Nicolin I.
Published: November 2022

The hydraulic steering simulation is done with SIMULINK, part of the MathWorks MATLAB® application. All parts, subassemblies, and assemblies that define the nose landing gear (NLG) and nose wheel steering are fully defined in 3D, with CATIA V5 - a computer-aided design software used for modeling, it is possible to carry out simulations that allow preliminary evaluation, theoretically and experimentally. The purpose of this simulation is to confirm the correctness of the steering gear kinematics, that the two hydraulic cylinders have been sized correctly and can overcome the resistive steering moment, and that the steering time complies with design specifications for the nose landing gear of a military training aircraft.
Properties of photo-curable polyurethane resins used in SLA manufacturing
Authors: Băilă D.I. , Tonoiu S.
Published: November 2022

Stereolithography (SLA) is the oldest additive manufacturing technology, and it is a 3D printing technology used to create industrial concept models, rapid prototypes or different parts with complex geometries in a very short time. By SLA technology, it is possible to manufacture parts with extremely high feature resolutions and quality surface finishes, using a wide selection of materials. SLA 3D printing is frequently used for manufacture: the parts requiring high accuracy and features as small as 0.07 mm, smooth surfaces with good rugosities and form and fit testing. In this article were presented the mechanical properties of the photo-curable polyurethane resins used in SLA technology, the SEM analysis and for establish the composition contain, it was used the ATR-FTIR analysis. In conclusion, new photo-curable polyurethane resins, used in SLA technology, allow the creation of parts with a high degree of accuracy, with good mechanical properties, which can be used both in industry and in medicine domain.
The influence of the cooling conditions and inclination of surfaces obtained by 3D printing on the roughness parameters
Authors: Hriţuc Adelina , Mihalache Andrei Marius , Slătineanu Laurenţiu , Dodun Oana , Nagîţ Gheorghe , Rîpanu Marius Ionuţ
Published: November 2022

A characteristic of the evolution of manufacturing processes in recent years is the expansion of technologies based on additive manufacturing, especially in the case of parts made of plastic materials. One of the accessible processes for making plastic parts is fused filament fabrication. In many situations, when using fused filament fabrication, it is necessary to obtain surfaces characterized by certain values of roughness parameters. Several factors can influence surface roughness. Some of these factors consider the materialization conditions of the 3D printing process. Starting from the hypothesis that the cooling conditions and the surface position can influence the roughness parameters values, experimental tests were carried out by modifying the values of the two factors. The experimental results were mathematically processed, and power function type mathematical models were determined for the roughness parameters Rz, Rt, Rp, Ra, Rq, Rc. These models provide information on the direction of action, the intensity of the influence exerted by the cooling conditions, and the angle of inclination of the test sample surface on the values of the mentioned roughness parameters.
Experimental studies on turning process, using the Prime turning processing strategy, proposed by Sandvik Coromant
Authors: Popan I. A. , Balc N. , Popan A. I. , Cerciu A.
Published: November 2022

CNC turning process is a common machining process in the industrial application. The requirement on turning process is to increase the productivity and cost reductions. The paper presents preliminary research of the turning process optimization by using the Prime Turning strategy, proposed by the Sandvik Coromant company. Using a CNC turning machine, parts with complex surfaces were manufactured and two process strategies were compared. The first machining strategy is conventional roughing and finishing in the longitudinal direction and the second is the strategy developed by Sandvik company, called Prime Turning. The experimental results show that by using the Prime turning strategy and tools the productivity can be increased, with lower power consumption.
Spectra-assisted laser focusing in quantitative analysis of laser-induced breakdown spectroscopy for copper alloys
Authors: LI Shoujie , ZHENG Ronger , DEGUCHI Yoshihiro , YE Wangquan , TIAN Ye , GUO Jinjia , LI Ying , LU Yuan
Published: November 2022

Laser-induced breakdown spectroscopy (LIBS) is a capable technique for elementary analysis, while LIBS quantitation is still under development. In quantitation, precise laser focusing plays an important role because it ensures the distance between the laser and samples. In the present work, we employed spectral intensity as a direct way to assist laser focusing in LIBS quantitation for copper alloys. It is found that both the air emission and the copper line could be used to determine the position of the sample surface by referencing the intensity maximum. Nevertheless, the fine quantitation was only realized at the position where the air emission (e.g. O (I) 777.4 nm) reached intensity maximum, and also in this way, a repeatable quantitation was successfully achieved even after 120 days. The results suggested that the LIBS quantitation was highly dependent on the focusing position of the laser, and spectra-assisted focusing could be a simple way to find the identical condition for different samples’ detection. In the future, this method might be applicable in field measurements for LIBS analysis of solids.
Attraction ofMyzus persicae(Hemiptera: Aphididae) to Volatiles Emitted From the Entomopathogenic FungusBeauveria bassiana
Authors: Geedi Ruchika , Canas Luis , Reding Michael E , Ranger Christopher M
Published: November 2022

Beauveria bassiana (Balsamo) Vuillemin infects a wide variety of insects, including the green peach aphid, Myzus persicae (Sulzer). Volatiles emitted from B. bassiana can act as semiochemical attractants or repellents, with most responses reported to date resulting in insects avoiding B. bassiana. Since insects can detect ‘enemy-specific volatile compounds’, we hypothesized the preference behavior of M. persicae would be influenced by volatile emissions from B. bassiana. We conducted Petri dish and Y-tube olfactometer bioassays to characterize the preference of M. persicae to B. bassiana strain GHA. During Petri dish bioassays, more apterous and alate M. persicae were recorded in the vicinity of agar colonized by B. bassiana compared to agar, or Fusarium proliferatum (Matsushima) Nirenberg and Ambrosiella grosmanniae Mayers, McNew, & Harrington as representatives of nonentomopathogenic fungi. Petri dish bioassays also determined that apterous and alate M. persicae preferred filter paper saturated with 1 × 107, 1 × 106, and 1 × 105B. bassiana conidia/ml compared to Tween 80. Y-tube bioassays documented that more apterous and alate M. persicae oriented upwind to volatiles from B. bassiana mycelia compared to agar. Apterous and alate Myzus persicae were also preferentially attracted to 1 × 107 and 1 × 106B. bassiana conidia/ml compared to Tween-80 during Y-tube bioassays. These results complement a previous finding that the mosquito Anopheles stephensi (Diptera: Culicidae) Liston is attracted to volatiles from B. bassiana. Future studies aimed at characterizing the olfactory mechanism leading to the attraction of M. persicae to B. bassiana could aid in optimizing lure-and-kill strategies.
The Nirenberg Problem on Half Spheres: A Bubbling-off Analysis
Authors: Ahmedou Mohameden , Ben Ayed Mohamed
Published: November 2022

In this paper, we perform a refined blow-up analysis of finite energy approximated solutions to a Nirenberg-type problem on half spheres. The latter consists of prescribing, under minimal boundary conditions, the scalar curvature to be a given function. In particular, we give a precise location of blow-up points and blow-up rates. Such an analysis shows that the blow-up picture of the Nirenberg problem on half spheres is far more complicated that in the case of closed spheres. Indeed, besides the combination of interior and boundary blow ups, there are nonsimple blow-up points for subcritical solutions having zero or nonzero weak limit. The formation of such nonsimple blowups is governed by a vortex problem, unveiling an unexpected connection with Euler equations in fluid dynamic and mean fields type equations in mathematical physics.
On the Equations of Poizat and Liénard
Authors: Freitag James , Jaoui Rémi , Marker David , Nagloo Joel
Published: November 2022

We study the structure of the solution sets in universal differential fields of certain differential equations of order two, the Poizat equations, which are particular cases of Liénard equations. We give a necessary and sufficient condition for strong minimality for equations in this class and a complete classification of the algebraic relations for solutions of strongly minimal Poizat equations. We also give an analysis of the non-strongly minimal cases as well as applications concerning the Liouvillian and Pfaffian solutions of some Liénard equations.
A Phase 1 pharmacokinetic study of a single-dose bioadhesive clindamycin 2% gel for bacterial vaginosis
Authors: Mauck Christine K , Atiee George J , McCulloh Jennifer , Reynolds Laurie , Zack Nadene , Friend David R
Published: November 2022

Objectives

To evaluate pharmacokinetics (PK) of a single dose of an investigational 2% clindamycin phosphate vaginal gel in healthy women by assessment of plasma and vaginal clindamycin concentrations over 7 days, and assess safety.

Methods

Single-centre, Phase 1, single-dose PK study. Blood and vaginal samples were collected daily and safety was evaluated through to Day 7.

Results

Twenty-one subjects were enrolled; 20 completed the study. Plasma clindamycin concentrations demonstrated quantifiable values in all subjects through to 24 h post-dose, remaining above the limits of quantification (LOQ) through to 48 h for the majority of subjects. Systemic exposure (AUC0–t) was 1179 (range 62–3822) h·ng/mL. Arithmetic mean AUC0–24 was 818 (range 51–3287) h·ng/mL. Vaginal clindamycin phosphate levels were relatively high 24 h following administration in 15/21 subjects (6 subjects had values >400 µg/g and 9 had values of 100–400 µg/g). The levels dropped in most participants to below the LOQ 2 days following dosing. In a few participants, levels remained elevated for several days. Maximal amounts of vaginal clindamycin occurred on Day 2 with a mean value of 30.3 µg. One treatment-emergent adverse event (TEAE) of moderate-severity headache not related to study drug was reported and resolved on Day 1. No TEAEs were related to physical examinations, pelvic examinations, laboratory values or vital signs.

Conclusions

The vaginal concentrations of clindamycin phosphate plus the clindamycin plasma profile over time are consistent with release of drug from the investigational gel over 24 to 72 h. A single dose was well tolerated.
Retrospective study of outcomes of short versus long duration of antibiotic therapy for residual osteomyelitis in surgically resected diabetic foot infection
Authors: Motaganahalli S , Batrouney A , Perera D , Vogrin S , Trubiano J A
Published: November 2022

Introduction

Optimal treatment duration for residual osteomyelitis (OM) post-amputation in diabetic foot infection (DFI) remains unclear, with resultant heterogeneity in prescribing noted in clinical practice. We aimed to identify a difference in outcomes of long duration of antibiotics (LD) with short duration (SD) in patients with culture-positive proximal bone specimen post-amputation.

Methods

In this single-centre retrospective cohort study (Melbourne, Australia), we analysed antibiotic duration of DFI patients requiring amputation with culture-positive proximal bone specimen over a 31 month period (January 2019–September 2021). Primary outcome was reamputation or debridement at the same and/or contiguous site of amputation at 6 months. Secondary outcomes were readmission to hospital and/or recommencement of antibiotics for DFI at the same and/or contiguous site at 6 months.

Results

Among 92 patients (83% male, median age 67 years), 26 received <4 weeks (SD) and 66 received ≥4 weeks (LD) antibiotic therapy. In the SD group, primary outcome occurred in 9 patients (35%) compared with 15 patients (23%) in the LD group (P = 0.246). Both secondary outcomes occurred in 12 patients (46%) in the SD group compared with 18 patients (27%) in the LD group (P = 0.086). Adjusted logistic regression analysis showed SD was not significantly associated with primary outcome [OR 1.12 (95% CI 0.38–3.31)] or secondary outcomes [OR 1.67 (95% CI 0.60–4.66)].

Conclusions

This single-centre experience did not demonstrate significant difference in outcomes between antibiotic duration of <4 weeks and ≥4 weeks in DFI patients with culture-positive proximal bone specimen post-amputation. These data provide background for larger international randomized control trials to establish optimal treatment duration.
Effects of lowering dietary protein content without or with increased protein-bound and feed-grade amino acids supply on growth performance, body composition, metabolism, and acute-phase protein of finishing pigs under daily cyclic heat stress
Authors: José Karpeggiane de Oliveira Marllon , Diego Brandão Melo Antonio , Alves Marçal Danilo , Alves da Cunha Valini Graziela , Alisson Silva Cleslei , Mari Veira Alini , Zem Fraga Alícia , Righetti Arnaut Pedro , Henrique Reis Furtado Campos Paulo , Sousa dos Santos Luan , Khun Kyaw Htoo John , Gastmann Brand Henrique , Hauschild Luciano
Published: November 2022

This study investigated the effects of a low-protein diet with or without an increase in dietary protein and feed-grade amino acids (AAs) on the growth performance, body composition, metabolism, and serum acute-phase proteins of finishing pigs reared in thermoneutrality or cyclic heat stress conditions. A total of 90 gilts (67.7 ± 6.2 kg) were distributed in a 2 × 3 factorial arrangement (two ambient temperatures and three diets). Ambient temperatures (AT) were thermoneutral (TN, 22 °C for 24 h) and cyclic heat stress (CHS, 12 h to 35 °C and 12 h to 22 °C). The evaluated diets (D) were high crude protein (HP); low CP-free AA-supplemented diets (LPAAs); low CP-free AA-supplemented diets and digestible Lys level (+20%), and Lys:AA ratios above recommendations (LPAA+). The experimental period lasted 48 d (two experimental phases: days 0–27 and days 28–48, respectively). CHS pigs had higher skin temperature (P < 0.05) than TN pigs. Pigs in CHS had higher rectal temperature (P < 0.05) than TN pigs until day 38 but similar (P > 0.10) to TN pigs from 38 to 45 d. For the entire experiment, CHS pigs had lower (P < 0.05) final BW, average daily gain and daily feed intake, net energy intake, body lipid, bone mineral, lipid deposition, energy retention, Lys and CP intake, and nitrogen excretion than TN pigs. The level of CP intake impacted nitrogen excretion, nitrogen retention efficiency, and urea as pigs fed HP had the highest values, and pigs fed LPAA had the lowest values (P < 0.05). On day 27, CHS pigs had lower (P < 0.05) free triiodothyronine than TN pigs. LPAA+ pigs had lower (P < 0.05) insulin than LPAA. On day 48, CHS pigs had lower (P < 0.05) thyroxine, albumin, and lactate than TN pigs. On day 27, pigs fed LPAA+ had higher (P < 0.05) lactate than pigs fed HP or LPAA. Both AT and D were enough to stimulate the immune system as CHS pigs had lower (P < 0.05) transferrin and 23-kDa protein levels than TN pigs, and HP pigs had higher haptoglobin than LPAA on day 27. These results confirm the deleterious effects of high AT on performance, body composition, metabolism, and immune system stimulation in finishing pigs. These data also show that a diet with low levels of CP can be provided to pigs in CHS without affecting performance and body composition while reducing nitrogen excretion. However, the use of a diet with an AA level above the requirements obtained by increasing intact protein and free AA did not attenuate the impact of CHS on performance and body composition of pigs.
Removal of an Aminopeptidase N From Midgut Brush Border Does Not Affect Susceptibility of Spodoptera litura (Lepidoptera: Noctuidae) Larvae to Four Insecticidal Proteins of Bacillus thuringiensis (Bacillales: Bacillaceae)
Authors: Wang Can , Deng Zhimin , Yuan Jin , Xu Kexin , Sha Li , Guan Xiong , Huang Zhipeng , Shao Ensi
Published: November 2022

Spodoptera litura is one of the most destructive lepidopteran insects of cabbages and cauliflowers in the world. Cry1 and Vip3 toxins from Bacillus thuringiensis have been reported to show toxicity in multiple lepidopteran insects. Binding of toxic molecules to specific receptors on the midgut epithelial cells is known to be a key step in the action mode of Bt toxins. Aminopeptidase N (APN) -like proteins have been reported to be binding sites of multiple Cry toxins in the midgut of Cry susceptible insects. In the present study, we identified six midgut APNs by analysis of the genome and midgut transcriptome of S. litura. CRISPR/Cas9 mediated gene-knockout system was utilized to mutate the GPI-anchor signal peptide at the C terminus of SlAPN1. SlAPN1 was verified to be removed from the midgut brush border membrane vesicles of a homozygous knockout strain of S. litura (SlAPN1-KO). Bioassay results indicated that susceptibility of the SlAPN1-KO strain to Cry1Aa, Cry1Ac, Cry1Ca, and Vip3Aa toxins was close to that of the wild-type strain of S. litura. RT–qPCR results showed that the transcriptional level of SlAPN2-6 was not up-regulated after knockout of the SlAPN1. Results in this study indicated that the SlAPN1 did not play a critical role in the pathway of toxicity of Cry1Aa, Cry1Ac, Cry1Ca, and Vip3Aa toxins in S. litura.
Multi-institutional phase II study of ultra-hypofractionated whole-breast irradiation after breast-conserving surgery for breast cancer in Japan: Kyoto Radiation Oncology Study Group (UPBEAT study)
Authors: Mitsuyoshi Takamasa , Ono Yuka , Ashida Ryo , Yamashita Mikiko , Tanabe Hiroaki , Takebe Sayaka , Tokiwa Mariko , Suzuki Eiji , Imagumbai Toshiyuki , Yoshimura Michio , Yamauchi Chikako , Mizowaki Takashi , Kokubo Masaki
Published: November 2022

Purpose

The UK-FAST-Forward study showed that ultra-hypofractionated whole-breast irradiation (ultra-HF-WBI) involving five fractions of 26 Gy radiation over 1 week was not inferior to HF-WBI. However, it is not used in Japan due to safety concerns. In April 2022, we commenced a multi-institutional, single-arm, phase II trial. Our aim is to confirm the safety of ultra-HF-WBI after breast-conserving surgery (BCS) for breast cancer in Japanese women.

Method

We plan to enroll 98 patients from 13 institutions. The primary endpoint is the proportion of late adverse events of grades ≥2 within 3 years.

Discussion

We believe that this highly promising clinical study can positively impact the Japanese guidelines for breast cancer treatment. The results will help us decide whether or not ultra-HF-WBI can be used as a more convenient alternative to WBI.

Registration number and date

This trial was registered in the UMIN Clinical Trials Registry (UMIN000047080) on March 4, 2022.
Highlights of Urban Entomology 2021: Chemical, Nonchemical, and Alternative Approaches to Urban Pest Management as We Adapt, Advance, Transform
Authors: Tay Jia-Wei
Published: November 2022

The 2021 annual meeting of the Entomological Society of America with the theme of “Adapt. Advance. Transform” guided the highlight compilation of urban entomology papers. Integrated pest management of urban pests relies on techniques and tools that adapt, advance, and transform over time to develop into new usable tactics and technologies; the review covers the following three themes: first, how science, researchers, and pest management professionals adapt to the changing environments; second, how urban pest management approaches and technologies advance using conventional and alternative strategies; and last, how transformation happens, leading to technological advances and sustainable pest management success. I selected papers on four groups of urban pests—ants, termites, bed bugs, and cockroaches—that were in the context of pest management in this highlights publication. Emphasis was placed on research regarding the efficacy of chemical (e.g., conventional pesticides, insect growth regulators), nonchemical, and alternative approaches (e.g., the use of heat, naturally derived compounds) for urban pests that help improve and implement sustainable pest management plans. These papers demonstrate the achievements of the urban entomology community while emphasizing the current challenges that we face from the far-reaching impact of climate change and insect pest adaptation and what should be prioritized.
Translocations are induced in hematopoietic stem cells after irradiation of fetal mice
Authors: Hamasaki Kanya , Matsumoto Tomoko , Cologne John , Mukai Mayumi , Kodama Yoshiaki , Noda Asao , Nakamura Nori
Published: November 2022

Although mammalian fetuses have been suggested to be sensitive to radiation, an increased frequency of translocations was not observed in blood lymphocytes from atomic bomb (A-bomb) survivors who were exposed to the bomb in utero and examined as adults. Since experiments using hematopoietic cells of mice and rats confirmed this finding, it was hypothesized that either irradiated fetal hematopoietic stem cells (f-HSCs) cannot generate exchange-type chromosomal aberrations or cells bearing induced aberrations are eliminated before the animals reach adulthood. In the present study, pregnant mice (12.5–15.5 days post coitum [dpc]) were irradiated with 2 Gy of X-rays and long-term HSCs (LT-HSCs) were isolated 24 h later. Multicolor fluorescence in situ hybridization (mFISH) analysis of LT-HSC clones proliferated in vitro showed that nine out of 43 (21%) clones from fetuses and 21 out of 41 (51%) clones from mothers bore translocations. These results indicate that cells with translocations can arise in mouse f-HSCs but exist at a lower frequency than in the mothers 24 h after X-ray exposure. Thus, it seems likely that translocation-bearing f-HSCs are generated but subsequently disappear, so that the frequency of lymphocyte translocations may decrease and reach the control level by the time the animals reach adulthood.
Statistical Analysis of Mortality Rates of Coronavirus Disease 2019 (COVID-19) Patients in Japan Across the 4C Mortality Score Risk Groups, Age Groups, and Epidemiological Waves: A Report From the Nationwide COVID-19 Cohort
Authors: Baba Hiroaki , Ikumi Saori , Aoyama Shotaro , Ishikawa Tetsuo , Asai Yusuke , Matsunaga Nobuaki , Ohmagari Norio , Kanamori Hajime , Tokuda Koichi , Ueda Takuya , Kawakami Eiryo
Published: November 2022

Background

The mortality rates of coronavirus disease 2019 (COVID-19) have been changed across the epidemiological waves. The aim was to investigate the differences in mortality rates of COVID-19 patients in Japan across the 6 epidemiological waves stratified by age group and Coronavirus Clinical Characterisation Consortium (4C) mortality score risk group.

Methods

A total of 56 986 COVID-19 patients in the COVID-19 Registry Japan from 2 March 2020 to 1 February 2022 were enrolled. These patients were categorized into 4 risk groups based on their 4C mortality score. Mortality rates of each risk group were calculated separately for different age groups: 18–64, 65–74, 75–89, and ≥90 years. In addition, mortality rates across the wave periods were calculated separately in 2 age groups: <75 and ≥75 years. All calculated mortality rates were compared with reported data from the United Kingdom (UK) during the early epidemic.

Results

The mortality rates of patients in Japan were significantly lower than in the UK across the board, with the exception of patients aged ≥90 years at very high risk. The mortality rates of patients aged ≥75 years at very high risk in the fourth and fifth wave periods showed no significant differences from those in the UK, whereas those in the sixth wave period were significantly lower in all age groups and in all risk groups.

Conclusions

The present analysis showed that COVID-19 patients had a lower mortality rate in the most recent sixth wave period, even among patients ≥75 years old at very high risk.
How Fast Do Investors Learn? Asset Management Investors and Bayesian Learning
Authors: Schwarz Christopher , Sun Zheng
Published: November 2022

We study the speed with which investors learn about managers’ skills by examining how quickly investor and managers’ beliefs converge. After showing our measure proxies for the change in the dispersion of beliefs, we find that hedge fund investors learn as fast as suggested by Bayes’ rule. However, we find mutual fund investors learn more slowly than suggested by Bayes’ rule. Mutual fund investors’ slow learning is not due to the use of different performance measures, institutional frictions, or lack of sophistication, but could be due to a low payoff from learning. Our results indicate learning speed depends on financial participants’ incentives.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Stratified Entry into Illegality: How Immigration Policy Shapes Being Undocumented
Authors: Aptekar Sofya , Hsin Amy
Published: November 2022

Research shows that legal status is a critical axis of stratification in the United States but is less clear about the variably permeable boundaries around illegality and the systematic ways in which migrants are channeled into and out of the liminal states of illegality. Drawing on analysis of 105 interviews with a diverse group of undocumented or formerly undocumented immigrant young adults in New York City collected in 2018–19, we introduce the concept of stratified entry into illegality to illustrate how migrants’ nationality, race, and socioeconomic status shape their mode of entry which, in turn, shapes opportunities to adjust legal status. Our comparison of migrants who entered the United States without inspection and those who overstayed visas reveals key differences in experience of illegality, including fear of deportation and future plans. We discuss the role of mandatory re-entry bans and hardship waivers on immigrants’ relationships, the “fix” of advance parole for the more privileged Deferred Action for Childhood Arrivals (DACA) recipients, and the gendered and racialized risks and pressures faced by visa overstayers seeking to adjust their status through marriage. Our comparison of undocumented young adults with and without DACA across mode of entry demonstrates how DACA serves as a class- and race-based filtering mechanism. We embed analysis of stratified entry into illegality within the US immigration regime and a global regime of racialized criminalization of migrants rooted in colonial and neocolonial relations of power and extraction.
Prevalence and Predictors of Preoperative Anxiety in Patients With An Intracranial Supratentorial Neoplasm Undergoing Surgery
Authors: Malik Ritu , Mathew Preethy , Panda Nidhi B. , Bhagat Hemant , Gupta Aakriti , Grover Vinod K. , Mohanty Manju
Published: November 2022

Background:

Preoperative anxiety is common among patients, particularly in neurosurgical patients. The aim of the study was to evaluate the incidence and predictive factors of preoperative anxiety using the state anxiety scale of the State-Trait Anxiety Inventory (STAI-S) among patients undergoing elective craniotomy for a supratentorial neoplasm. This study also determined the optimal Amsterdam Preoperative Anxiety and Information Scale (APAIS) score for the identification of preoperative anxiety in this cohort.

Methods:

Sixty patients aged 18 to 65 years with American Society of Anesthesiologists physical status score I/II scheduled for elective craniotomy for a supratentorial neoplasm were recruited into this prospective, observational study. Preoperative anxiety was assessed using STAI-S and APAIS questionnaires. Using STAI-S ≥37 to define preoperative anxiety, the optimal APAIS to identify preoperative anxiety was determined using receiver operating characteristic curve analysis. Logistic regression was performed to identify independent predictive factors for preoperative anxiety.

Results:

Sixty percent of patients had preoperative anxiety (STAI-S ≥37). An APAIS score of 10 identified preoperative anxiety with a sensitivity, specificity, and positive predictive value of 97%, 96%, and 97%, respectively. Right-sided tumor location (P=0.047) and need-for-information on surgery (P=0.007) were independent predictors of preoperative anxiety.

Conclusions:

Patients with supratentorial neoplasms have a high incidence of preoperative anxiety; an APAIS score of 10 is the optimal cutoff to identify anxious patients in the preoperative period. Need-for-information about surgery and right-sided tumor laterality are independent predictors of preoperative anxiety.
Reproductive phenology of the eastern oyster,Crassostrea virginica(Gmelin, 1791), along a temperate estuarine salinity gradient
Authors: Gregory Kaili M. , McFarland Katherine , Hare Matthew P.
Published: November 2022

Low salinity can negatively affect reproduction in estuarine bivalves. The spatial and temporal extent of these effects are important to inform models of population dynamics, environmental risk assessments, restoration efforts, and predictions of climate change effects. We hypothesized that oysters at low salinity sites would have delayed gametogenesis compared to their higher salinity counterparts in downstream experimental cages. The timing of gametogenesis and spawning was observed June – August for 2-year-old oysters from three distinct ancestries (Native, Hatchery, Aquaculture), outplanted at age 1 month along the salinity gradient (3–30 psu) of a temperate estuary. A second season of data was collected from 3-year-old Aquaculture oysters (comparable to year 1 data) and Native adult oysters transplanted one year prior. Dermo was very low both years. A delay in gametogenesis and spawning was observed for all ancestries at low salinity relative to higher salinity sites during July and August of the first year but not the second year. In contrast, June showed the reverse pattern with northern low salinity sites having more advanced gonad index (2.65) than a high salinity site (1.46). This difference in average gonad index was 2.65 vs 1.46, respectively, for the Native line and 2.62 vs 2.08 for Aquaculture. Low salinity seemed to not only induce earlier gametogenesis in June, but also extended the reproductive season relative to higher salinity sites. Among oyster ancestries, the Aquaculture line stood out as having 30 – 48% lower gametogenic synchrony within sites, but only in 2018. Despite some dependence of reproductive phenology on salinity variation, the Native low salinity population demonstrates notable reproductive plasticity in the completion of a reproductive cycle across a wide range of salinities, an encouraging result for potential future restoration strategies.
Organism-wide secretome mapping uncovers pathways of tissue crosstalk in exercise
Authors: Wei Wei , Riley Nicholas M. , Lyu Xuchao , Shen Xiaotao , Guo Jing , Zhao Meng , Moya-Garzon Maria Dolores , Basu Himanish , Tung Alan , Li Veronica L. , Huang Wentao , Svensson Katrin J. , Snyder Michael P. , Bertozzi Carolyn R. , Long Jonathan Z.
Published: November 2022

There has been growing interest in identifying blood-borne factors that mediate tissue crosstalk and function as molecular effectors of physical activity. Although past studies have focused on an individual molecule or cell type, the organism-wide secretome response to physical activity has not been evaluated. Here, we use a cell type-specific proteomic approach to generate a 21-cell type, 10-tissue map of exercise-regulated secretomes in mice. Our dataset identifies >200 exercise-regulated cell type-secreted protein pairs, the majority of which have not been previously reported.Pdgfra-cre-labeled secretomes were the most responsive to exercise training. Elevated lactate levels can directly regulate protein secretion. Lastly, we establish an anti-obesity and anti-diabetic role for a proteoform of an intracellular carboxylesterase whose secretion from the liver is induced by exercise training. Together, our data uncover the dynamic remodeling of cell and tissue crosstalk by physical activity.
Inclusion of database outgroups improves accuracy of fungal meta-amplicon taxonomic assignments
Authors: Rawson Clayton , Zahn Geoffrey
Published: November 2022

Meta-amplicon studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other non-fungal environmental sequences that are amplified during PCR are inherently assigned taxonomy by these same databases, possibly leading to ambiguous non-fungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including non-fungal outgroups in a fungal taxonomic database to aid in detecting and removing these non-target amplicons. We processed 15 publicly available fungal meta-amplicon data sets and discovered that roughly 40% of the reads from these studies were not fungal, though they were assigned asFungus sp. when using a database without non-fungal outgroups. We discuss implications for meta-amplicon studies and recommend assigning taxonomy using a database with outgroups to better detect these non-fungal amplicons.
Higher-order dissimilarity in biodiversity: Identifying dissimilarities of spatial or temporal dissimilarity structures
Authors: Nakadai Ryosuke , Fukasawa Keita , Kadoya Taku , Ishihama Fumiko
Published: November 2022

Elucidating biodiversity patterns and their background processes is critical in biodiversity science. Dissimilarity, which is calculated based on multivariate biological quantities, is a major component of biodiversity. As spatial and temporal biodiversity information availability increases, the scope of dissimilarity studies has been expanded to cover various levels and types of spatio-temporal biodiversity facets (e.g., gene, community, and ecosystem function), and diverse pairwise dissimilarity indices have been developed. However, further development of the dissimilarity concept is required in comparative studies on spatio-temporal structures of biodiversity compositional patterns, such as those exploring commonalities of biogeographical boundaries among taxa, compared to the conventional ones to consider higher dimensions of dissimilarity: dissimilarity of dissimilarity structures.

This study proposes a novel and general concept, high-order dissimilarity (HOD), for quantitatively evaluating the dissimilarities of spatial or temporal dissimilarity structures among different datasets, proposes specific implementations of HOD as operational indices, and illustrates the potential resolution of scientific and practical questions through HOD.

We further demonstrate the advantages of the HOD concept by applying it to actual patterns, such as long-term and/or large-spatial hypothetical monitoring datasets.

Our conceptual framework on HOD extends the existing framework of biodiversity science and is versatile, with many potential applications in acquiring more valuable information from ever-increasing biodiversity data.
A fast blind source separation algorithm for decomposing ultrafast ultrasound images into spatiotemporal muscle unit kinematics
Authors: Rohlén Robin , Lundsberg Jonathan , Malesevic Nebojsa , Antfolk Christian
Published: November 2022

Objective

Ultrasound can detect individual motor unit (MU) activity during voluntary isometric contractions based on their subtle axial displacements. The detection pipeline, currently performed offline, is based on displacement velocity images and identifying the subtle axial displacements. This identification can preferably be made through a blind source separation (BSS) algorithm with the feasibility of translating the pipeline from offline toonline. However, the question remains how to reduce the computational time for the BSS algorithm, which includes demixing tissue velocities from many different sources, e.g., the active MU displacements, arterial pulsations, bones, connective tissue, and noise.

Approach

This study proposes a fast velocity-based BSS (velBSS) algorithm suitable for online purposes that decomposes velocity images from low-force voluntary isometric contractions into spatiotemporal components associated with single MU activities. The proposed algorithm will be compared against stICA, i.e., the method used in previous papers, for various subjects, ultrasound- and EMG systems, where the latter acts as MU reference recordings.

Main results

We found that the spatial and temporal correlation between the MU-associated components from velBSS and stICA was high (0.86 ± 0.05 and 0.87 ± 0.06). The spike-triggered averaged twitch responses (using the MU spike trains from EMG) had an extremely high correlation (0.99 ± 0.01). In addition, the computational time for velBSS was at least 50 times less than for stICA.

Significance

The present algorithm (velBSS) outperforms the currently available method (stICA). It provides a promising translation towards an online pipeline and will be important in the continued development of this research field of functional neuromuscular imaging.
Characterization of Genomic Diversity In Bacteriophages InfectingRhodococcus
Authors: Garza Dominic R. , Di Blasi Daria , Bruns James A. , Empson Brianna , Light Isabel , Ghannam Maisam , Castillo Salvador , Quijada Britney , Zorawik Michelle , Garcia-Vedrenne Ana E. , Freise Amanda C.
Published: November 2022

Bacteriophages are globally ubiquitous viruses that infect bacteria. With nearly 4,000 sequenced genomes of phages infecting the phylum Actinobacteria available, genomic analyses of these actinobacteriophage genomes has been instrumental in uncovering a diverse genomic landscape often characterized by genome mosaicism. Here, we describe the genomic characterization of 57 sequenced phages capable of infecting the genusRhodococcus.These phages were previously isolated at multiple institutions by students in the SEA-PHAGES program using four different species ofRhodococcus.MostRhodococcusphages have been grouped into 4 clusters based on their genomic similarities; 13 phages are singletons too genetically distinct for clustering. These clusters and singletons containSiphoviridaeandMyoviridaephages, and most contain integrase and repressor genes indicative of a potential lysogenic life cycle. The genome size of these phages varies from 14,270 bp to 142,586 bp and their G+C% content ranges from 41.2–68.4%, while that of theirRhodococcushosts typically exceeds 60%. Through comparative genomic analyses, it was revealed that theseRhodococcusphages display high intracluster similarity but low intercluster similarity, despite their shared ability to infect the same host genus. Additionally, theseRhodococcusphages share similarities with phages that infect other Actinobacterial hosts such asGordonia, StreptomycesandArthrobacter.
Retinal microvascular and neuronal pathologies probedin vivoby adaptive optical two-photon fluorescence microscopy
Authors: Zhang Qinrong , Yang Yuhan , Cao Kevin J. , Chen Wei , Paidi Santosh , Xia Chun-Hong , Kramer Richard H. , Gong Xiaohua , Ji Na
Published: November 2022

The retina, behind the transparent optics of the eye, is the only neural tissue whose physiology and pathology can be non-invasively probed by optical microscopy. The aberrations intrinsic to the mouse eye, however, prevent high-resolution investigation of retinal structure and functionin vivo. Optimizing the design of a two-photon fluorescence microscope (2PFM) and sample preparation procedure, we found that adaptive optics (AO), by measuring and correcting ocular aberrations, is essential for resolving synapses and achieving three-dimensional cellular resolution in the mouse retinain vivo. Applying AO-2PFM to longitudinal retinal imaging in transgenic models of retinal pathology, we characterized microvascular lesions and observed microglial migration in a proliferative vascular retinopathy model, and found Lidocaine to effectively suppress retinal ganglion cell hyperactivity in a retinal degeneration model. Tracking structural and functional changes at high resolution longitudinally, AO-2PFM enables microscopic investigations of retinal pathology and pharmacology for disease diagnosis and treatmentin vivo.
A model for Scc2p Stimulation of Cohesin’s ATPase and its Inhibition by Acetylation of Smc3p
Authors: Boardman Kevin M. , Xiang Siheng , Chatterjee Fiona , Mbonu Udochi , Guacci Vincent , Koshland Douglas
Published: November 2022

The evolutionarily conserved cohesin complex mediates sister chromatid cohesion and facilitates mitotic chromosome condensation, DNA repair, and transcription regulation. These biological functions require cohesin’s two ATPases, formed by the Smc1p and Smc3p subunits. Cohesin’s ATPase activity is stimulated by the Scc2p auxiliary factor. This stimulation is inhibited by Eco1p acetylation of Smc3p at an interface with Scc2p. It was unclear how cohesin’s ATPase activity is stimulated by Scc2p, or how acetylation inhibits Scc2p, given that the acetylation site is distal to cohesin’s ATPase active sites. Here, we identify mutations in budding yeast that suppressed the in vivo defects caused by Smc3p acetyl-mimic and acetyl-defective mutations. We provide compelling evidence that Scc2p activation of cohesin ATPase depends upon an interface between Scc2p and a region of Smc1p proximal to cohesin’s Smc3p ATPase active site. Furthermore, substitutions at this interface increase or decrease ATPase activity to overcome ATPase modulation by acetyl-mimic and - null mutations. Using these observations and a cryo-EM structure, we propose a model for regulating cohesin ATPase activity. We suggest that Scc2p binding to Smc1p causes a shift in adjacent Smc1p residues and ATP, stimulating the Smc3p ATPase. This stimulatory shift is inhibited through acetylation of the distal Scc2p-Smc3 interface.
Analyzing rare mutations in metagenomes assembled using long and accurate reads
Authors: Fedarko Marcus W. , Kolmogorov Mikhail , Pevzner Pavel A.
Published: November 2022

The advent of long and accurate “HiFi” reads has greatly improved our ability to generate complete metagenome-assembled genomes (MAGs), enabling “complete metagenomics” studies that were nearly impossible to conduct with short reads. In particular, HiFi reads simplify the identification and phasing of mutations in MAGs: It is increasingly feasible to distinguish between positions that are prone to mutations and positions that rarely ever mutate, and to identify co-occurring groups of mutations. However, the problems of identifying rare mutations in MAGs, estimating the false-discovery rate (FDR) of these identifications, and phasing identified mutations remain open in the context of HiFi data. We present strainFlye, a pipeline for the FDR-controlled identification and analysis of rare mutations in MAGs assembled using HiFi reads. We show that deep HiFi sequencing has the potential to reveal and phase tens of thousands of rare mutations in a single MAG, identify hotspots and coldspots of these mutations, and detail MAGs’ growth dynamics.