bluuebunny/crossref_metadata_2025 huggingface dataset:
The Octopus processor for the CMS L1 muon trigger for High Luminosity LHC
Authors: Bachtis M. , Campos D. , Jones J. , Tepper M.
Published: March 2022

The upgraded L1 muon trigger system of the CMS experiment in the High Luminosity Large Hadron Collider is based on custom processors featuring large Field Programmable Gate Arrays (FPGAs) connected by large numbers of optical links. These provide the I/O bandwidth and power necessary to process the complex algorithms used during the collection of physics data. The design and performance requirements of these processors creates significant challenges in signal integrity, power delivery, and thermal management. In this paper we describe the Octopus processor, featuring a large Xilinx Virtex Ultrascale+ FPGA and up to 128 links interfaced to optics through high quality twin-ax copper cables. Results on signal integrity at 25 Gb/s and the first demonstration of 50+ Gb/s links with pluggable optics in CMS are also shown, demonstrating bit error rates below 10−15 at a 95% confidence level. The thermal performance is measured inside an Advanced-TCA crate with acceptable thermal margins up to 200 W of chip power. Future improvements are mentioned, potentially allowing operation at up to 300 W.
The isolated USB programmer board for lpGBT configuration in ATLAS-HGTD upgrade
Authors: Han L. , Zhang J. , Liang Z. , Zhang L. , Qi M. , Chen S.
Published: March 2022

To configure the lpGBT chips that will be used on the peripheral electronics boards of the ATLAS-HGTD upgrade for the HL-LHC, a miniature and isolated USB programmer board for lpGBT (UPL) was developed based on an USB-protocol converter. Compared with the currently-used lpGBT programmer piGBT, the UPL has the advantages of compact profile, electrical isolation and cross-platform compatibility. In addition, it has a 14-pin header connector with one I2C port and six GPIOs available, and a dedicated GUI for lpGBT configuration. In particular, its isolation performance is completely determined by its I2C isolator and power isolator, both of which have the high isolation voltages of more than 1000 V AC RMS and 2000 V DC. The UPL was extensively tested by configuring a lpGBT-based board, and the lpGBT can always be successfully configured, and the bit error rate of the data transmission is always less than 1 × 10−13.
Adsorption performance of magnetic Mg0.5Ni0.5Fe2O4 nanoparticles for reactive red 2BF
Authors: Ouyang Hezhong , Liu Shuyan , Wang Zhou , Liu Aihua , Liu Dandan , Xu Shuping
Published: March 2022

A novel nitrate solution combustion process for formation of magnetic Mg0.5Ni0.5Fe2O4 nanoparticles was introduced, and XRD, VSM, SEM, TEM, and BET techniques were employed to characterize the nanoparticles. For Mg0.5Ni0.5Fe2O4 nanoparticles prepared at 400 °C for 2 h with 20 ml absolute ethanol, the average size and the saturation magnetization were approximately 22 nm and 8.1 A·m2 kg−1, respectively. Mg0.5Ni0.5Fe2O4 nanomaterials were subjected to reactive red 2BF adsorption, and the adsorption performances were investigated. The results revealed that the experimental data fit the Temkin isotherm model and the pseudo-second-order kinetics model, suggesting that the RR-2BF adsorption process was a monolayer-multilayer-associated chemisorption mechanism. The effects of pH on the adsorption capacity and cycle capacity of the magnetic Mg0.5Ni0.5Fe2O4 nanoparticles for the adsorption of reactive red 2BF were revealed.
Quantum trees which maximize higher eigenvalues are unbalanced
Authors: Rohleder Jonathan
Published: March 2022

The isoperimetric problem of maximizing all eigenvalues of the Laplacian on a metric tree graph within the class of trees of a given average edge length is studied. It turns out that, up to rescaling, the unique maximizer of the

k
k

-th positive eigenvalue is the star graph with three edges of lengths

2
k
−
1

2 k - 1

,

1
1

and

1
1

. This complements the previously known result that the first nonzero eigenvalue is maximized by all equilateral star graphs and indicates that optimizers of isoperimetric problems for higher eigenvalues may be less balanced in their shape—an observation which is known from numerical results on the optimization of higher eigenvalues of Laplacians on Euclidean domains.
Understanding the Psychology of Social Order
Authors: Tyler Tom
Published: March 2022

Looking across different societies it is clear that there have been many viable systems for managing social order. Each system has particular strengths and weaknesses and its utility depends upon its compatibility to the features of the society within which it exists. This suggestion is supported by empirical research showing that rewards and punishments, social norms, moral values, and legitimacy-based legal orders are all successful in some societies, under some conditions. Social science theories and research findings provide a guide for predicting those situations within with a particular form of authority is most likely to lead to a viable and sustainable social order.
Failed Performance on the Test of Memory Malingering and Misdiagnosis in Individuals with Early-Onset Dysexecutive Alzheimer’s Disease
Authors: Corriveau-Lecavalier Nick , Alden Eva C , Stricker Nikki H , Machulda Mary M , Jones David T
Published: March 2022

Objective

Individuals with early-onset dysexecutive Alzheimer’s disease (dAD) have high rates of failed performance validity testing (PVT), which can lead to symptom misinterpretation and misdiagnosis.

Method

The aim of this retrospective study is to evaluate rates of failure on a common PVT, the test of memory malingering (TOMM), in a sample of clinical patients with biomarker-confirmed early-onset dAD who completed neuropsychological testing.

Results

We identified seventeen patients with an average age of symptom onset at 52.25 years old. Nearly fifty percent of patients performed below recommended cut-offs on Trials 1 and 2 of the TOMM. Four of six patients who completed outside neuropsychological testing were misdiagnosed with alternative etiologies to explain their symptomatology, with two of these patients’ performances deemed unreliable based on the TOMM.

Conclusions

Low scores on the TOMM should be interpreted in light of contextual and optimally biological information and do not necessarily rule out a neurodegenerative etiology.
Integrating specific and common topologies of heterogeneous graphs and pairwise attributes for drug-related side effect prediction
Authors: Xuan Ping , Wang Meng , Liu Yong , Wang Dong , Zhang Tiangang , Nakaguchi Toshiya
Published: March 2022

Motivation

Computerized methods for drug-related side effect identification can help reduce costs and speed up drug development. Multisource data about drug and side effects are widely used to predict potential drug-related side effects. Heterogeneous graphs are commonly used to associate multisourced data of drugs and side effects which can reflect similarities of the drugs from different perspectives. Effective integration and formulation of diverse similarities, however, are challenging. In addition, the specific topology of each heterogeneous graph and the common topology of multiple graphs are neglected.

Results

We propose a drug-side effect association prediction model, GCRS, to encode and integrate specific topologies, common topologies and pairwise attributes of drugs and side effects. First, multiple drug-side effect heterogeneous graphs are constructed using various kinds of similarities and associations related to drugs and side effects. As each heterogeneous graph has its specific topology, we establish separate module based on graph convolutional autoencoder (GCA) to learn the particular topology representation of each drug node and each side effect node, respectively. Since multiple graphs reflect the complex relationships among the drug and side effect nodes and contain common topologies, we construct a module based on GCA with sharing parameters to learn the common topology representations of each node. Afterwards, we design an attention mechanism to obtain more informative topology representations at the representation level. Finally, multi-layer convolutional neural networks with attribute-level attention are constructed to deeply integrate the similarity and association attributes of a pair of drug-side effect nodes. Comprehensive experiments show that GCRS’s prediction performance is superior to other comparing state-of-the-art methods for predicting drug-side effect associations. The recall rates in top-ranked candidates and case studies on five drugs further demonstrate GCRS’s ability in discovering potential drug-related side effects.

Contact

zhang@hlju.edu.cn
LOCAN: a python library for analyzing single-molecule localization microscopy data
Authors: Doose Sören
Published: March 2022

Single-molecule localization microscopy has become an important part of the super-resolution microscopy toolbox in biomedical research. Software platforms for applying analytical methods to the point-based data structures are needed that offer both routine application and flexible customization of analysis procedures. We present a python library called LOCAN that consists of well-defined data structures and analysis methods for analyzing localization data in a script or computable notebook.

Availability and implementation

The package source code is released open-source under a BSD-3 license at https://github.com/super-resolution/Locan. It can be installed from the Python Package Index at https://pypi.org/project/locan. Documentation is available at https://locan.readthedocs.io.
Placental structure, function, and mitochondrial phenotype relate to fetal size in each fetal sex in mice
Authors: Salazar-Petres Esteban , Pereira-Carvalho Daniela , Lopez-Tello Jorge , Sferruzzi-Perri Amanda Nancy
Published: March 2022

Fetal growth depends on placental function, which requires energy from mitochondria. Here we investigated whether mitochondrial function in the placenta relates to the growth of the lightest and heaviest fetuses of each sex within the litter of mice. Placentas from the lightest and heaviest fetuses were taken to evaluate placenta morphology (stereology), mitochondrial energetics (high-resolution respirometry), mitochondrial regulators, nutrient transporters, hormone handling, and signaling pathways (qPCR and Western blotting). We found that mitochondrial complex I and II oxygen consumption rate was greater for placentas supporting the lightest female fetuses, although placental complex I abundance of the lightest females and complexes III and V of the lightest males were decreased compared to their heaviest counterparts. Expression of mitochondrial biogenesis (Nrf1) and fission (Drp1 and Fis1) genes was lower in the placenta from the lightest females, whilst biogenesis-related gene Tfam was greater in the placenta of the lightest male fetuses. In addition, placental morphology and steroidogenic gene (Cyp17a1 and Cyp11a1) expression were aberrant for the lightest females, but glucose transporter (Slc2a1) expression was lower in only the lightest males versus their heaviest counterparts. Differences in intra-litter placental phenotype were related to changes in the expression of hormone-responsive (androgen receptor) and metabolic signaling (AMPK, AKT, and PPARγ) pathways. Thus, in normal mouse pregnancy, placental structure, function, and mitochondrial phenotype are differentially responsive to the growth of the female and male fetus. This study may inform the design of sex-specific therapies for placental insufficiency and fetal growth abnormalities with life-long benefits for the offspring.
COVID-19 and the paediatric acute abdomen—the emerging dilemma of PIMS-TS
Authors: Walker Eleanor T. , Humphrey Hannah N. , Daniels Ian R. , McDermott Frank D.
Published: March 2022

PIMS-TS is a newly emerging complication of COVID-19 infection in paediatric patients. A common presenting complaint is that of the 'acute abdomen', however only a small proportion of patients are eventually diagnosed with a GI pathology requiring surgical intervention. A high level of suspicion and close working with the MDT is therefore required by surgical teams involved in the care of these patients.
Unbiased metabolome screen leads to personalized medicine strategy for amyotrophic lateral sclerosis
Authors: Boddy Sarah , Islam Mahjabin , Moll Tobias , Kurz Julian , Burrows David , McGown Alexander , Bhargava Anushka , Julian Thomas H , Harvey Calum , Marshall Jack NG , Hall Benjamin PC , Allen Scott P , Kenna Kevin P , Sanderson Eleanor , Zhang Sai , Ramesh Tennore , Snyder Michael P , Shaw Pamela J , McDermott Christopher , Cooper-Knock Johnathan
Published: March 2022

Amyotrophic lateral sclerosis is a rapidly progressive neurodegenerative disease that affects 1/350 individuals in the United Kingdom. The cause of amyotrophic lateral sclerosis is unknown in the majority of cases. Two-sample Mendelian randomization enables causal inference between an exposure, such as the serum concentration of a specific metabolite, and disease risk. We obtained genome-wide association study summary statistics for serum concentrations of 566 metabolites which were population matched with a genome-wide association study of amyotrophic lateral sclerosis. For each metabolite, we performed Mendelian randomization using an inverse variance weighted estimate for significance testing. After stringent Bonferroni multiple testing correction, our unbiased screen revealed three metabolites that were significantly linked to the risk of amyotrophic lateral sclerosis: Estrone-3-sulphate and bradykinin were protective, which is consistent with literature describing a male preponderance of amyotrophic lateral sclerosis and a preventive effect of angiotensin-converting enzyme inhibitors which inhibit the breakdown of bradykinin. Serum isoleucine was positively associated with amyotrophic lateral sclerosis risk. All three metabolites were supported by robust Mendelian randomization measures and sensitivity analyses; estrone-3-sulphate and isoleucine were confirmed in a validation amyotrophic lateral sclerosis genome-wide association study. Estrone-3-sulphate is metabolized to the more active estradiol by the enzyme 17β-hydroxysteroid dehydrogenase 1; further, Mendelian randomization demonstrated a protective effect of estradiol and rare variant analysis showed that missense variants within HSD17B1, the gene encoding 17β-hydroxysteroid dehydrogenase 1, modify risk for amyotrophic lateral sclerosis. Finally, in a zebrafish model of C9ORF72-amyotrophic lateral sclerosis, we present evidence that estradiol is neuroprotective. Isoleucine is metabolized via methylmalonyl-CoA mutase encoded by the gene MMUT in a reaction that consumes vitamin B12. Multivariable Mendelian randomization revealed that the toxic effect of isoleucine is dependent on the depletion of vitamin B12; consistent with this, rare variants which reduce the function of MMUT are protective against amyotrophic lateral sclerosis. We propose that amyotrophic lateral sclerosis patients and family members with high serum isoleucine levels should be offered supplementation with vitamin B12.
Neurochemical and cognitive changes precede structural abnormalities in the TgF344-AD rat model
Authors: Fowler Caitlin F. , Goerzen Dana , Devenyi Gabriel A. , Madularu Dan , Chakravarty M. Mallar , Near Jamie
Published: March 2022

Alzheimer’s disease is a progressive neurodegenerative disorder with a decades-long pre-symptomatic phase, substantiating the need for prodromal biomarker development and early intervention. To deconstruct the processes underlying disease progression and identify potential biomarkers, we used neuroimaging techniques with high translational potential to human clinical studies in the TgF344-AD rat model which recapitulates the full spectrum of Alzheimer’s neuropathology (progressive amyloid deposition, tauopathy, frank neuronal loss, gliosis, and cognitive dysfunction). We employed longitudinal MRI and magnetic resonance spectroscopy in conjunction with behavioural testing to characterize multiple facets of disease pathology in male and female TgF344-AD rats (n = 26, 14M/12F) relative to wildtype littermates (n = 24, 12M/12F). Testing was performed at 4, 10, 16, and 18 months, covering much of the adult rat lifespan and multiple stages of disease progression. The TgF344-AD model demonstrated impaired spatial reference memory in the Barnes Maze by 4 months of age, followed by neurochemical abnormalities in the hippocampus by 10 months and major structural changes by 16 months. Specifically, TgF344-AD rats displayed increased total choline and lactate, and decreased total creatine, taurine, and N-acetylaspartate to myo-inositol ratio, dentate gyrus hypertrophy, and atrophy in the hippocampus, hypothalamus, and nucleus accumbens. Overall, these findings support the use of MRI and magnetic resonance spectroscopy for the development of non-invasive biomarkers of disease progression, clarify the timing of pathological feature presentation in this model, and contribute to the validation of the TgF344-AD rat as a highly relevant model for pre-clinical Alzheimer’s disease research.
AI analysis and modified type classification for endocytoscopic observation of esophageal lesions
Authors: Kumagai Youichi , Takubo Kaiyo , Sato Taku , Ishikawa Hiroyasu , Yamamoto Eisuke , Ishiguro Toru , Hatano Satoshi , Toyomasu Yoshitaka , Kawada Kenro , Matsuyama Takatoshi , Mochiki Erito , Ishida Hideyuki , Tada Tomohiro
Published: March 2022

Endocytoscopy (EC) facilitates real-time histological diagnosis of esophageal lesions in vivo. We developed a deep-learning artificial intelligence (AI) system for analysis of EC images and compared its diagnostic ability with that of an expert pathologist and nonexpert endoscopists. Our new AI was based on a vision transformer model (DeiT) and trained using 7983 EC images of the esophagus (2368 malignant and 5615 nonmalignant). The AI evaluated 114 randomly arranged EC pictures (33 ESCC and 81 nonmalignant lesions) from 38 consecutive cases. An expert pathologist and two nonexpert endoscopists also analyzed the same image set according to the modified type classification (adding four EC features of nonmalignant lesions to our previous classification). The area under the curve calculated from the receiver-operating characteristic curve for the AI analysis was 0.92. In per-image analysis, the overall accuracy of the AI, pathologist, and two endoscopists was 91.2%, 91.2%, 85.9%, and 83.3%, respectively. The kappa value between the pathologist and the AI, and between the two endoscopists and the AI showed moderate concordance; that between the pathologist and the two endoscopists showed poor concordance. In per-patient analysis, the overall accuracy of the AI, pathologist, and two endoscopists was 94.7%, 92.1%, 86.8%, and 89.5%, respectively. The modified type classification aided high overall diagnostic accuracy by the pathologist and nonexpert endoscopists. The diagnostic ability of the AI was equal or superior to that of the experienced pathologist. AI is expected to support endoscopists in diagnosing esophageal lesions based on EC images.
Fatty acid desaturase genetic variations and dietary omega-3 fatty acid intake associate with arterial stiffness
Authors: Bäck Magnus , Xhaard Constance , Rouget Raphael , Thuillier Quentin , Plunde Oscar , Larsson Susanna C. , Girerd Nicolas , Ferreira João Pedro , Boivin Jean-Marc , Bozec Erwan , Mercklé Ludovic , Zannad Faiez , Hoge Axelle , Guillaume Michèle , Dandine-Roulland Claire , Floch Edith Le , Bacq-Daian Delphine , Deleuze Jean-François , Van den Berghe Laurie , Nazare Julie-Anne , Laville Martine , Branlant Christiane , Behm-Ansmant Isabelle , Wagner Sandra , Rossignol Patrick
Published: March 2022

Aims

Long-chain polyunsaturated fatty acids (PUFAs) generate diverse bioactive lipid mediators, which tightly regulate vascular inflammation. The effects of omega-3 PUFA supplementation in cardiovascular prevention however remain controversial. In addition to direct dietary intake, fatty acid desaturases (FADS) determine PUFA levels. Increased arterial stiffness represents an independent predictor of mortality and cardiovascular events. The aim of the present study was to determine the association of PUFA intake, FADS1 genotype, and FADS expression with arterial stiffness.

Methods and results

A cross-sectional population-based cohort study of 1464 participants without overt cardiovascular disease was conducted. Dietary intake was assessed using a food frequency questionnaire. Arterial stiffness was assessed by carotid–femoral pulse wave velocity (cfPWV), and the FADS1 locus variant was determined. Blood cell transcriptomics was performed in a subset of 410 individuals. Pulse wave velocity was significantly associated with the FADS1 locus variant. Differential associations between PWV and omega-3 PUFA intake were observed depending on the FADS1 genotype. High omega-3 PUFA intake attenuated the FADS1 genotype-dependent associations. Carriers of the minor FADS1 locus variant exhibited increased expression of FADS2, which is associated with PWV.

Conclusion

Taken together, these findings point to FADS1 genotype-dependent associations of omega-3 PUFA intake on subclinical cardiovascular disease. These findings may have implications for identifying responders and non-responders to omega-3 PUFA supplementation and open up for personalized dietary counselling in cardiovascular prevention.
Genotype-independent plant transformation
Authors: Maren Nathan A , Duan Hui , Da Kedong , Yencho G Craig , Ranney Thomas G , Liu Wusheng
Published: March 2022

Plant transformation and regeneration remain highly species- and genotype-dependent. Conventional hormone-based plant regeneration via somatic embryogenesis or organogenesis is tedious, time-consuming, and requires specialized skills and experience. Over the last 40 years, significant advances have been made to elucidate the molecular mechanisms underlying embryogenesis and organogenesis. These pioneering studies have led to a better understanding of the key steps and factors involved in plant regeneration, resulting in the identification of crucial growth and developmental regulatory genes that can dramatically improve regeneration efficiency, shorten transformation time, and make transformation of recalcitrant genotypes possible. Co-opting these regulatory genes offers great potential to develop innovative genotype-independent genetic transformation methods for various plant species, including specialty crops. Further developing these approaches has the potential to result in plant transformation without the use of hormones, antibiotics, selectable marker genes, or tissue culture. As an enabling technology, the use of these regulatory genes has great potential to enable the application of advanced breeding technologies such as genetic engineering and gene editing for crop improvement in transformation-recalcitrant crops and cultivars. This review will discuss the recent advances in the use of regulatory genes in plant transformation and regeneration, and their potential to facilitate genotype-independent plant transformation and regeneration.
Mitogen-activated protein kinase 4 is obligatory for late pollen and early fruit development in tomato
Authors: Wang Jie , Li Mengzhuo , Zhuo Shibin , Liu Yue , Yu Xiaolin , Mukhtar Sidra , Ali Muhammad , Lu Gang
Published: March 2022

Mitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules regulating vegetative and reproductive development of plants. However, the molecular mechanisms of the SlMPK4 gene in tomato pollen and fruit development remain elusive. SlMPK4 is preferentially and highly expressed in tomato stamens and its mRNA levels increase during early flower development, peaking at the mature pollen stage. Either up- or downregulation of SlMPK4 expression had no significant effect on tomato vegetative growth. However, RNAi-mediated suppression of SlMPK4 caused defects in pollen development, resulting in pollen abortion. The aborted pollen grains were either malformed or collapsed and completely lacked viability, resulting in a predominantly reduced fruit set rate in RNAi lines compared with control and overexpressing transgenic plants. Interestingly, seed development was inhibited in RNAi lines. Moreover, >12% of emasculated RNAi flowers developed seedless fruits without pollination. Anthers can produce typical microspore mother cells as well as uninucleate microspores, according to cytological investigations, while binucleate pollen ceased to produce typical mature pollen. Pollen abortion was further confirmed by transmission electron microscopy analysis at the binucleate stage in RNAi plants. The exine layer in aberrant pollen had a normal structure, while the intine layer appeared thicker. Suppression of SlMPK4 affects the transcript level of genes related to cell wall formation and modification, cell signal transduction, and metabolic and biosynthetic processes. A subset of genes that may be putative substrates of plant MAPKs were also differentially changed in RNAi transgenic flowers. Taken together, these results suggest that SlMPK4 plays a critical role in regulating pollen development and fruit development in tomato plants.
Ocean model-based covariates improve a marine fish stock assessment when observations are limited
Authors: du Pontavice Hubert , Miller Timothy J , Stock Brian C , Chen Zhuomin , Saba Vincent S
Published: March 2022

The productivity of many fish populations is influenced by the environment, but developing environment-linked stock assessments remain challenging and current management of most commercial species assumes that stock productivity is time-invariant. In the Northeast United States, previous studies suggest that the recruitment of Southern New England-Mid Atlantic yellowtail flounder is closely related to the strength of the Cold Pool, a seasonally formed cold water mass on the continental shelf. Here, we developed three new indices that enhance the characterization of Cold Pool interannual variations using bottom temperature from a regional hindcast ocean model and a global ocean data assimilated hindcast. We associated these new indices to yellowtail flounder recruitment in a state–space, age-structured stock assessment framework using the Woods Hole Assessment Model. We demonstrate that incorporating Cold Pool effects on yellowtail flounder recruitment reduces the retrospective patterns and may improve the predictive skill of recruitment and, to a lesser extent, spawning stock biomass. We also show that the performance of the assessment models that incorporated ocean model-based indices is improved compared to the model using only the observation-based index. Instead of relying on limited subsurface observations, using validated ocean model products as environmental covariates in stock assessments may both improve predictions and facilitate operationalization.
Boyden’s triad in the left lung: an interesting phenomenon
Authors: Zhang Min , Sun Wei-Jie , Wu Qing-Chen , Ge Ming-Jian
Published: March 2022

OBJECTIVES

Boyden’s triad of the right lung was first proposed in 2021. Here, we report 5 cases of this malformation found in the left lung.

METHODS

A total of 5280 patients with pulmonary lesions underwent three-dimensional computed tomography bronchography and angiography between January 2019 and January 2021, prior to surgery; 5 cases of this malformation were identified in the left lung. Bronchovascular patterns were analysed in each patient.

RESULTS

The incidence rate of Boyden’s triad in the left lung was 0.1%. This malformation was further divided into B3 on B4+5 type and B3 on B4 type. In B3 on B4+5 type, B3 was shifted downwards on the common trunk of B4+5, and A3 arose from the common trunk of A4+5 running alongside B3. In B3 on B4 type, B3 was shifted downwards on B4. A4 and A5 appeared separately. A3 arose from A4, running alongside B3; A5 arose from the common trunk of A8 − 10, and there was also an extraordinary ‘posterior vein’ (V. post): V1+2c. The incidence of V. post was 0.17%. An additional ‘fissure’ lies longitudinally between S1+2 and S3+4+5, nearly perpendicular to the oblique fissure, dividing the upper lobe into ‘two lobes’.

CONCLUSIONS

The B3 downwards-shifting malformation can be found on both lungs, and this is the first description of Boyden’s triad in the left lung; it appears to be much rarer than that in the right lung, with some accompanying unique variations.
The consequence of financial incentives for not prescribing antibiotics: a Japan’s nationwide quasi-experiment
Authors: Okubo Yusuke , Nishi Akihiro , Michels Karin B , Nariai Hiroki , Kim-Farley Robert J , Arah Onyebuchi A , Uda Kazuhiro , Kinoshita Noriko , Miyairi Isao
Published: March 2022

Background

For addressing antibiotic overuse, Japan designed a health care policy in which eligible medical facilities could claim a financial reward when antibiotics were not prescribed for early-stage respiratory and gastrointestinal infections. The policy was introduced in a pilot manner in paediatric clinics in April 2018.

Methods

We conducted a quasi-experimental, propensity score-matched, difference-in-differences (DID) design to determine whether the nationwide financial incentives for appropriate non-prescribing of antibiotics as antimicrobial stewardship [800 JPY (≈7.3 US D) per case] were associated with changes in prescription patterns, including antibiotics, and health care use in routine paediatric health care settings at a national level. Data consisted of 9 253 261 cases of infectious diseases in 553 138 patients treated at 10 180 eligible or ineligible facilities.

Results

A total of 2959 eligible facilities claimed 316 770 cases for financial incentives and earned 253 million JPY (≈2.29 million USD). Compared with ineligible facilities, the introduction of financial incentives in the eligible facilities was associated with an excess reduction in antibiotic prescriptions [DID estimate, -228.6 days of therapy (DOTs) per 1000 cases (95% CI, -272.4 to -184.9), which corresponded to a relative reduction of 17.8% (95% CI, 14.8 to 20.7)]. The introduction was also associated with excess reductions in drugs for respiratory symptoms [DID estimates, -256.9 DOTs per 1000 cases (95% CI, -379.3 to -134.5)] and antihistamines [DID estimate, -198.5 DOTs per 1000 cases (95% CI, -282.1 to -114.9)]. There was no excess in out-of-hour visits [DID estimate, -4.43 events per 1000 cases (95% CI, -12.8 to 3.97)] or hospitalizations [DID estimate, -0.08 events per 1000 cases (95% CI, -0.48 to 0.31)].

Conclusions

Our findings suggest that financial incentives to medical facilities for not prescribing antibiotics were associated with reductions in prescriptions for antibiotics without adverse health care consequences. Japan’s new health policy provided us with policy options for immediately reducing inappropriate antibiotic prescriptions by relatively small financial incentives.
A Blunted GPR183/Oxysterol Axis During Dysglycemia Results in Delayed Recruitment of Macrophages to the Lung During Mycobacterium tuberculosis Infection
Authors: Ngo Minh Dao , Bartlett Stacey , Bielefeldt-Ohmann Helle , Foo Cheng Xiang , Sinha Roma , Arachchige Buddhika Jayakody , Reed Sarah , Mandrup-Poulsen Thomas , Rosenkilde Mette Marie , Ronacher Katharina
Published: March 2022

Background

We previously reported that reduced GPR183 expression in blood from tuberculosis (TB) patients with diabetes is associated with more severe TB.

Methods

To further elucidate the role of GPR183 and its oxysterol ligands in the lung, we studied dysglycemic mice infected with Mycobacterium tuberculosis (Mtb).

Results

We found upregulation of the oxysterol-producing enzymes CH25H and CYP7B1 and increased concentrations of 25-hydroxycholesterol upon Mtb infection in the lungs of mice. This was associated with increased expression of GPR183 indicative of oxysterol-mediated recruitment of GPR183-expressing immune cells to the lung. CYP7B1 was predominantly expressed by macrophages in TB granulomas. CYP7B1 expression was significantly blunted in lungs from dysglycemic animals, which coincided with delayed macrophage infiltration. GPR183-deficient mice similarly had reduced macrophage recruitment during early infection.

Conclusions

Taken together, we demonstrate a requirement of the GPR183/oxysterol axis for positioning of macrophages to the site of infection and add an explanation to more severe TB in diabetes patients.
Antibiotic resistance: calling time on the ‘silent pandemic’
Authors: Mendelson Marc , Sharland Michael , Mpundu Mirfin
Published: March 2022

It is time to stop referring to the antibiotic resistance pandemic as ‘silent’. Continuing to use such a term denies the reality that antibiotic-resistant bacterial infections, driven by misuse and abuse of antibiotics by humans against microbial ecosystems that we should be living in symbiosis with, is wrong. Both our terminology and who the real ‘enemy’ is in relation to antibiotic resistance demands serious reconsideration.
Determination of Orellanine in Human Biological Matrices Using Liquid Chromatography with High-Resolution Mass Spectrometry Detection: A Validated Method Applied to Suspected Poisoning Cases
Authors: Flament Estelle , Guitton Jérôme , Gicquel Thomas , Paret Nathalie , Jarrier Nathalie , Creusat Gaelle , Tournoud Christine , Labadie Magali , Gaulier Jean-Michel , Gaillard Yvan
Published: March 2022

Consumption of mushrooms can become unsafe for the consumer in case of confusion. Some fungi of Cortinarius genus contain the nephrotoxic mycotoxin orellanine responsible for their toxicity. Related case poisoning diagnosis is a challenge for both clinicians and analysts because of a long latency period between intake and toxic syndrome, the lack of available information in literature and the numerous pitfalls of orellanine identification/quantification in biological samples. In this situation, we propose an analytical method designed for the orellanine detection and/or quantification in biological matrices such as plasma, urine and whole blood, in a context of related intoxication suspected case. Using 1 mL biological sample volume, this liquid chromatographic with high-resolution mass spectrometry detection method (i) exhibits a limit of quantification for orellanine of 0.5 µg/L in plasma and urine and (ii) enables orellanine detection in whole blood with a limit of detection of 0.5 µg/L. This validated analytical method was successfully applied to 10 suspected intoxication cases.
Heavy drought reduces the decomposition rate of the mixed litters of two composite invasive alien plants
Authors: Yu Youli , Cheng Huiyuan , Wang Congyan , Du Daolin
Published: March 2022

Compositae family comprises the largest number of species of invasive alien plants (IAPs) in China. Two IAPs can co-invade the same habitat. Drought can alter the litter decomposition of IAPs and soil enzyme activities. This study aims to estimate the independent and combined effects of two composite IAPs (Bidens pilosa and Solidago canadensis) on litter decomposition and soil enzyme activities under drought. A polyethylene litterbags experiment (5 g litters of B. pilosa, 5 g litters of S. canadensis or 5 g litters of B. pilosa and S. canadensis in an equal proportion per polyethylene litterbag) was performed. The polyethylene litterbags were treated with a gradient of drought, i.e. control, light level of drought and heavy level of drought. The decomposition coefficient of the two composite IAPs and soil enzyme activities was determined. The co-invasion of the two composite IAPs posed a synergistic effect on urease activity. The mixed litters of two composite IAPs and the litters of B. pilosa had higher decomposition rates than S. canadensis. Urease activity was increased in light droughts, but it was decreased in heavy drought. Heavy drought reduced the decomposition rate of the mixed litters of two composite IAPs and the litters of B. pilosa. Drought did not affect the decomposition rate of S. canadensis litters. Thus, heavy drought can decrease the nutrient cycling rate under the co-invasion of the two composite IAPs and the independent invasion of B. pilosa rather than the independent invasion of S. canadensis.
Estimating cluster masses from SDSS multiband images with transfer learning
Authors: Lin Sheng-Chieh , Su Yuanyuan , Liang Gongbo , Zhang Yuanyuan , Jacobs Nathan , Zhang Yu
Published: March 2022

The total masses of galaxy clusters characterize many aspects of astrophysics and the underlying cosmology. It is crucial to obtain reliable and accurate mass estimates for numerous galaxy clusters over a wide range of redshifts and mass scales. We present a transfer-learning approach to estimate cluster masses using the ugriz-band images in the SDSS Data Release 12. The target masses are derived from X-ray or SZ measurements that are only available for a small subset of the clusters. We designed a semisupervised deep learning model consisting of two convolutional neural networks. In the first network, a feature extractor is trained to classify the SDSS photometric bands. The second network takes the previously trained features as inputs to estimate their total masses. The training and testing processes in this work depend purely on real observational data. Our algorithm reaches a mean absolute error (MAE) of 0.232 dex on average and 0.214 dex for the best fold. The performance is comparable to that given by redMaPPer, 0.192 dex. We have further applied a joint integrated gradient and class activation mapping method to interpret such a two-step neural network. The performance of our algorithm is likely to improve as the size of training data set increases. This proof-of-concept experiment demonstrates the potential of deep learning in maximizing the scientific return of the current and future large cluster surveys.
Particle-in-cell simulations of high-frequency waves driven by pickup ion ring-beam distributions in the outer heliosheath
Authors: Mousavi Ameneh , Liu Kaijun , Sadeghzadeh Sina
Published: March 2022

Scattering of pickup ion ring-beam distributions in the outer heliosheath is a fundamental element in the spatial retention scenario of the energetic neutral atom (ENA) ribbon observed by the Interstellar Boundary EXplorer (IBEX). According to our earlier linear instability analysis, pickup ion ring-beam distributions trigger magnetic field-aligned, right-hand polarized unstable waves in two separate frequency ranges which are near and far above the proton cyclotron frequency, respectively. We have performed hybrid simulations to study the unstable waves near the proton cyclotron frequency. However, the high-frequency waves well above the proton cyclotron frequency are beyond the reach of hybrid simulations. In this paper, particle-in-cell simulations are carried out to study the parallel- and antiparallel-propagating high-frequency waves excited by the outer heliosheath pickup ions at different pickup angles as well as the scattering of the pickup ions by the waves excited. In the early stages of the simulations, the results confirm the excitation of the parallel-propagating, right-hand polarized high-frequency waves as predicted by the earlier linear analysis. Later in the simulations, enhanced antiparallel-propagating modes also emerge. Furthermore, the evolution of the pickup ion ring-beam distributions of the selected pickup angles reveals that the high-frequency waves do not significantly contribute to the pickup ion scattering. These results are favourable regarding the plausibility of the spatial retention scenario of the IBEX ENA ribbon.
Instability from high-order resonant chains in wide-separation massive planet systems
Authors: Murphy Matthew M , Armitage Philip J
Published: March 2022

Diversity in the properties of exoplanetary systems arises, in part, from dynamical evolution that occurs after planet formation. We use numerical integrations to explore the relative role of secular and resonant dynamics in the long-term evolution of model planetary systems, made up of three equal mass giant planets on initially eccentric orbits. The range of separations studied is dominated by secular processes, but intersects chains of high-order mean-motion resonances. Over time-scales of 108 orbits, the secular evolution of the simulated systems is predominantly regular. High-order resonant chains, however, can be a significant source of angular momentum deficit (AMD), leading to instability. Using a time series analysis based on a Hilbert transform, we associate instability with broad islands of chaotic evolution. Previous work has suggested that first-order resonances could modify the AMD of nominally secular systems and facilitate secular chaos. We find that higher order resonances, when present in chains, can have similar impacts.
Variations of magnetic multipoles in the X-ray binary pulsars Her X-1 and A 0535+26
Authors: Christodoulou Dimitris M , Laycock Silas G T , Kazanas Demosthenes , Contopoulos Ioannis
Published: March 2022

The X-ray binaries (XRBs) Her X-1 and A 0535+26 have been extensively studied over the years during outbursts and in deep quiescence. Cyclotron resonance scattering features (CRSFs) have been observed in absorption correlating with X-ray luminosities, though recently, an anticorrelation was seen in the 2020 giant outburst of A 0535+26 at higher luminosities. These types of behaviour have been observed in several other XRBs, yet there are sources showing extended periods of no correlation at all. Such aperiodic changes and periods of no change in CRSFs can be explained by changes in the surface magnetic fields of the X-ray pulsars. In particular, we show here that CRSF variations occur in Her X-1 and A 0535+26 due to corresponding changes in the strong nondipolar components of their surface magnetic fields, while the magnetic dipoles reaching out to the accretion discs remain largely unchanged.
Large-amplitude periodic outbursts and long-period variables in the VVV VIRAC2-β data base
Authors: Guo Zhen , Lucas P W , Smith L C , Clarke C , Contreras Peña C , Bayo A , Briceño C , Elias J , Kurtev R G , Borissova J , Alonso-García J , Minniti D , Catelan M , Nikzat F , Morris C , Miller N
Published: March 2022

The VISTA Variables in the Via Lactea (VVV) survey obtained near-infrared photometry towards the Galactic bulge and the southern disc plane for a decade (2010–2019). We designed a modified Lomb–Scargle method to search for large-amplitude ($\Delta K_{s, 2-98{{\ \rm per\ cent}}}$ > 1.5 mag) mid to long-term periodic variables (P> 10 d) in the 2nd version of VVV Infrared Astrometric Catalogue (VIRAC2-β). In total, 1520 periodic sources were discovered, including 59 candidate periodic outbursting young stellar objects (YSOs), based on the unique morphology of the phase-folded light curves, proximity to Galactic H ii regions and mid-infrared colours. Five sources are spectroscopically confirmed as accreting YSOs. Both fast-rise/slow-decay and slow-rise/fast-decay periodic outbursts were found, but fast-rise/slow-decay outbursts predominate at the highest amplitudes. The multiwavelength colour variations are consistent with a variable mass accretion process, as opposed to variable extinction. The cycles are likely to be caused by dynamical perturbations from stellar or planetary companions within the circumstellar disc. An additional search for periodic variability amongst YSO candidates in published Spitzer-based catalogues yielded a further 71 candidate periodic accretors, mostly with lower amplitudes. These resemble cases of pulsed accretion but with unusually long periods and greater regularity. The majority of other long-period variables are pulsating dusty Miras with smooth and symmetric light curves. We find that some Miras have redder W3 − W4 colours than previously thought, most likely due to their surface chemical compositions.
Confirmed Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections After a Second Wave With Predominance of Lambda in Lima and Callao, Peru
Authors: Pampa-Espinoza Luis , Padilla-Rojas Carlos , Silva-Valencia Javier , Jimenez-Vasquez Victor , Silva Iris , Mestanza Orson , Lope Pari Priscila , Cáceres Omar , Bailón-Calderón Henry , Bárcena-Flores Luis , Galarza Marco , García Mendoza María , Gavilán Ronnie , Rojas Serrano Nancy , Palomino Rodriguez Miryam , Huaringa Maribel , Rios Monteza Pamela , Ordoñez Luis , Fernandez-Navarro Manuel , Vargas-Herrera Natalia , Solari Lely
Published: March 2022

Background

Coronavirus disease 2019 (COVID-19) infection is a major public health problem in the world and reinfections are becoming more frequent. Our main objective was to describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the capital of Lima and Callao, Peru.

Methods

We searched in the Peruvian laboratory information system from April 2020 up to May 2021, looking for cases having 2 positive molecular tests for SARS-CoV-2 with more than 90 days between them. We performed genomic sequencing to the available pairs of samples and described the clinical characteristics, epidemiological impact, and genomic analysis of the confirmed reinfections.

Results

There were 1 694 164 people with a positive diagnostic test for SARS-CoV-2 in Lima/Callao during the study period. Of these, 1695 had 2 positive molecular tests with more than 90 days between them. Two hundred eleven had both samples available for genomic analysis according to our selection criteria, and these were retrieved and submitted to sequencing. Thirty cases were confirmed to be SARS-CoV-2 reinfections with 2 different lineages in the 2 episodes. The variant Lambda (C.37) was the most common during the second infection and accounted for 19 (63.3%) of the 30 cases.

Conclusions

We report 30 cases of confirmed SARS-CoV-2 reinfections. The Lambda variant was the most common cause of the second infections, in concordance with its predominant circulation during Peru’s second wave. This report describes the largest series of confirmed reinfections by SARS-CoV-2 in Latin America.

We describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 in Lima and Callao, durante la segunda ola en Peru. The Lambda variant (C.37) was the most common cause of the second infections.