bluuebunny/crossref_metadata_2025 huggingface dataset:
Fisher matrix for the one-loop galaxy power spectrum: measuring expansion and growth rates without assuming a cosmological model
Authors: Amendola Luca , Pietroni Massimo , Quartin Miguel
Published: November 2022

We introduce a methodology to extend the Fisher matrix forecasts to mildly non-linear
scales without the need of selecting a cosmological model. We make use of standard non-linear
perturbation theory for biased tracers complemented by counterterms, and assume that the
cosmological distances can be measured accurately with standard candles. Instead of choosing a
specific model, we parametrize the linear power spectrum and the growth rate in several k and
z bins. We show that one can then obtain model-independent constraints of the expansion rate
E(z) = E(z)/H
0 and the growth rate f(k,z), besides the bias functions. We apply the technique
to both Euclid and DESI public specifications in the range 0.6 ≤ z ≤ 1.8 and show that the
gain in precision when going from k
max = 0.1 to 0.2 h/Mpc is around two- to threefold,
while it reaches four- to ninefold when extending to k
max = 0.3 h/Mpc. In absolute
terms, with k
max = 0.2 h/Mpc, one can reach high precision on E(z) at each z-shell:
8–10% for DESI with Δz = 0.1, 5–6% for Euclid with Δz = 0.2–0.3. This improves to
1–2% if the growth rate f is taken to be k-independent. The growth rate itself has in
general much weaker constraints, unless assumed to be k-independent, in which case the gain is
similar to the one for E(z) and uncertainties around 5–15% can be reached at each z-bin. We
also discuss how neglecting the non-linear corrections can have a large effect on the constraints
even for k
max = 0.1 h/Mpc, unless one has independent strong prior information on the
non-linear parameters.
Reheating with effective potentials
Authors: Katuwal S. , Miao S.P. , Woodard R.P.
Published: November 2022

We consider reheating for a charged inflaton which is minimally coupled to
electromagnetism. The evolution of such an inflaton induces a time-dependent
mass for the photon. We show how the massive photon propagator can be
expressed as a spatial Fourier mode sum involving three different sorts of
mode functions, just like the constant mass case. We develop accurate
analytic approximations for these mode functions, and use them to approximate
the effective force exerted on the inflaton 0-mode. This effective force
allows one to simply compute the evolution of the inflaton 0-mode and to
follow the progress of reheating.
A Self-learning Neural Network Approach for Radio Frequency Interference Detection and Removal in Radio Astronomy
Authors: Saliwanchik Benjamin R. B. , Slosar Anže
Published: November 2022

We present a novel neural network (NN) method for the detection and removal of radio frequency interference (RFI) from the raw digitized signal in the signal processing chain of a typical radio astronomy experiment. The main advantage of our method is that it does not require a training set. Instead, our method relies on the fact that the true signal of interest coming from astronomical sources is thermal and therefore described as a Gaussian random process, which cannot be compressed. We employ a variational encoder/decoder network to find the compressible information in the data stream that can explain the most variance with the fewest degrees of freedom. We demonstrate it on a set of toy problems and stored ring buffers from the Baryon Mapping eXperiment prototype. We find that the RFI subtraction is effective at cleaning simulated time streams: While we find that the power spectra of the RFI-cleaned time streams output by the NN suffer from extra signal consistent with additive noise, we find that it is generally around percent level across the band and sub 10% in contaminated spectral channels even when RFI power is an order of magnitude larger than the signal. We discuss the advantages and limitations of this method and possible implementation in the front end of future radio experiments.
Investigating the laser metal deposition of Inconel 718 superalloy using the numerical and experimental methods
Authors: Afshari Mahmoud , Khandaei Mehrdad , Shoja Razavi Reza
Published: November 2022

In this research, a volume of fluid (VOF) model was developed to investigate the effect of laser deposition parameters on the geometry of molten pool and deposited layer in the Inconel 718 superalloy. For this purpose, the process parameters of laser power, laser beam diameter and scanning speed were considered to estimate the geometric characteristics of the molten pool and deposited layer. In the following, the laser deposition process of Inconel 718 superalloy was carried out experimentally to validate the results of simulation. It was observed that an increase in the laser power from 100 to 400 W resulted in an improvement in the length, width and depth of molten pool, while an increase in the values of laser beam diameter (from 1 to 2 mm) and scanning speed (from 2 to 10 mm s−1) was associated with a reduction in the length, width and depth of molten pool. From the results of both simulation and experiments, a reduction was observed in the wetting angle of deposited layer when the values of laser power and scanning speed increased up to 400 W and 10 mm s−1 respectively, while the increase of feeding rate from 48 to 62 mgr s−1 indicated an improvement in the wetting angle. It was also observed that the maximum penetration depth was obtained in the rear part of molten pool due to Marangoni convection currents that pushed the melt toward the end of molten pool. The comparison of the experimental results and those predicted by the VOF model indicated that the model is capable of predicting the shape of deposition layer with sensible error.
Integrate a high precision scan magnet power supply in NSRRC
Authors: Huang Jhao-Cyuan , Wong Yong-Seng , Liu Kuo-Bin , Jan Jyh-Chyuan , Lin Fu-Yuan , Chu Yun-Liang , Hsu Yang-Yang
Published: November 2022

This work describes the integration of a high precision power supply in a scan magnet in National Synchrotron Radiation Research Center (NSRRC). Horizontal and vertical energy transmission to the scan magnet are independent. The high precision and sinewave are utilised to produce a smooth circle field. This power supply has an air cooling system and a more protective function to keep the machine and magnet from being damaged. During the scan magnet application, the maximum current is 12.5 A, and the inductor is 30 mH at 20 Hz sine wave. Accordingly, Kecpo BOP 72-14 model with a maximum current of 14 A and maximum output voltage of 72 V is chosen. Finally, an integrated high-precision scan magnet power supply is created in the laboratory. Experimental result shows the output current ripple and bandwidth, with the output current being 14 A and the maximum ripple being 0.45 A. This combination is simple because no resistor is in parallel with the magnet coils. Lastly, this work demonstrates the magnetic field, output current ripple, and frequency variation with output current to prove that this power supply meets the requirements.
Measurement catastrophe and ballistic spread of charge density with vanishing current
Authors: Zadnik L , Bocini S , Bidzhiev K , Fagotti M
Published: November 2022

One of the features of many-body quantum systems with Hilbert-space fragmentation are stationary states manifesting quantum jamming. It was recently shown that these are ‘states with memory’, in which, e.g. measuring a localised observable has everlasting macroscopic effects. We study such a measurement catastrophe with an example that stands out for its clarity. We show in particular that at late times the expectation value of a charge density becomes a nontrivial function of the ratio between distance and time notwithstanding the corresponding current approaching zero.
Myasthenia gravis: What does a pharmacist need to know?
Authors: Marriott Morgan , Schwery Abbey , VandenBerg Amy
Published: November 2022

Purpose

Myasthenia gravis (MG) is not commonly covered in pharmacy school curricula. However, many medications that have been reported to cause exacerbations of MG are among the top 200 most prescribed drugs. The purpose of this therapeutic update is to provide pharmacists with a general understanding of the pathophysiology and treatment of MG and describe common medications with the potential to cause new onset or acute worsening of this disease.

MG is an autoimmune disorder in which patients develop autoantibodies to a component of the neuromuscular junction, most frequently the acetylcholine receptor, resulting in impairment of skeletal muscle contraction. Although MG is not highly prevalent, there are up to 60,000 individuals with MG in the US, making it a disease that many pharmacists will likely encounter at least once in their career. Immunosuppressant medications and acetylcholinesterase inhibitors are the mainstays of treatment, although there is limited evidence as to which agents are most efficacious. Medications that activate the immune system, such as immune checkpoint inhibitors, may cause new onset of disease, while those with actions on the neuromuscular junction, such as macrolides and fluoroquinolones, can cause acute worsening of disease.

Conclusion

MG, although not frequently covered in pharmacy school curricula, is a disease state for which it is not uncommon for pharmacists to provide care. Treatment tends to be patient specific, and evidence is often weak. Many medications that cause new onset or worsening of MG are among the most prescribed. Key classes of medications to use with caution include macrolides, fluoroquinolones, β-blockers, and magnesium.
Greeting in English as a Foreign Language: A Problem for Speakers of Chinese
Authors: House Juliane , Kádár Dániel Z , Liu Fengguang , Liu Shiyu
Published: November 2022

This paper investigates the phenomenon of greeting in English, which can be surprisingly challenging for speakers of other languages, such as Chinese. By ‘greeting’ we mean the seemingly ‘simple’ act of choosing conventionalized expressions at the opening of an encounter. Following pilot interviews with Chinese learners of English who reported puzzlement concerning greeting in English, we pursue a two-fold approach to explore conventions of greeting in English and Chinese. First, we use corpora to investigate pragmatic differences and similarities between conventionalized uses of English and Chinese comparable Greet expressions, examining them separately and then conducting a contrastive analysis. This step helps us capture the contextual spread of Greet expressions in English and Chinese. Second, we elicit production data from speakers of English and Chinese to investigate their behaviour in the broader opening phase of an interaction across various contexts. The results of the study help us understand in a differentiated way the puzzlement that certain groups of learners of English feel when it comes to greeting.
Plant specialized metabolites in the rhizosphere of tomatoes: secretion and effects on microorganisms
Authors: Nakayasu Masaru , Takamatsu Kyoko , Yazaki Kazufumi , Sugiyama Akifumi
Published: November 2022

Plants interact with microorganisms in the phyllosphere and rhizosphere. Here the roots exude plant specialized metabolites (PSMs) that have diverse biological and ecological functions. Recent reports have shown that these PSMs influence the rhizosphere microbiome, which is essential for the plant's growth and health. This review summarizes several specialized metabolites secreted into the rhizosphere of the tomato plant (Solanum lycopersicum), which is an important model species for plant research and a commercial crop. In this review, we focused on the effects of such plant metabolites on plant-microbe interactions. We also reviewed recent studies on improving the growth of tomatoes by analyzing and reconstructing the rhizosphere microbiome and discussed the challenges to be addressed in establishing sustainable agriculture.
Achieving improved accuracy for imputation of ancient DNA
Authors: Ausmees Kristiina , Nettelblad Carl
Published: November 2022

Motivation

Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.

Results

We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.

Availability and implementation

The C++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser.

Supplementary information

Supplementary information is available at Bioinformatics online.
Power enhancement using improved maximum power point tracking for solar photovoltaic systems under partial shading
Authors: Bhos Chandrakant D , Sayyad Javed , Nasikkar Paresh
Published: November 2022

One of the key reasons contributing to a reduction in the performance of a solar photovoltaic (SPV) system is the presence of partial shade on the solar panels. It is necessary to use maximum power point tracking (MPPT) in SPV systems to get around the non-linear behaviour of photovoltaic panels. This research analyses the reduction in power output of SPV systems caused by partial shading. In the latter part of the paper, the improved dynamic behaviour-based ant colony optimization MPPT approach under the effect of module-level partial shading is implemented in MATLAB®/Simulink®. Various partial shading levels were applied to SPV modules to evaluate the system performance. The proposed system follows the maximum power point with 99.9% accuracy and a response time of 2 ms. The addition of a weight coefficient accelerates the convergence of the algorithm.
Black and White Patients With Staphylococcus aureus Bacteremia Have Similar Outcomes but Different Risk Factors
Authors: Ruffin Felicia , Dagher Michael , Park Lawrence P , Wanda Lisa , Hill-Rorie Jonathan , Mohnasky Michael , Marshall Julia , Souli Maria , Lantos Paul , Sharma-Kuinkel Batu K , Maskarinec Stacey A , Eichenberger Emily M , Muiruri Charles , Broadnax Brittney , Fowler Vance G
Published: November 2022

Background

Staphylococcus aureus bacteremia (SAB) disproportionately affects Black patients. The reasons for this disparity are unclear.

Methods

We evaluated a prospectively ascertained cohort of patients with SAB from 1995 to 2020. Clinical characteristics, bacterial genotypes, and outcome were compared among Black and White patients with SAB. Multivariable logistic regression models were used to determine factors independently associated with the outcomes.

Results

Among 3068 patients with SAB, 1107 (36%) were Black. Black patients were younger (median, 56 years vs 63 years; P < .001) and had higher rates of diabetes (47.5% vs 34.5%, P < .001), hemodialysis dependence (40.0% vs 7.3%, P < .001), and human immunodeficiency virus (6.4% vs 0.6%, P < .001). Black patients had higher rates of methicillin-resistant S. aureus (49.3% vs 44.9%, P = .020), including the USA300 hypervirulent clone (11.5% vs 8.4%, P = .007). White patients had higher rates of corticosteroid use (22.4% vs 15.8%, P < .0001) and surgery in the preceding 30 days (28.1% vs 18.7%, P < .001). Although the median Acute Physiology Score (APS) at the time of initial SAB diagnosis was significantly higher in Black patients (median APS, 9; interquartile range [IQR], 5–14 vs median APS, 7; IQR, 4–12; P < .001), race was not associated with 90-day mortality (risk ratio, 1.02; 95% confidence interval, .93–1.12), and rates of metastatic infection were lower among Black patients (37.2% vs 41.3% White, P = .029).

Conclusions

Despite differences in Black patients' higher APS on presentation and more risk factors, including a 5 times higher risk of hemodialysis dependence, 90-day mortality among Black and White patients with SAB was similar.
Ecological Drivers and Consequences of Bumble Bee Body Size Variation
Authors: Fitzgerald Jacquelyn L , Ogilvie Jane E , CaraDonna Paul J
Published: November 2022

Body size is arguably one of the most important traits influencing the physiology and ecology of animals. Shifts in animal body size have been observed in response to climate change, including in bumble bees (Bombus spp. [Hymenoptera: Apidae]). Bumble bee size shifts have occurred concurrently with the precipitous population declines of several species, which appear to be related, in part, to their size. Body size variation is central to the ecology of bumble bees, from their social organization to the pollination services they provide to plants. If bumble bee size is shifted or constrained, there may be consequences for the pollination services they provide and for our ability to predict their responses to global change. Yet, there are still many aspects of the breadth and role of bumble bee body size variation that require more study. To this end, we review the current evidence of the ecological drivers of size variation in bumble bees and the consequences of that variation on bumble bee fitness, foraging, and species interactions. In total we review: (1) the proximate determinants and physiological consequences of size variation in bumble bees; (2) the environmental drivers and ecological consequences of size variation; and (3) synthesize our understanding of size variation in predicting how bumble bees will respond to future changes in climate and land use. As global change intensifies, a better understanding of the factors influencing the size distributions of bumble bees, and the consequences of those distributions, will allow us to better predict future responses of these pollinators.
Gravid Periplaneta americana (Blattodea: Blattidae) Fails to Detect or Respond to the Presence of the Oothecal Parasitoid Aprostocetus hagenowii (Hymenoptera: Eulophidae)
Authors: Smith C M , Chicas-Mosier A M , Appel A G , Fadamiro H Y
Published: November 2022

Several families of parasitic Hymenoptera have evolved traits that allow them to exploit cockroach oothecae. Cockroaches may bury and conceal their oothecae to prevent parasitoid attack. However, these protective measures require additional investment by females. We hypothesized that gravid cockroaches would reduce parental care in the absence of oothecal parasitoids and increase care when parasitoids were detected. Behavior bioassays consisted of glass jars containing a gravid American cockroach, Periplaneta americana (L.) (Blattodea: Blattidae), expanded polystyrene (EPS), and a dog food pellet. A fruit fly (Drosophila melanogaster Meigen) (Diptera: Drosophilidae) or parasitoid Aprostocetus hagenowii (Ratzburg) (Hymenoptera: Eulophidae) was added for the fly and parasitoid treatments, respectively. There was no significant difference among treatments in the proportion of oothecae buried or in mean cover of oothecae with EPS particles. Cover had no effect on parasitism success or failure. Electroantennogram (EAG) assays using P. americana antennae were also conducted. The EAG responses to dead parasitoid stimuli (0.111–0.124 mV) were significantly (p < 0.05) greater than the negative control, but responses to living parasitoid stimuli (0.075–0.089 mV) were nonsignificant. These findings suggest that burial and concealment of oothecae is a general defensive behavior employed regardless of the presence or absence of a natural enemy. The results also indicate that gravid P. americana are unable to detect, and therefore, differentiate A. hagenowii from other insects and that A. hagenowii can successfully locate and parasitize oothecae completely concealed with EPS particles.
The impact of a community health worker intervention on uptake of antenatal care: a cluster-randomized pragmatic trial in Dar es Salaam
Authors: Regan Mathilda , Cheng Chao , Mboggo Eric , Larson Elysia , Lema Irene Andrew , Magesa Lucy , Machumi Lameck , Ulenga Nzovu , Sando David , Mwanyika-Sando Mary , Barnhart Dale A , Hong Biling , Mungure Ester , Li Nan , Siril Hellen , Mujinja Phares , Naburi Helga , Kilewo Charles , Ekström Anna Mia , Geldsetzer Pascal , Fawzi Wafaie , Bärnighausen Till , Sudfeld Christopher R , Spiegelman Donna
Published: November 2022

The provision of high-quality antenatal care (ANC) is important for preventing maternal and newborn mortality and morbidity, but only around half of pregnant women in Tanzania attended four or more ANC visits in 2019. Although there is emerging evidence on the benefit of community health worker (CHW) interventions on ANC uptake, few large-scale pragmatic trials have been conducted. This pragmatic cluster-randomized trial, implemented directly through the public sector health system, assessed the impact of an intervention that trained public sector CHWs to promote the uptake of ANC. We randomized 60 administrative wards in Dar es Salaam to either a targeted CHW intervention or a standard of care. The impact of the intervention was assessed using generalized estimating equations with an independent working correlation matrix to account for clustering within wards. A total of 243 908 women were included in the analysis of our primary outcome of four or more ANC visits. The intervention significantly increased the likelihood of attending four or more ANC visits [relative risk (RR): 1.42; 95% confidence interval (CI): 1.05, 1.92] and had a modest beneficial effect on the total number of ANC visits (percent change: 7.7%; 95% CI: 0.2%, 15.5%). While slightly more women in the intervention arm attended ANC in their first trimester compared with the standard-of-care arm (19% vs 18.7%), the difference was not significant (RR: 1.02; 95% CI: 0.84, 1.22). Our findings suggest that trained CHWs can increase attendance of ANC visits in Dar es Salaam and similar settings. However, additional interventions appear necessary to promote the early initiation of ANC. This study demonstrates that routine health system data can be leveraged for outcome assessment in trials and programme evaluation and that the results are likely superior, both in terms of bias and precision, to data that are collected specifically for science.
Guide for Laboratory Animal Facilities and Care
Authors:   Prepared by the Animal Facilities Standards Committee of the Animal Care Panel
Published: November 2022

The Animal Care Panel is a nonprofit educational association of individuals and institutions concerned with the production, care, and study of laboratory animals. The entire United States and several foreign countries are represented in its membership. The Panel provides for the exchange of scientific information on all phases of laboratory animal care. It compiles and distributes information on films dealing with the handling of laboratory animals, and has initiated an animal technicians’ training program. It publishes a bimonthly journal, “Laboratory Animal Care;” sponsors annual awards designed to encourage and reward outstanding accomplishment in the improvement of the care and quality of laboratory animals; and maintains close liaison with the Institute of Laboratory Resources (National Research Council), the American Veterinary Medical Association (through the American College of Laboratory Animal Medicine), the Laboratory Animal Breeders Association, and the National Society for Medical Research. Through its Animal Facilities Standards Committee, the Panel gathers and examines information that will aid in the establishment of high standards for the care of animals. The Guide for  Laboratory  Animal  Facilities and  Care was adopted by the Institute of Laboratory Animal Resources, National Academy of Sciences-National Research Council, on January 28, 1963.
Relative bioavailability of crushed tebipenem administered through a nasogastric tube with and without enteral feeding
Authors: Fouad Aliaa , Quintiliani Richard , Nicolau David P , Asempa Tomefa E
Published: November 2022

Objective

Tebipenem pivoxil hydrobromide is an orally bioavailable carbapenem prodrug of the active agent tebipenem with broad-spectrum activity against drug-resistant Enterobacterales. This study aimed to evaluate the relative bioavailability of crushed tebipenem tablets administered via nasogastric tube (NGT) with or without concomitant enteral feeds.

Methods

This Phase 1, open label study randomized 12 healthy subjects to receive a crushed tebipenem tablet via NGT (n = 6) or via NGT with concomitant Osmolite® enteral feeds (n = 6) on Study Day 1, followed by oral administration of tebipenem whole tablet (reference formulation) on Study Day 2. Tebipenem plasma concentrations were measured by LC with mass spectrometry. Bioequivalence was determined using pharmacokinetic parameters derived through non-compartmental analyses.

Results

Mean ± SD tebipenem pharmacokinetic parameters in plasma for subjects who received a crushed tablet via NGT (relative to whole tablet) and a crushed tablet with enteral feeds (relative to whole tablet) were as follows: maximum total plasma concentration (Cmax), 11.1 ± 3.9 (12 ± 3.4) and 10.2 ± 1.9 (10 ± 4) mg/L; area under the curve (AUC0–8), 17.5 ± 3.5 (17.9 ± 2.3) and 15 ± 4.3 (13.4 ± 5.3) mg•h/L. Using the 90% CI criteria, Cmaxand AUC0–8 values for tebipenem were found to be bioequivalent following alternative methods of administration compared with oral dosing of the whole tablet. The three methods of administration were well tolerated.

Conclusion

Results demonstrate that tebipenem maintained bioequivalence when crushed and administered via NGT with and without accompanying enteral feeds in healthy subjects, relative to whole tablet oral administration. Data therefore support alternative methods of tebipenem administration depending on patient condition.
Subcutaneously administered antibiotics: a review
Authors: Jumpertz Marie , Guilhaumou Romain , Million Matthieu , Parola Philippe , Lagier Jean-Christophe , Brouqui Philippe , Cassir Nadim
Published: November 2022

Background

Subcutaneous (SC) administration of antibiotics represents an attractive alternative to the intravenous (IV) route.

Methods

We performed a systematic electronic search of PubMed and the Cochrane Library for all articles published prior to April 2022, using the key terms and MeSH terms ‘subcutaneous’, ‘antibiotic’ and the international non-proprietary name of antibiotics.

Results

A total of 30 studies were selected including data on the efficacy and tolerability of antibiotics, and seven studies that were conducted in healthy subjects, for relevant information regarding the safety and tolerability of antibiotics. Comparative studies have shown that efficacy is similar for the SC and IV routes for ceftriaxone, teicoplanin and ertapenem. The SC use of other antibiotics such as ampicillin, ceftazidime, cefepime, piperacillin/tazobactam, metronidazole and fosfomycin has also been described. These results have largely been corroborated by pharmacokinetic/pharmacodynamic analyses, especially for time-dependent antibiotics. Complications of SC treatment are rarely severe, with no reports of bacteraemia or other invasive infection related to this route of administration. Therapeutic drug monitoring has been proposed to adapt the dose and avoid toxicity.

Discussion

The rationale for using SC administration of ceftriaxone, ertapenem and teicoplanin is strong in patients with non-severe infections. It is already commonly practised in some countries, particularly in France. Other antibiotics could be administered subcutaneously, but further studies are needed to validate their use in clinical practice. Further research is needed to safely generalize and optimize this route of administration whenever possible. This would reduce the risk of catheter-related infections and their complications, together with the length of hospital stay.
Gastrointestinal dynamics, immune response, and nutrient digestibility of weanling pigs fed diets supplemented with enzymatically treated yeast
Authors: Alagbe Emmanuel O , Aderibigbe Ayodeji S , Schulze Hagen , Ajuwon Kolapo M , Adeola Olayiwola
Published: November 2022

The objective of this trial was to investigate the effect of enzymatically treated yeast (ETY) on the growth performance, nutrient digestibility, immune response, and gut health of weanling pigs. A total of 192 weanling pigs (6.0 ± 1.04 kg) were allocated to 4 corn and soybean-based diets with increasing concentrations of ETY (0, 1, 2, or 4 g/kg) for a 43-d trial. There were 8 replicate pens (4 replicate pens per sex) and 6 pigs per replicate. The experiment was set up as a randomized complete block design with body weight used as a blocking factor. Pigs had ad libitum access to water and diets for the duration of the study. There was no effect of ETY supplementation on the growth performance indices of weanling pigs. At day 14, there was a quadratic decrease (P < 0.05) in the apparent total tract digestibility (ATTD) of acid detergent fiber (ADF). At day 28, there was a linear increase (P < 0.05) in the ATTD of neutral detergent fiber and a quadratic decrease (P < 0.05) in the ATTD of ADF. On day 14, there was a linear increase (P < 0.05) in serum catalase activity with ETY supplementation. There was a linear increase (P < 0.01) in the gene expression of glutathione peroxidase-4 in the ileal mucosa of pigs. Increasing dietary ETY supplementation linearly decreased (P < 0.05) the gene expression of ileal peptide transporter 1. There was a tendency for a quadratic effect (P = 0.07) in the ileal villus height to crypt depth ratio with ETY supplementation. In addition, there was a tendency for a linear increase (P = 0.06) in ileal digesta butyrate with ETY supplementation. In conclusion, the current study demonstrated that dietary ETY supplementation could partly ameliorate the deleterious effects of post-weaning stress by enhancing the antioxidative status of weanling pigs. However, prolonged supplementation of ETY may be needed to see its effect on growth performance.
A comparative study of fatigue behavior between S-shaped and involute POM gears
Authors: Wu Ruo , Wei Peitang , Lu Zehua , Liu Huaiju , Zorko Damijan , Xie Huaijie
Published: November 2022

Applications of polymer gears have been gradually expanding from motion transmission to power transmission fields. Design of new gear teeth profiles plays a crucial role in meeting the requirement of replacing metallic gears with polymer ones. This work develops a computational framework consisting of tooth profile generation and fatigue life prediction of S-shaped and involute POM gears. The contact and bending fatigue performances of S-shaped and involute POM gears under oil lubrication are comparatively studied. It is found that the S-shaped profile reduces the tooth root stress by 25% and significantly improves the bending fatigue life by 10 times compared with the involute profile, especially under medium or high loading levels. Furthermore, the S-shaped gear with a single circular-filleted root curve benefits a 20% reduction of tooth root stress and a 30% increase in bending fatigue life compared to a double circular-filleted root curve S-shaped gear.
Additional evidence that Fomalhaut b might be a non-exoplanet
Authors: Del Vecchio Alexa , Stone Jonathon Rick
Published: November 2022

Fomalhaut b is an extrasolar object that was imaged directly in 2008. Its status since has changed from exoplanet – including super-Earth and low-mass candidates – to neutron star to dust cloud, generating contention, controversy, and confusion. We contribute to the discussion by reporting additional evidence that, given a set containing celestial objects classified as exoplanets, Fomalhaut b might be a non-member. We conducted a principal component (PC) analysis on a data set containing 425 extrasolar objects and 7 variables and found a single isolated point in PC space representing Fomalhaut b. Whatever its existential status, Fomalhaut b is characterized by properties very different from those characterizing exoplanets.
NPInter v5.0: ncRNA interaction database in a new era
Authors: Zheng Yu , Luo Huaxia , Teng Xueyi , Hao Xinpei , Yan Xiaoyu , Tang Yiheng , Zhang Wanyu , Wang Yuanxin , Zhang Peng , Li Yanyan , Zhao Yi , Chen Runsheng , He Shunmin
Published: November 2022

Noncoding RNAs (ncRNAs) play key regulatory roles in biological processes by interacting with other biomolecules. With the development of high-throughput sequencing and experimental technologies, extensive ncRNA interactions have been accumulated. Therefore, we updated the NPInter database to a fifth version to document these interactions. ncRNA interaction entries were doubled from 1 100 618 to 2 596 695 by manual literature mining and high-throughput data processing. We integrated global RNA–DNA interactions from iMARGI, ChAR-seq and GRID-seq, greatly expanding the number of RNA–DNA interactions (from 888 915 to 8 329 382). In addition, we collected different types of RNA interaction between SARS-CoV-2 virus and its host from recently published studies. Long noncoding RNA (lncRNA) expression specificity in different cell types from tumor single cell RNA-seq (scRNA-seq) data were also integrated to provide a cell-type level view of interactions. A new module named RBP was built to display the interactions of RNA-binding proteins with annotations of localization, binding domains and functions. In conclusion, NPInter v5.0 (http://bigdata.ibp.ac.cn/npinter5/) provides informative and valuable ncRNA interactions for biological researchers.
Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers
Authors: Takeuchi Chikara , Yokoshi Moe , Kondo Shu , Shibuya Aoi , Saito Kuniaki , Fukaya Takashi , Siomi Haruhiko , Iwasaki Yuka W
Published: November 2022

Telomeres in Drosophila are composed of sequential non-LTR retrotransposons HeT-A, TART and TAHRE. Although they are repressed by the PIWI-piRNA pathway or heterochromatin in the germline, the regulation of these retrotransposons in somatic cells is poorly understood. In this study, we demonstrated that specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells. Among the variants, we found that the Mod(mdg4)-N variant represses HeT-A expression the most efficiently. Subtelomeric sequences bound by Mod(mdg4)-N block enhancer activity within subtelomeric TAS-R repeats. This enhancer-blocking activity is increased by the tandem association of Mod(mdg4)-N to repetitive subtelomeric sequences. In addition, the association of Mod(mdg4)-N couples with the recruitment of RNA polymerase II to the subtelomeres, which reinforces its enhancer-blocking function. Our findings provide novel insights into how telomeric retrotransposons are regulated by the specific variants of insulator proteins associated with subtelomeric sequences.
Incorporating cell hierarchy to decipher the functional diversity of single cells
Authors: Chen Lingxi , Li Shuai Cheng
Published: November 2022

Cells possess functional diversity hierarchically. However, most single-cell analyses neglect the nested structures while detecting and visualizing the functional diversity. Here, we incorporate cell hierarchy to study functional diversity at subpopulation, club (i.e., sub-subpopulation), and cell layers. Accordingly, we implement a package, SEAT, to construct cell hierarchies utilizing structure entropy by minimizing the global uncertainty in cell–cell graphs. With cell hierarchies, SEAT deciphers functional diversity in 36 datasets covering scRNA, scDNA, scATAC, and scRNA-scATAC multiome. First, SEAT finds optimal cell subpopulations with high clustering accuracy. It identifies cell types or fates from omics profiles and boosts accuracy from 0.34 to 1. Second, SEAT detects insightful functional diversity among cell clubs. The hierarchy of breast cancer cells reveals that the specific tumor cell club drives AREG-EGFT signaling. We identify a dense co-accessibility network of cis-regulatory elements specified by one cell club in GM12878. Third, the cell order from the hierarchy infers periodic pseudo-time of cells, improving accuracy from 0.79 to 0.89. Moreover, we incorporate cell hierarchy layers as prior knowledge to refine nonlinear dimension reduction, enabling us to visualize hierarchical cell layouts in low-dimensional space.
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase
Authors: Krysiak Kilannin , Danos Arpad M , Saliba Jason , McMichael Joshua F , Coffman Adam C , Kiwala Susanna , Barnell Erica K , Sheta Lana , Grisdale Cameron J , Kujan Lynzey , Pema Shahil , Lever Jake , Ridd Sarah , Spies Nicholas C , Andric Veronica , Chiorean Andreea , Rieke Damian T , Clark Kaitlin A , Reisle Caralyn , Venigalla Ajay C , Evans Mark , Jani Payal , Takahashi Hideaki , Suda Avila , Horak Peter , Ritter Deborah I , Zhou Xin , Ainscough Benjamin J , Delong Sean , Kesserwan Chimene , Lamping Mario , Shen Haolin , Marr Alex R , Hoang My H , Singhal Kartik , Khanfar Mariam , Li Brian V , Lin Wan-Hsin , Terraf Panieh , Corson Laura B , Salama Yasser , Campbell Katie M , Farncombe Kirsten M , Ji Jianling , Zhao Xiaonan , Xu Xinjie , Kanagal-Shamanna Rashmi , King Ian , Cotto Kelsy C , Skidmore Zachary L , Walker Jason R , Zhang Jinghui , Milosavljevic Aleksandar , Patel Ronak Y , Giles Rachel H , Kim Raymond H , Schriml Lynn M , Mardis Elaine R , Jones Steven J M , Raca Gordana , Rao Shruti , Madhavan Subha , Wagner Alex H , Griffith Malachi , Griffith Obi L
Published: November 2022

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.
ANGI-02. EPIGENETIC REGULATION OF GLIOMA INVASION BY CHITINASE-3-LIKE PROTEIN 1 (CHI3L1) CPG PROMOTER METHYLATION
Authors: Schreiner Sophie , Cialini Camille , Salcedo Uxue , Mittelbronn Michel , Hau Ann-Christin , Müller Tanja
Published: November 2022

Epigenetically controlled processes play an important role in development but also in the formation and progression of many common diseases. Molecular signatures are increasingly incorporated into cancer classifications and DNA methylation-based analyses of brain tumors including glioma is currently the gold standard. Glioblastoma (GBM), CNS WHO grade 4, is characterized by a very diffuse infiltrative growth into the adjacent brain parenchyma. Due to these highly invasive but also genetically heterogeneous and plastic cellular phenotypes, standard treatment, including maximum resection, radio- and chemotherapy, has limited efficacy. It can be assumed that intertumoral or molecular heterogeneity of gliomas at the transcriptome level is caused by altered epigenetic changes within the individual tumor cells. Considering this, we hypothesize that tumor cell invasion being one of the major hallmarks of highly malignant gliomas can be associated with altered DNA methylation and therefore transcript expression. To analyze this, we isolated fractions of glioma cells with increased invasive properties and performed Illumina® array-based methylation profiling as well as RNA sequencing analysis to identify methylation-driven, invasion-promoting genes. Among other, we focused on Chitinase-3-like protein 1 (CHI3L1) as a candidate gene with significantly decreased promoter methylation in invasive cell fractions and overall strong transcript expression in high-grade gliomas. Differential expression and methylation correlation of TCGA data combined with our own dataset revealed that CHI3L1 expression is dependent on the methylation status of at least three CpG sites within the gene promoter region. We validated these findings using several in vitro experimental settings and propose an upstream regulatory mechanism in which single CpG DNA demethylation within the CHI3L1 promoter facilitates transcription factor binding resulting in gene expression.
ANGI-04. DEPLETION OF CHITINASE-3-LIKE PROTEIN 1 (CHI3L1) IN HUMAN U87-MG GLIOMA CELLS AFFECTS TUMOUR GROWTH AND NEOVASCULATURE IN INTRACRANIAL MOUSE MODEL
Authors: Cyranowski Salwador , Zawadzka Malgorzata , Wojtas Bartosz , Swatler Julian , Kaminska Bozena
Published: November 2022

Chitinase-3-like protein 1 (CHI3L1) plays multiple roles in inflammation, tissue remodelling, and wound healing. It is a new, potentially druggable target for the treatment of cancer due to its association with both extracellular matrix (ECM) modifications and potential involvement in neoangiogenesis. Expression of CHI3L1 is upregulated in glioblastoma (GBM), the most common and aggressive primary brain tumour. The role of CHI3L1 in GBM progression is not fully understood and calls for further research. We generated a knockout (KO) of CHI3L1 in human glioblastoma U87-MG cells. To evaluate the effects of CHI3L1 KO on tumour growth, wild-type (WT) or CHI3L1 KO cells were intracranially implanted into athymic mice and tumour volume was assessed with magnetic resonance imaging. We have measured the serum level of CHI3L1 in both groups and correlated it with the tumour burden. Immunofluorescent staining against endothelium marker – von Willebrand factor (vWF), and perivascular water channel – aquaporin 4 (AQP4) were employed to evaluate the tumour vasculature in both groups. We found that CHI3L1 KO in glioblastoma cells significantly reduced volume of established tumors. Blood serum level of CHI3L1 positively correlated with tumour burden of experimental animals, which corroborates its role as a biomarker. Immunostaining for vWF revealed that in CHI3L1 KO gliomas there were more non-capillary blood vessels than in controls. We observed a higher level of AQP4 in CHI3L1 KO tumours, which suggests a difference in the structure of perivascular space, and thus vasculature functionality, in CHI3L1 depleted gliomas. In conclusion, we demonstrated the involvement of glioma-derived CHI3L1 in the growth and neovasculature of experimental human gliomas. Our findings suggest that the depletion of CHI3L1 in glioma cells results in a higher number and possibly different structure of non-capillary blood vessels in the tumour. Studies supported by the grant N 2020/39/B/NZ4/02683 from the National Science Center.
BIOM-06. IDENTIFICATION OF AN INFLAMMATORY BIOMARKER SIGNATURE IN PLASMA-DERIVED EXTRACELLULAR VESICLES OF GLIOBLASTOMA PATIENTS
Authors: Giamas Georgios , Cilibrasi Chiara , Simon Thomas , Stewart Nicolas , Critchley Giles , Eravci Murat
Published: November 2022

Diagnosis of Glioblastoma (GBM) remains a clinical challenge, currently relying on symptomatic presentation of the tumour, brain imaging and invasive biopsy. Description of effective biomarkers in biofluids could prove invaluable in GBM diagnosis. Extracellular vesicles (EVs) are essential to intercellular crosstalk in the tumour bulk and circulating EVs have been described as a potential reservoir of GBM biomarkers. Our work focuses on the: (i) isolation of EVs from blood liquid biopsies of GBM patients. (ii) Characterisation of their transcriptomic and proteomic cargoes to identify/validate novel candidate GBM biomarkers that could improve GBM diagnosis/prognosis. (iii) For cases where the original GBM tumour tissues are available, we will examine the expression of the identified biomarker signatures (derived from blood-EVs) to see if the content of EVs mirrors the transcriptomic/proteomic profile of the original tissue. Similar comparisons will be performed in GBM cohorts available in TCGA. Ultimately, in future studies, transcriptomic/proteomic analyses will be assessed during patients’ follow-ups to correlate the observed biomarker profiles with MRI data,treatment,recurrence, including molecular and clinical features.Our preliminary data comparing the proteomic cargoes of EVs derived from GBM patients (n=15) and those from healthy volunteers (n=10) indicated the presence of a GBM inflammatory biomarker signature comprising members of the complement and regulators of inflammation and coagulation. Bioinformatic analysis highlighted that all potential markers exclusively identified in patient samples have been linked with either GBM diagnosis,prognosis or associated signalling, suggesting that sEVs protein cargo could mirror the landscape of the original tumour and that selective circulating sEV-derived proteins might be used as hallmarks for GBM patients.Overall, this study is a step forward in the development of a non-invasive liquid biopsy approach for the identification of valuable biomarkers that could significantly improve GBM diagnosis and, consequently, patients’ prognosis and quality of life.