bluuebunny/crossref_metadata_2025 huggingface dataset:
Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa
Authors: Tapela Kesego , Oyawoye Fatima O. , Olwal Charles Ochieng’ , Opurum Precious C. , Amponsah Jones Amo , Segbedzi Kekeli Aku Lumor , Tetteh Becky , Kumi-Ansah Frederick , Mutungi Joe K. , Obodai Evangeline , Amoako Emmanuella , Agyemang Seth , Ndam Nicaise Tuikue , Ampofo William Kwabena , Rayner Julian C. , Awandare Gordon A. , Paemka Lily , Bediako Yaw , Quashie Peter Kojo
Published: October 2022

Background

West Africa has recorded a relatively higher proportion of asymptomatic coronavirus disease 2019 (COVID-19) cases than the rest of the world, and West Africa-specific host factors could play a role in this discrepancy. Here, we assessed the association between COVID-19 severity among Ghanaians with their immune profiles and ABO blood groups.

Methods

Plasma samples were obtained from Ghanaians PCR-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive individuals. The participants were categorized into symptomatic and asymptomatic cases. Cytokine profiling and antibody quantification were performed using Luminex™ multiplex assay whereas antigen-driven agglutination assay was used to assess the ABO blood groups. Immune profile levels between symptomatic and asymptomatic groups were compared using the two-tailed Mann-Whitney U test. Multiple comparisons of cytokine levels among and between days were tested using Kruskal-Wallis with Dunn’s post hoc test. Correlations within ABO blood grouping (O’s and non-O’s) and between cytokines were determined using Spearman correlations. Logistic regression analysis was performed to assess the association of various cytokines with asymptomatic phenotype.

Results

There was a trend linking blood group O to reduced disease severity, but this association was not statistically significant. Generally, symptomatic patients displayed significantly (p < 0.05) higher cytokine levels compared to asymptomatic cases with exception of Eotaxin, which was positively associated with asymptomatic cases. There were also significant (p < 0.05) associations between other immune markers (IL-6, IL-8 and IL-1Ra) and disease severity. Cytokines’ clustering patterns differ between symptomatic and asymptomatic cases. We observed a steady decrease in the concentration of most cytokines over time, while anti-SARS-CoV-2 antibody levels were stable for at least a month, regardless of the COVID-19 status.

Conclusions

The findings suggest that genetic background and pre-existing immune response patterns may in part shape the nature of the symptomatic response against COVID-19 in a West African population. This study offers clear directions to be explored further in larger studies.
‘It’s the same thing as giving them CPR training’: rural first responders’ perspectives on naloxone
Authors: Filteau Matthew R. , Green Brandn , Kim Frances , McBride Ki-Ai
Published: October 2022

The Substance Abuse and Mental Health Services Administration’s (SAMHSA) Harm Reduction grant program expanded access to several harm reduction strategies to mitigate opioid overdose fatalities, including expanding access to naloxone. Interviews with first responders in a frontier and remote (FAR) state were conducted to understand their job responsibilities in relation to overdose response and prevention and their perceptions of training laypersons to administer naloxone. This study includes 22 interviews with law enforcement, EMS and/or fire personnel, and members of harm reduction-focused community organizations. The study finds widespread support for increasing access to naloxone and training laypersons in naloxone administration throughout Montana, due to rural first responders’ inability to meet the needs of residents and an overall lack of resources to address addiction and the effects of fentanyl. Participants from harm reduction-focused community organizations convey support for training lay persons, but also illuminate that real and perceived cultural opposition to harm reduction strategies could reduce the likelihood that laypeople enroll in naloxone training. This study adds to the literature because it focuses on first responders in a FAR area that would benefit from layperson naloxone education and administration training due to its geographic expansiveness and the area’s overall lack of access to medications for opioid use disorder or other treatment services. Expanding harm reduction approaches, like increasing access and training laypersons to administer naloxone, might be FAR residents’ best chance for surviving an opioid overdose.
Incomplete penetrance of NOD2 C483W mutation underlining Blau syndrome
Authors: Chang Shao-Yu , Kambe Naotomo , Fan Wen-Lang , Huang Jing-Long , Lee Wen-I , Wu Chao-Yi
Published: October 2022

Background

Blau syndrome (BS) is a rare autoinflammatory disorder with NOD2 gain-of-function mutation and characterized by autoactivation of the NFκB pathway. Classically considered a disease of high penetrance, reports on NOD2 mutations underlining BS with incomplete penetrance is limited.

Case presentation

The proband is a 9-year-old girl presented with brownish annular infiltrative plaques and symmetric boggy polyarthritis over bilateral wrists and ankles. Her skin biopsy revealed noncaseating granulomas inflammation with multinucleated giant cells. A novel C483W NOD2 mutation was identify in the proband and her asymptomatic father. Functional examinations including autoactivation of the NFκB pathway demonstrated by in vitro HEK293T NOD2 overexpression test as well as intracellular staining of phosphorylated-NFκB in patient’s CD11b+ cells were consistent with BS.

Conclusions

We reported a novel C483W NOD2 mutation underlining BS with incomplete penetrance. Moreover, a phosphorylated-NFκB intracellular staining assay of CD11b+ was proposed to assist functional evaluation of NFκB autoactivation in patient with BS.
An interactive mobile application versus an educational booklet to promote job retention in women undergoing adjuvant chemotherapy for breast cancer: a randomized controlled trial
Authors: Blinder Victoria S. , Patil Sujata , Finik Jackie , Makower Della , Muppidi Monica , Lichtenthal Wendy G. , Parker Patricia A. , Claros Maria , Suarez Jennifer , Narang Bharat , Gany Francesca
Published: October 2022

Background

Job loss after a cancer diagnosis can lead to long-term financial toxicity and its attendant adverse clinical consequences, including decreased treatment adherence. Among women undergoing (neo)adjuvant chemotherapy for breast cancer, access to work accommodations (e.g., sick leave) is associated with higher job retention after treatment completion. However, low-income and/or minority women are less likely to have access to work accommodations and, therefore, are at higher risk of job loss. Given the time and transportation barriers that low-income working patients commonly face, it is crucial to develop an intervention that is convenient and easy to use.

Methods

We designed an intervention to promote job retention during and after (neo)adjuvant chemotherapy for breast cancer by improving access to relevant accommodations. Talking to Employers And Medical staff about Work (TEAMWork) is an English/Spanish mobile application (app) that provides (1) suggestions for work accommodations tailored to specific job demands, (2) coaching/strategies for negotiating with an employer, (3) advice for symptom self-management, and (4) tools to improve communication with the medical oncology team. This study is a randomized controlled trial to evaluate the app as a job-retention tool compared to a control condition that provides the app content in an informational paper booklet. The primary outcome of the study is work status after treatment completion. Secondary outcomes include work status 1 and 2 years later, participant self-efficacy to ask an employer for accommodations, receipt of workplace accommodations during and following adjuvant therapy, patient self-efficacy to communicate with the oncology provider, self-reported symptom burden during and following adjuvant therapy, and cancer treatment adherence.

Discussion

This study will assess the use of mobile technology to improve vulnerable breast cancer patients’ ability to communicate with their employers and oncology providers, work during treatment and retain their jobs in the long term, thereby diminishing the potential consequences of job loss, including decreased treatment adherence, debt, and bankruptcy.

Trial registration

ClincalTrials.govNCT03572374. Registered on 08 June 2018.
Mitochondrial neurogastrointestinal encephalomyopathy in a Pakistani female: a case report
Authors: Khan Zaraq Rashid , Karam Alvina , ul Haq Mian Ayaz , Aman Aleena , Karam Ahmad Sharjeel
Published: October 2022

Background

Mitochondrial neurogastrointestinal encephalopathy is a rare multisystem autosomal recessive disease caused by mutations in the TYMP gene, that encodes for thymidine phosphorylase. Mitochondrial neurogastrointestinal encephalopathy is a progressive degenerative disease characterized by a distinctive tetrad of gastrointestinal dysmotility, peripheral neuropathy, ophthalmoplegia with ptosis, and asymptomatic leukoencephalopathy. It provides a diagnostic dilemma to physicians in regions like Pakistan because of a lack of genetic study availability and associated financial constraints of the population. However, with careful examination and a few basic investigations, mitochondrial neurogastrointestinal encephalopathy can be diagnosed by ruling out most of the close differentials.

Case presentation

We report the case of a 23-year-old Asian female whose chief complaints were epigastric pain, bilious emesis, weight loss for 3 months, and bilateral lower limb weakness for 20 days. All clinical signs and symptoms along with relevant investigations including nerve conduction studies, electromyography, and magnetic resonance imaging of the brain were highly suggestive of mitochondrial neurogastrointestinal encephalopathy syndrome. Because of financial constraints, genetic studies could not be performed. The patient was managed with a multidisciplinary approach involving gastroenterology, physiotherapy, and nutrition departments. Currently, therapeutic options for the disease include allogeneic hematopoietic stem cell transplant and carrier erythrocyte entrapped thymidine phosphorylase; however, these could not be provided to the patient owing to certain limitations.

Conclusions

As misdiagnosis and delayed diagnosis are quite common in this disease, the prime objective of this case report is to increase the basic understanding of this disease, especially its signs and symptoms, and address the limitations regarding the diagnostic investigations and management of patients with mitochondrial neurogastrointestinal encephalopathy.
Lactobacillus rhamnosus and Staphylococcus epidermidis in gut microbiota: in vitro antimicrobial resistance
Authors: Hindieh Pamela , Yaghi Joseph , Khoury André El , Chokr Ali , Atoui Ali , Louka Nicolas , Assaf Jean Claude
Published: October 2022

The gastrointestinal tract is one of the most complex microbiological niches containing beneficial and non-pathogenic bacterial strains of which some may evolve into virulent under specific conditions. Lactobacillus rhamnosus GG is of the most known beneficial species with an ability to protect the intestine as opposed to Staphylococcus epidermidis 444 which causes serious health risks due to its high antimicrobial resistance. This study investigates first the survival and coexistence ability of L. rhamnosus GG, and S. epidermidis 444 at different pH levels. Subsequently, lysozyme's antimicrobial and antibiofilm effect on these two strains was elucidated before adding different concentrations of oxytetracycline hydrochloride antibiotic. Results showed that 50% inhibition of L. rhamnosus GG, S. epidermidis 444, and a co-culture of these planktonic strains were obtained respectively at a lysozyme concentration of 30, 18, and 26 mg/mL after the addition of ethylenediamine tetra-acetic acid (EDTA). At a pH of 7.5, mixing lysozyme (at IC50) and EDTA with oxytetracycline hydrochloride (700 μg/mL) showed an additional bactericidal effect as compared to its known bacteriostatic effect. Similarly, the addition of lysozyme to the antibiotic further increased the biofilm eradication of S. epidermidis 444 and L. rhamnosus GG where a maximal eradication of 70% was reached. Therefore, the potential development of new drugs based on adding a lysozyme-EDTA mixture to different types of antibiotics may be highly promising.
Gabapentin, a human therapeutic medication and an environmental substance transferring at trace levels to horses: a case report
Authors: Brewer Kimberly , Machin Jacob , Maylin George , Fenger Clara , Morales-Briceño Abelardo , Tobin Thomas
Published: October 2022

Gabapentin, 1-(Aminomethyl)cyclohexaneacetic acid, MW 171.240, is a frequently prescribed high dose human medication that is also used recreationally. Gabapentin is orally absorbed; the dose can be 3,000 mg/day and it is excreted essentially unchanged in urine. Gabapentin is stable in the environment and routinely detected in urban wastewater. Gabapentin randomly transfers from humans to racing horses and is at times detected at pharmacologically ineffective / trace level concentrations in equine plasma and urine. In Ohio racing between January 2019 and July 2020,18 Gabapentin identifications, all less than 2 ng/ml in plasma, were reported. These identifications were ongoing because the horsemen involved were unable to pin down and therefore avoid the source of these identifications. Given that 44 ng/ml or less is an Irrelevant Plasma Concentration (IPC) of Gabapentin in horses, we proposed a 5 ng/ml plasma interim Screening Limit of Detection for Gabapentin identifications in Ohio racing, and an essentially similar 8 ng/ml plasma Screening Limit of Detection was suggested by a scientific advisor to the Ohio Horse Racing Commission. As such, an analytical Screening Limit of 8 ng /ml in plasma is an appropriate and pharmacologically conservative analytical “cut-off” or Screening Limit of Detection (SLOD) for Gabapentin in equine competitive events to avoid the calling of “positive” identifications on random unavoidable trace level identifications of this widely prescribed human therapeutic medication in equine forensic samples.
Pathologic complete response following low-dose radiation for advanced oral cavity cancer in a patient with human immunodeficiency virus
Authors: Leming Amy B. , Johnston Andrea L. , Krempl Greg A. , Fowle Evan J. , Morton Daniel J. , Henson Christina E.
Published: October 2022

Background

Advanced squamous cell carcinoma (SCCa) of the oral cavity is often not amenable to curative-intent therapy due to tumor location, tumor size, or comorbidities.

Case presentation

A 51-year-old male patient with human immunodeficiency virus and on highly active antiretroviral therapy (HAART) presented with a cT4aN2c SCCa of the tongue. He received a preoperative single course of Quad-Shot radiation therapy to 14 Gy in 4 fractions followed by surgical resection. Patient had no residual carcinoma on surgical pathology and no evidence of disease on subsequent clinical and radiological exams.

Conclusions

To our knowledge, this is the first case of pathologic complete response for a patient on HAART following a single cycle of the Quad-Shot regimen for advanced oral cavity SCCa. Protease inhibitors in HAART can induce spontaneous tumor regression via inhibition of proteasome function and activation of apoptosis, and thus act as a cancer therapeutic.

Graphical abstract
Investigating the potential of the Nd:YAG and Er:YAG lasers for the cleaning of feathers: a pilot study
Authors: Bertasa Moira , Korenberg Capucine
Published: October 2022

A dual-wavelength Q-switched Nd:YAG laser emitting at 1064 nm and 532 nm and an Er:YAG laser were tested on a range of feathers containing melanin, carotenoids and psittacofulvins. Dyed, white and iridescent feathers, as well as down feathers, were also included in the study. First, the damage threshold fluence was determined for each type of feather and then, as appropriate, laser tests were conducted on feathers artificially soiled with dust or carbon black. The Nd:YAG laser was unsuccessful at cleaning feathers soiled with carbon black. Better outcomes were obtained on feathers soiled with dust: the Nd:YAG laser was effective at both wavelengths at removing dust from white feathers, dyed feathers and yellow feathers containing psittacofulvins. Feathers containing melanin, as their main colourant, were found to have a much lower damage threshold fluence than other feathers. Also, laser radiation at 532 nm at high fluences can cause discolouration on pink feathers containing carotenoids. Finally, it was not possible to remove dust from down feathers without causing thermal damage. This investigation showed that laser cleaning using a Q-switched Nd:YAG laser can remove dust from certain types of feathers. However, further research is needed to assess any potential chemical or long-term effects of laser cleaning on feathers. Finally, the Er:YAG laser was found to be unsuitable for laser cleaning resulting in thermal damage to all feathers at low fluences.
Exfoliation of stone cultural relics under the microclimate in the Yongling Mausoleum of the Former Shu Dynasty
Authors: Zhang Yao , Cui Deshan , Bao Xun , Liu Shiyi , Guo Hong , Li Bo
Published: October 2022

Many degradation processes of cultural heritage objects are associated with unsuitable microclimatic conditions. One of the most ubiquitous deteriorations is the crystallization of salts in pores, which can accelerate the erosion rate of masonry historical relics. In this study, the microclimate of the burial tomb and exfoliation of sandstone in the Yongling Mausoleum of the Former Shu Dynasty in Chengdu were monitored for 1 year to determine the development of the degradation. We established a connection between the monitoring data and exfoliation variations of the stone with time. To predict the deterioration of the stone, a three-dimensional computational finite element model was used to simulate the detailed process of the thermo-hygrometric performance that led to salt crystallization and artwork deterioration. Two results were obtained. In the simulation of the microclimate, the temperature ranged from 15 to 22.6 °C, and the relative humidity was heterogeneous and varied between 60 and 100%. The other was the relationship between the microclimate and exfoliation. It was found that the exfoliation was more severe in the higher relative humidity areas where the water vapor frequently interacted with the relics. The crystallization and hydration of sulfate produced stress, which damaged the stone relics. These results provide a rationale analysis and a reference for better management of the environmental interactions and reduction of the environmental impacts in the subsequent scientific conservation of ancient Chinese cultural relics in tombs.
The effectiveness of value-based messages to engage gun owners on firearm policies: a three-stage nested study
Authors: Boine Claire , Siegel Michael , Maiga Abdine
Published: October 2022

Background

Although gun owners overwhelmingly support violence prevention policies, they are hesitant to speak up publicly to advocate for these policies. We tested a series of communication messages on gun owners’ level of support for various firearm violence prevention policies and on their willingness to engage in gun violence prevention advocacy.

Methods

We conducted three consecutive experiments, testing a total of thirteen messages on a sample of gun owners over 18 years old who live in the U.S. The first was a random experiment, the second a quasi-experiment, and the third a randomized control trial. The goal of having these varied methods was to develop messages applicable to different contexts with different levels of information about the audience.

Results

The most effective message was a script showing respect for gun owners’ decisions to purchase a firearm and proposing a balanced policy roadmap to end gun violence, which led to an increase in gun owner’s willingness to engage in eight different advocacy activities. We also found a value-based message conveying loyalty to increase support for domestic violence related prohibitions and willingness to engage in advocacy for gun violence prevention policies.

Conclusions

Public health professionals need to develop communication strategies that are aligned with gun owners’ values and that affirm respect for gun culture and for gun owners’ decisions to own a gun.
Therapeutic non-invasive brain treatments in Alzheimer’s disease: recent advances and challenges
Authors: Wu Chongyun , Yang Luoman , Feng Shu , Zhu Ling , Yang Luodan , Liu Timon Cheng-Yi , Duan Rui
Published: October 2022

Alzheimer’s disease (AD) is one of the major neurodegenerative diseases and the most common form of dementia. Characterized by the loss of learning, memory, problem-solving, language, and other thinking abilities, AD exerts a detrimental effect on both patients’ and families’ quality of life. Although there have been significant advances in understanding the mechanism underlying the pathogenesis and progression of AD, there is no cure for AD. The failure of numerous molecular targeted pharmacologic clinical trials leads to an emerging research shift toward non-invasive therapies, especially multiple targeted non-invasive treatments. In this paper, we reviewed the advances of the most widely studied non-invasive therapies, including photobiomodulation (PBM), transcranial magnetic stimulation (TMS), transcranial direct current stimulation (tDCS), and exercise therapy. Firstly, we reviewed the pathological changes of AD and the challenges for AD studies. We then introduced these non-invasive therapies and discussed the factors that may affect the effects of these therapies. Additionally, we review the effects of these therapies and the possible mechanisms underlying these effects. Finally, we summarized the challenges of the non-invasive treatments in future AD studies and clinical applications. We concluded that it would be critical to understand the exact underlying mechanisms and find the optimal treatment parameters to improve the translational value of these non-invasive therapies. Moreover, the combined use of non-invasive treatments is also a promising research direction for future studies and sheds light on the future treatment or prevention of AD.
A Low-Frequency APOB p.(Pro955Ser) Variant Contributes to the Severity of/Variability in Familial Hypercholesterolemia
Authors: Hori Mika , Takahashi Atsushi , Hosoda Kiminori , Ogura Masatsune , Harada-Shiba Mariko
Published: October 2022

Context

Heterozygous familial hypercholesterolemia (HeFH) is caused by a rare pathogenic variant in the LDLR, APOB, and PCSK9 genes. However, the causative variants in these genes have not been identified in approximately 40% of HeFH patients.

Objective

Our aim was to identify novel (or additional) genes/variants that contribute to HeFH.

Methods

Whole-exome sequencing was performed for 215 family members from 122 families with HeFH without pathogenic variants in the LDLR or PCSK9 genes.

Results

We could not find novel causative familial hypercholesterolemia (FH) genes/variants by family analysis. Next, we examined all APOB variants. Twenty-four nonsynonymous APOB variants were identified. The allele frequencies of the c.2863C > T:p.(Pro955Ser) variant in the HeFH probands and the general Japanese population were 0.15 and 0.034, respectively [odds ratio 4.9 (95% CI 3.4-7.1); P = 6.9 × 10−13]. The patients harboring the c.2863C > T:p.(Pro955Ser) variant accounted for 9.8% (n = 63) of unrelated patients with HeFH (n = 645). The penetrance of the c.2863C > T:p.(Pro955Ser) variant was low in the pedigree-based genetic analysis. In an in vitro assay, low-density lipoprotein (LDL) uptake from patients with the homozygous c.2863C > T:p.(Pro955Ser) variant was 44% of the LDL uptake from control subjects, and it was similar to that of the LDL uptake from patients with the known pathogenic heterozygous p.(Arg3527Gln) variant.

Conclusions

The low-frequency APOB c.2863C > T:p.(Pro955Ser) variant is not an FH-causative variant, but it has a moderate effect size in HeFH. These findings suggest that the combination of the APOB c.2863C > T:p.(Pro955Ser) variant and age, environmental factors, or other genetic factors contributes to the severity of or variability in the HeFH phenotype.
Sequential and additive expression of miR-9 precursors control timing of neurogenesis
Authors: Soto Ximena , Burton Joshua , Manning Cerys S. , Minchington Thomas , Lea Robert , Lee Jessica , Kursawe Jochen , Rattray Magnus , Papalopulu Nancy
Published: October 2022

MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.
Formation and function of a highly specialised type of organelle in cardiac valve cells
Authors: Meyer Christian , Breitsprecher Leonhard , Bataille Laetitia , Vincent Alain J. M. , Drechsler Maik , Meyer Heiko , Paululat Achim
Published: October 2022

Within a cell, vesicles play a crucial role in the transport of membrane material and proteins to a given target membrane, and thus regulate a variety of cellular functions. Vesicular transport occurs by means of, among others, endocytosis, where cargoes are taken up by the cell and are processed further upon vesicular trafficking, i.e. transported back to the plasma membrane via recycling endosomes or the degraded by fusion of the vesicles with lysosomes. During evolution, a variety of vesicles with individual functions arose, with some of them building up highly specialised subcellular compartments. In this study, we have analysed the biosynthesis of a new vesicular compartment present in the valve cells of Drosophila melanogaster. We show that the compartment is formed by invaginations of the plasma membrane and grows via re-routing of the recycling endosomal pathway. This is achieved by inactivation of other membrane-consuming pathways and a plasma membrane-like molecular signature of the compartment in these highly specialised heart cells.
Imaging findings of urosymphyseal fistulas
Authors: Patel Kunj , Butt Hayan , Patel Shlok , Roux Jacques , Bhagat Ashish
Published: October 2022

Prostate cancer accounts for 13% of all new cancer diagnoses in the UK. Urosymphyseal fistulas are a rare complication that can occur post-radiotherapy and surgery for prostate cancer. Patients often present with non-specific symptoms such as suprapubic tenderness, poor mobility, recurrent urinary infections, and difficulty passing urine. These can be difficult to diagnose clinically and extremely problematic and debilitating for patients. The management of these patients is often complex and requires input from urology, orthopaedics, and microbiology. At present, there are no clear guidelines for diagnosing these conditions. Recommended investigations include blood tests, urine culture, and imaging. The preferred imaging modality is pelvic MRI. This article explores three rare cases of such complications and the classic imaging findings on CT and MRI to aid the diagnosis of urosymphyseal fistula.
iSnoDi-LSGT: identifying snoRNA-disease associations based on local similarity constraint and global topological constraint
Authors: Zhang Wenxiang , Liu Bin
Published: October 2022

Growing evidences prove that small nucleolar RNAs (snoRNAs) have important functions in various biological processes, malfunction of which leads to the emergence and development of complex diseases. However, identifying snoRNA-disease associations is an ongoing challenging task due to the considerable time-consuming and money-consuming for biological experiments. Therefore, it is urgent to design efficient and economical methods for the identification of snoRNA-diseases associations. In this regard, we propose a computational method named iSnoDi-LSGT, which utilizes snoRNA sequence similarity and disease similarity as local similarity constraint. The iSnoDi-LSGT predictor further employs network embedding technology to extract topological features of snoRNAs and diseases, based on which snoRNA topological similarity and disease topological similarity are calculated as global topological constraint. To the best knowledge of ours, iSnoDi-LSGT is the first computational method for snoRNA-disease association identification. The experimental results indicate that iSnoDi-LSGT predictor can effectively predict the unknown snoRNA-disease associations. The web server of iSnoDi-LSGT predictor is freely available at http://bliulab.net/iSnoDi-LSGT/.
Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance
Authors: Ganesan Robin , Mangkalaphiban Kotchaphorn , Baker Richard , He Feng , Jacobson Allan
Published: October 2022

Upf1, Upf2, and Upf3, the central regulators of nonsense-mediated mRNA decay (NMD), appear to exercise their NMD functions while bound to elongating ribosomes, and evidence for this conclusion is particularly compelling for Upf1. Hence, we employed selective profiling of yeast Upf1:ribosome association to define that step in greater detail, understand whether the nature of the mRNA being translated influences Upf1:80S interaction, and elucidate the functions of ribosome-associated Upf1. Our approach has allowed us to clarify the timing and specificity of Upf1 association with translating ribosomes, obtain evidence for a Upf1 mRNA surveillance function that precedes the activation of NMD, identify a unique ribosome state that generates 37-43 nt ribosome footprints whose accumulation is dependent on Upf1’s ATPase activity, and demonstrate that a mutated form of Upf1 can interfere with normal translation termination and ribosome release. In addition, our results strongly support the existence of at least two distinct functional Upf1 complexes in the NMD pathway.
Regret Analysis of a Markov Policy Gradient Algorithm for Multiarm Bandits
Authors: Walton Neil , Denisov Denis
Published: October 2022

We consider a policy gradient algorithm applied to a finite-arm bandit problem with Bernoulli rewards. We allow learning rates to depend on the current state of the algorithm rather than using a deterministic time-decreasing learning rate. The state of the algorithm forms a Markov chain on the probability simplex. We apply Foster–Lyapunov techniques to analyze the stability of this Markov chain. We prove that, if learning rates are well-chosen, then the policy gradient algorithm is a transient Markov chain, and the state of the chain converges on the optimal arm with logarithmic or polylogarithmic regret.
Best Practices of Fostering Undergraduates’ Cross-Cultural Competence Involving Training Them in Foreign Languages: Systemic Review
Authors: Nozhovnik Oleh , Harbuza Tetiana , Starosta Hanna , Radchenko Yuliia , Zatserkovnyi Oleh
Published: October 2022

The purpose of the study was to identify and categorise the criteria-specified instructional approaches to fostering undergraduates’ cross-cultural skills involving training them in foreign languages and to evaluate their effectiveness and feasibility. It was a systemic review of the effectiveness type. The descriptive content analysis was used as a methodology within the study to analyse the relevant short-listed sources. The triangular assessment method (TAM) was applied by instructors from Ukraine to rate each approach’s/programme/course’s potential effectiveness and/or feasibility for the context of higher education in Ukraine. This review identified potentially effective and feasible approaches/programmes/courses that can be converged to produce more efficient instructional models for fostering undergraduates’ cross-cultural skills. The selected approaches or courses or programmes could be categorised as technology-driven approaches, approaches based on classroom activities or using specific instruction models, psychological effect-driven approaches, and combined or converged approaches. The use of technology-driven approaches seems to be the emerging instructional trend specifically in training students’ cross-cultural skills.
Quantitative focused laser differential interferometry with hypersonic turbulent boundary layers
Authors: Benitez Elizabeth K. , Borg Matthew P. , Luke Hill J. , Aultman Matthew T. , Duan Lian , Running Carson L. , Jewell Joseph S.
Published: October 2022

The effect of turbulent
wind-tunnel-wall boundary
layers on density change measurements obtained with focused laser
differential interferometry (FLDI) was studied using a detailed direct
numerical simulation (DNS) of the wall from the Boeing/AFOSR Mach-6
Quiet Tunnel run in its noisy configuration. The DNS was probed with
an FLDI model that is capable of reading in three-dimensional
time-varying density fields and computing the FLDI response. Simulated
FLDI measurements smooth the boundary-layer root-mean-square (RMS)
profile relative to true values obtained by directly extracting the
data from the DNS. The peak of the density change RMS measured by the
FLDI falls within 20% of the true density change RMS. A relationship
between local spatial density change and temporal density fluctuations
was determined and successfully used to estimate density fluctuations
from the FLDI measurements. FLDI measurements of the freestream
fluctuations are found to be dominated by the off-axis tunnel-wall
boundary layers for lower frequencies despite spatial suppression
provided by the technique. However, low-amplitude (0.05%–5% of the
mean density) target signals placed along the tunnel centerline were
successfully measured over the noise of the boundary layers (which
have RMS values of about 12% of the mean). Overall, FLDI was shown to
be a useful technique for making quantitative turbulence measurements
and to measure finite-width sinusoidal signals through turbulent
boundary layers, but may not provide enough off-focus suppression to
provide accurate freestream noise measurements, particularly at lower
frequencies.
Practical technique for balancing the optical aberrations among conceptual thin-lens components of optical zoom lenses
Authors: Chen Chaohsien
Published: October 2022

Solving conceptual thin-lens components with balanced optical aberrations among
different optical configurations is essential for lens design from
scratch. This paper presents a general and practical method for
building conceptual thin-lens components that can be further optimized
by Code V (a well-known optical design program) to approach specific
aberration targets. The conceptual component consists of a Code V’s
lens module and a hologram with zero diffraction order. The latter
provides spaces for storing the reference data of incident marginal
and chief rays, spherical aberration, central coma, and longitudinal
chromatic aberration without affecting the paraxial ray tracing. Those
reference data are used to evaluate the real aberrations at different
optical configurations by our earlier aberration variation algorithms
[Appl.
Opt. 55, 10363
(2016)APOPAI0003-693510.1364/AO.55.010363]. The model helps
investigate the properties of lenses and solve the balanced
aberrations by the optimization process. An example of solving a zoom
lens with different optimization goals is given to demonstrate the
usage of the method. Detailed design data are listed for
verification.
Motion modeling and blurred image simulation of the star tracker used for deep-space missions
Authors: Yuan Honglin , Lu Ke , Liu Qingshan
Published: October 2022

The star tracker is the most accurate attitude measurement device among different types of attitude measurement devices. It is based on captured star images to extract star centroids and then determine attitude. However, images taken by the star tracker under dynamic conditions are often blurred, which limits its dynamic performance. In this paper, we first classify and model motions of the star tracker under dynamic conditions, including rotations and angular vibrations. Then, a motion kernel consisting of three individual descriptors (trajectory, intensity, and point spread function) is proposed to model the motion blurring process and simulate blurred images. Experimental results show that our approach can model a wide variety of blurs including uniform and non-uniform blurs, and it can provide extremely realistic blurred images. These findings are crucial to the subsequent centroid extraction of stars and the dynamic performance of the star tracker.
Highly sensitive refractive index sensor based on the lossy mode resonance enhanced photonic spin Hall effect
Authors: Wang Huixin , He Ying , Zhang Jing , Xu Yi
Published: October 2022

Different from surface plasmon resonance (SPR) that only can be excited by

p

-polarized light, lossy mode resonance (LMR) can be achieved with both

p

- and

s

-polarized light, thus providing a pathway for enhanced transverse spin-dependent shift (SDS) of the photonic spin Hall effect (PSHE) for the horizontal and vertical polarization states. The maximum transverse SDSs of 13.28 µm and 7.64 µm for the horizontal and vertical polarization states are achieved, respectively, which are about 12 and 7 times the wavelength of incident light. A refractive index sensor based on the LMR enhanced PSHE is proposed, and the maximum refractive index sensitivity of 13500 µm/RIU (RIU, refractive index unit) can be obtained. Our investigation provides an alternative method for the enhancement of PSHE, thus opening up opportunities for the design of various photonic devices based on PSHE.
Dark current and single photon detection by 1550 nm avalanche photodiodes: dead time corrected probability distributions and entropy rates
Authors: Menkart Nicole , Hart Joseph D. , Murphy Thomas E. , Roy Rajarshi
Published: October 2022

Single photon detectors have dark count rates that depend strongly on the bias level for detector operation. In the case of weak light sources such as novel lasers or single-photon emitters, the rate of counts due to the light source can be comparable to that of the detector dark counts. In such cases, a characterization of the statistical properties of the dark counts is necessary. The dark counts are often assumed to follow a Poisson process that is statistically independent of the incident photon counts. This assumption must be validated for specific types of photodetectors. In this work, we focus on single-photon avalanche photodiodes (SPADs) made for 1550 nm. For the InGaAs detectors used, we find the measured distributions often differ significantly from Poisson due to the presence of dead time and afterpulsing with the difference increasing with the bias level used for obtaining higher quantum efficiencies. We find that when the dead time is increased to remove the effects of afterpulsing, it is necessary to correct the measured distributions for the effects of the dead time. To this end, we apply an iterative algorithm to remove dead time effects from the probability distribution for dark counts as well as for the case where light from an external weak laser source (known to be Poisson) is detected together with the dark counts. We believe this to be the first instance of the comprehensive application of this algorithm to real data and find that the dead time corrected probability distributions are Poisson distributions in both cases. We additionally use the Grassberger-Procaccia algorithm to estimate the entropy production rates of the dark count processes, which provides a single metric that characterizes the temporal correlations between dark counts as well as the shape of the distribution. We have thus developed a systematic procedure for taking data with 1550 nm SPADs and obtaining accurate photocount statistics to examine novel light sources.
Hand gestures recognition in videos taken with a lensless camera
Authors: Zhang Yinger , Wu Zhouyi , Lin Peiying , Pan Yang , Wu Yuting , Zhang Liufang , Huangfu Jiangtao
Published: October 2022

A lensless camera is an imaging system that uses a mask in place of a lens, making it thinner, lighter, and less expensive than a lensed camera. However, additional complex computation and time are required for image reconstruction. This work proposes a deep learning model named Raw3dNet that recognizes hand gestures directly on raw videos captured by a lensless camera without the need for image restoration. In addition to conserving computational resources, the reconstruction-free method provides privacy protection. Raw3dNet is a novel end-to-end deep neural network model for the recognition of hand gestures in lensless imaging systems. It is created specifically for raw video captured by a lensless camera and has the ability to properly extract and combine temporal and spatial features. The network is composed of two stages: 1. spatial feature extractor (SFE), which enhances the spatial features of each frame prior to temporal convolution; 2. 3D-ResNet, which implements spatial and temporal convolution of video streams. The proposed model achieves 98.59% accuracy on the Cambridge Hand Gesture dataset in the lensless optical experiment, which is comparable to the lensed-camera result. Additionally, the feasibility of physical object recognition is assessed. Further, we show that the recognition can be achieved with respectable accuracy using only a tiny portion of the original raw data, indicating the potential for reducing data traffic in cloud computing scenarios.
Parallel optical coherent dot-product architecture for large-scale matrix multiplication with compatibility for diverse phase shifters
Authors: Xu Shaofu , Wang Jing , Yi Sicheng , Zhao Xinrui , Liu Binshuo , Shao Jiayi , Zou Weiwen
Published: October 2022

Photonics physically promises high-speed and low-consumption computing of matrix multiplication. Nevertheless, conventional approaches are challenging to achieve large throughput, high precision, low power consumption, and high density simultaneously in a single architecture, because the integration scale of conventional approaches is strongly limited by the insertion loss of cascaded optical phase shifters. Here, we present a parallel optical coherent dot-product (P-OCD) architecture, which deploys phase shifters in a fully parallel way. The insertion loss of phase shifters does not accumulate at large integration scale. The architecture decouples the integration scale and phase shifter insertion loss, making it possible to achieve superior throughput, precision, energy-efficiency, and compactness simultaneously in a single architecture. As the architecture is compatible with diverse integration technologies, high-performance computing can be realized with various off-the-shelf photonic phase shifters. Simulations show that compared with conventional architectures, the parallel architecture can achieve near 100× higher throughput and near 10× higher energy efficiency especially with lossy phase shifters. The parallel architecture is expected to perform its unique advantage in computing-intense applications including AI, communications, and autonomous driving.
Accurate analysis of the efficiency of Bessel Gauss beams passing through two Cassegrain optical antennas in atmospheric turbulence
Authors: Shang Shunyuan , Yang Huajun , Jiang Ping
Published: October 2022

The Bessel Gauss beam has shown good performance in solving occlusion by the secondary mirror of Cassegrain antenna. In this work, the analytical expression for the optical field of the Bessel Gauss beam after passing through the optical communication system comprising two Cassegrain antennas in atmospheric turbulence is derived. The light filed is obtained more precisely by optimising the parameters of the hard-edged optical aperture. And the energy efficiency of the whole system is investigated more accurately taking into account the efficiency of two antennas and the reflection losses. For the 3 order Bessel Gauss beam, the optimal parameters of the system are obtained by calculation. When b = 0.1m, a = 0.0162 m, η
T
of Bessel Gauss beams when l = 1 ∼ 5 are 64%, 91%, 96%, 96%, 96%, respectively. At the same time, the light field expressions we have derived allow us to easily analyze the effect of atmospheric turbulence and antenna defocus on the efficiency of the system. So the effect of turbulent atmosphere and antenna defocus on the efficiency of the system and the corresponding reasons are studied as well.
Ultra-intense laser field amplification from a petawatt-class laser focusing in moderate density plasma
Authors: Li Niehong , Zou Debin , Zhao Na , Jiang Xiangrui , Shao Fuqiu , Yu Tongpu
Published: October 2022

The rapid development of laser technologies promises a significant growth of peak laser intensity from 1022 W/cm2 to >1023 W/cm2, allowing the experimental studies of strong field quantum-electrodynamics physics and laser nuclear physics. Here, we propose a method to realize the ultra-intense laser field amplification of petawatt-class laser pulse in moderate density plasma via relativistic self-focusing and tapered-channel focusing. Three-dimensional particle-in-cell simulations demonstrate that almost an order of magnitude enhancement of laser intensity is possible even though the γ-ray radiation results in massive laser energy loss. In particular, with a seed laser intensity of ∼1023 W/cm2, duration of 82.5 fs and power of 31 petawatt, one can obtain ∼1024 W/cm2 intensity and up to ∼60% energy conversion efficiency from the initial seed laser to the focused laser in plasma with density of 3.3 × 1022/cm3. This may pave the way to the new research field of ultra-intense laser plasma interaction in the upcoming laser facilities.