bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations
Authors: Landis Elizabeth A. , Fogarty Emily , Edwards John C. , Popa Otilia , Eren A. Murat , Wolfe Benjamin E.
Published: June 2022

Through an integration of metagenomic and experimental approaches, our work reveals the diversity and nature of interactions among key taxa in kombucha microbiomes through the construction of synthetic microbial pairs. Manipulation of these microbes in kombucha has the potential to shape both the fermentation qualities of kombucha and the production of biofilms and is valuable for kombucha beverage producers, biofilm engineers, and synthetic ecologists.
Molecular Surveillance of Artemisinin-Based Combination Therapies Resistance in Plasmodium falciparum Parasites from Bioko Island, Equatorial Guinea
Authors: Liu YaQun , Liang XueYan , Li Jian , Chen JiangTao , Huang HuiYing , Zheng YuZhong , He JinQuan , Ehapo Carlos Salas , Eyi Urbano Monsuy , Yang PeiKui , Lin LiYun , Chen WeiZhong , Sun GuangYu , Liu XiangZhi , Zha GuangCai , Wang JunLi , Wang ChunFang , Wei HuaGui , Lin Min
Published: June 2022

Malaria, one of the tropical parasitic diseases with a high transmission rate in Bioko Island, Equatorial Guinea, especially caused by
P. falciparum
is highly prevalent in this region and is commonly treated locally with ACTs. The declining antimalarial susceptibility of artemisinin-based drugs suggested that resistance to artemisinin and its derivatives is developing in
P. falciparum
.
Simulation of Medium Wave Propagation in the Magnetosphere
Authors: Blagoveshchensky D. V. , Maltseva O. A.
Published: June 2022

A model of the medium of the ionosphere and magnetosphere, including the distributions of the concentrations and temperatures, collision frequencies, and magnetic field parameters, is described. The ray-tracing method was used to simulate the parameters of medium radio waves in this environment. The wave trajectories were calculated in the approximation of geometric optics. When the level of solar and geomagnetic activity and the location of the transmitter and the frequency are set, the parameters of the wave paths can be calculated. Numerical modeling of the characteristics of experimental echo signals has shown that the mechanism of magnetospheric propagation is of paramount importance. In this case, the main ionospheric trough turned out to be an unusual channel. Medium waves propagate inside the trough along the plasmapause. This is possible with sufficiently clear relationships between the positions of the trough, plasmapause, and transmitter. The considered effect of medium wave channeling can be used to diagnose the position of the trough and plasmapause.
Primary Burkitt lymphoma of the thyroid associated with Hashimoto’s thyroiditis
Authors: Bergsma Patrick , Riemenschnitter Cosima , Gruber-Mösenbacher Ulrike , Brand Yves
Published: June 2022

Primary Burkitt lymphoma of the thyroid is an extremely rare entity with only a few reported cases. A female patient in her 70s with Hashimoto’s thyroiditis presented with a 2-month history of progressive left-sided neck swelling. Ultrasound examination revealed a multinodular goitre and fine needle aspiration (FNA) showed no signs of malignancy. The rapid growth of the thyroid mass raised the concern of a lymphoproliferative process. After left thyroid lobectomy and histopathological examination, the diagnosis of Burkitt lymphoma was made and the patient was included in a randomised study providing chemotherapy following a dose adjusted EPOCH-R regimen. Clinical remission was reached after 6 cycles of chemotherapy. There were no signs of relapse on follow-up, 1.5 years after the end of the treatment. Fast growing thyroid nodules in HT warrant a high index of suspicion. Despite no signs of malignancy after FNA cytology, these nodules may need further investigations.
Nomogram model and risk score predicting overall survival and guiding clinical decision in patients with Hodgkin’s lymphoma: an observational study using SEER population-based data
Authors: Liang Xiangping , Zhang Mingtao , Zhang Zherui , Tan Shuzhen , Li Yingqi , Zhong Yueyuan , Shao Yingqi , Kong Yi , Yang Yue , Li Shang , Xu Jiayi , Li Zesong , Zhu Xiao
Published: June 2022

Introduction

This study developed a prognostic nomogram of Hodgkin lymphoma (HL) for purpose of discussing independent risk factors for HL patients with Surveillance, Epidemiology and End Results (SEER) database.

Methods

We collected data of HL patients from 2010 to 2015 from the SEER database and divided it into two cohorts: the training and the verification cohort. Then the univariate and the multivariate Cox regression analyses were conducted in the training, the verification as well as the total cohort, after which the intersection of variables with statistical significance was taken as independent risk factors to establish the nomogram. The predictive ability of the nomogram was validated by the Concordance Index. Additionally, the calibration curve and receiver operating characteristic curve were implemented to evaluate the accuracy and discrimination. Finally, we obtained 1-year, 3-year and 5-year survival rates of HL patients.

Results

10 912 patients were eligible for the study. We discovered that Derived American Joint Committee on Cancer (AJCC) Stage Group, lymphoma subtype, radiotherapy and chemotherapy were four independent risk factors affecting the prognosis of HL patients. The 1-year, 3-year and 5-year survival rates for high-risk patients were 85.4%, 79.9% and 76.0%, respectively. It was confirmed that patients with stage I or II had a better prognosis. Radiotherapy and chemotherapy had a positive impact on HL outcomes. However, patients with lymphocyte-depleted HL were of poor prognosis.

Conclusions

The nomogram we constructed could better predict the prognosis of patients with HL. Patients with HL had good long-term outcomes but novel therapies are still in need for fewer complications.
Evaluation of the strategy for implementing the GLA:D programme in Switzerland: protocol for an implementation-effectiveness hybrid type 3 design study with a mixed-method approach
Authors: Ettlin Lea , Bruderer-Hofstetter Marina , Rausch-Osthoff Anne-Kathrin , Nast Irina , Gaugler Olivier , Niedermann Karin
Published: June 2022

Introduction

International guidelines recommend the use of exercise, education and weight reduction, when appropriate, as first-line treatment for the conservative management of knee osteoarthritis (OA). These guidelines have not been applied systematically in Switzerland, resulting in an evidence-performance gap. After an analysis of available programmes, the Good Life with osteoArthritis Denmark (GLA:D) programme was determined as the most applicable exercise and education programme for its implementation in Switzerland. The implementation of GLA:D Switzerland OA was initiated to encourage the wider implementation of the clinical guideline recommendations and to improve conservative management of knee OA. The aim of this study protocol is to describe the evaluation of the implementation strategy and its impact on implementation, service and clinical outcomes; as well as to identify contributing barriers and facilitators.

Methods and analysis

The Implementation Research Logic Model will be used to evaluate the strategy and analyse its impact on the implementation outcomes by means of a mixed methods approach. This protocol outlines the proposed measures, data sources and strategies for the evaluation. Predefined implementation outcomes will help to identify the implementation impact and analyse barriers and facilitators systematically. The study population will be the healthcare professionals who are involved in the conservative management of knee OA in Switzerland, that is, physiotherapists and medical doctors, and their patients.

Ethics and dissemination

The use of the registry data containing data of patients participating in the GLA:D Switzerland OA programme does not fall within the scope of the Swiss Human Research Act (BASEC-Nr. Req-2019-00274). However, all participants involved in the evaluation will be asked to give informed written consent and all measures are taken to protect data and privacy of participants. Research findings will be submitted to journals relevant for the topic.

Trial registration number

Not applicable.
Exploring the role of Microbiome in Susceptibility, Treatment Response and Outcome among Tuberculosis Patients from Pakistan: study protocol for a prospective cohort study (Micro-STOP)
Authors: Shahzad Muhammad , Andrews Simon C , Ul-Haq Zia
Published: June 2022

Introduction

Tuberculosis (TB) caused by Mycobacterium tuberculosis is a common infectious disease associated with significant morbidity and mortality, especially in low-income and middle-income countries. Successful treatment of the disease requires prolonged intake (6–8 months) of multiple antibiotics with potentially detrimental consequences on the composition and functional potential of the human microbiome. The protocol described in the current study aims to identify microbiome (oral and gut) signatures associated with TB pathogenesis, treatment response and outcome in humans.

Methods and analysis

Four hundred and fifty, newly diagnosed patients with TB from three district levels (Peshawar, Mardan and Swat) TB diagnosis and treatment centres, will be recruited in this non-interventional, prospective cohort study and will be followed and monitored until treatment completion. Demographic and dietary intake data, anthropometric measurement and blood, stool and salivary rinse samples will be collected at baseline, day 15, month-2 and end of the treatment. Additionally, we will recruit age (±3 years) and sex-matched healthy controls (n=30). Blood sampling will allow monitoring of the immune response during the treatment, while salivary rinse and faecal samples will allow monitoring of dynamic changes in oral and gut microbiome diversity. Within this prospective cohort study, a nested case–control study design will be conducted to assess perturbations in oral and gut microbiome diversity (microbial dysbiosis) and immune response and compare between the patients groups (treatment success vs failure).

Ethics and dissemination

The study has received ethics approval from the Ethic Board of Khyber Medical University Peshawar, and administrative approval from Provincial TB Control Programme of Khyber Pakhtunkhwa, Pakistan. The study results will be presented in national and international conferences and published in peer-reviewed journals.

Trial registration number

NCT04985994.
Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites
Authors: Bai Xiaowu , Wei Hong , Liu Weixin , Coker Olabisi Oluwabukola , Gou Hongyan , Liu Changan , Zhao Liuyang , Li Chuangen , Zhou Yunfei , Wang Guoping , Kang Wei , Ng Enders Kwok-wai , Yu Jun
Published: June 2022

Objective

Cigarette smoking is a major risk factor for colorectal cancer (CRC). We aimed to investigate whether cigarette smoke promotes CRC by altering the gut microbiota and related metabolites.

Design

Azoxymethane-treated C57BL/6 mice were exposed to cigarette smoke or clean air 2 hours per day for 28 weeks. Shotgun metagenomic sequencing and liquid chromatography mass spectrometry were parallelly performed on mice stools to investigate alterations in microbiota and metabolites. Germ-free mice were transplanted with stools from smoke-exposed and smoke-free control mice.

Results

Mice exposed to cigarette smoke had significantly increased tumour incidence and cellular proliferation compared with smoke-free control mice. Gut microbial dysbiosis was observed in smoke-exposed mice with significant differential abundance of bacterial species including the enrichment ofEggerthella lentaand depletion ofParabacteroides distasonisandLactobacillusspp. Metabolomic analysis showed increased bile acid metabolites, especially taurodeoxycholic acid (TDCA) in the colon of smoke-exposed mice. We found thatE. lentahad the most positive correlation with TDCA in smoke-exposed mice. Moreover, smoke-exposed mice manifested enhanced oncogenic MAPK/ERK (mitogen-activated protein kinase/extracellular signal‑regulated protein kinase 1/2) signalling (a downstream target of TDCA) and impaired gut barrier function. Furthermore, germ-free mice transplanted with stools from smoke-exposed mice (GF-AOMS) had increased colonocyte proliferation. Similarly, GF-AOMS showed increased abundances of gutE. lentaand TDCA, activated MAPK/ERK pathway and impaired gut barrier in colonic epithelium.

Conclusion

The gut microbiota dysbiosis induced by cigarette smoke plays a protumourigenic role in CRC. The smoke-induced gut microbiota dysbiosis altered gut metabolites and impaired gut barrier function, which could activate oncogenic MAPK/ERK signalling in colonic epithelium.
Decreased risk of treatment failure with vedolizumab and thiopurines combined compared with vedolizumab monotherapy in Crohn’s disease
Authors: Kirchgesner Julien , Desai Rishi J , Schneeweiss Maria C , Beaugerie Laurent , Schneeweiss Sebastian , Kim Seoyoung C
Published: June 2022

Objective

While infliximab combined to thiopurines is more effective than infliximab monotherapy in patients with Crohn’s disease (CD) and UC, the impact of adding thiopurines to vedolizumab remains controversial. We emulated two target trials comparing the effectiveness of combination therapy versus vedolizumab monotherapy in CD and UC.

Design

Based on two US and the French nationwide healthcare databases, patients with CD and UC who initiated vedolizumab were identified. The study methodology, including confounding adjustment and outcome definitions, were previously validated in successful emulations of the SONIC and SUCCESS trials. Risk ratios for treatment failure based on hospitalisation or surgery related to disease activity, treatment switch, or prolonged corticosteroids use, were estimated after 1:1 propensity score (PS) matching.

Results

Among a total of 10 299 vedolizumab users, 804 CD and 1088 UC pairs of combination therapy versus vedolizumab monotherapy users were PS matched. Treatment failure occurred at week 26 in 236 (29.3%) and 376 (34.3%) patients with CD and at week 16 in 236 (21.7%) and 263 (24.2%) patients with UC initiating combination therapy and vedolizumab monotherapy, respectively. The risk of treatment failure was decreased with combination therapy compared with vedolizumab monotherapy in CD (RR 0.85, 95% CI: 0.74 to 0.98) and to a lesser extent in UC (RR 0.90, 95% CI: 0.77 to 1.05). Findings were consistent across databases.

Conclusion

Using validated methodologies, combination therapy with vedolizumab and thiopurines was associated with lower treatment failure compared with vedolizumab monotherapy in CD but not UC across the USA and France.
Parasites and priorities: the early evolution of ‘neglected disease’ initiatives and the history of a global health agenda
Authors: Webel Mari Kathryn
Published: June 2022

This article explores the development and evolution of ‘neglected tropical diseases’ (NTDs) as an operative and imaginative category in global public health, focusing on the early intellectual and institutional development of the category in the 1970s. It examines early work around ‘neglected’ diseases in the Rockefeller Foundation’s Health Sciences Division, specifically the Foundation’s ‘Great Neglected Diseases of Mankind’ initiative that ran between 1978 and 1988, as well as intersections with the WHO’s parallel Special Programme for Research and Training in Tropical Diseases and efforts by the US-based Edna McConnell Clark and MacArthur Foundations. A key concern of advocates who influenced initial programmes focused around ‘neglect’ was a lack of sophistication in medical parasitological research globally. Central to the NTDs’ capacity to animate diverse energies were claims about parasitic diseases and their place in new biotechnological approaches to medicine. This article explores how the emphasis on ‘neglected’, ‘tropical’ or even ‘endemic’ diseases encoded specific concerns and desires of parasitologists in the early 1970s. Despite the desire to prioritise the needs of ‘endemic’ countries and the recognition of a widening cohort of experts from both high-income and low-income nations, NTD advocates often recapitulated historic power dynamics privileging research institutions in the USA and Europe. Historicising and contextualising ‘neglect’ illuminates the contingent and changing politics of global health in a formative period in the late twentieth century.
Pandemic and the human factor
Authors: Szawarski Piotr
Published: June 2022

As the staffing crisis in the UK deepens, it is time for the policy-makers and professional bodies to rethink the approach to the most vital and yet most fragile component of the healthcare system—the human beings. The austerity measures, combined with pandemic and more recently the vision of a backlog with attached unrealistic expectations of tackling it, have brought the NHS and many other healthcare systems to the brink of a crisis. It is a human factors approach, which emphasises clinician's well-being as the core aspect of optimising performance that should become our goal. Delivery of healthcare under circumstances of physical, legal or moral threat cannot be optimal and is not sustainable. The pandemic served to highlight this quite clearly. Also, an injured, tired or burn-out healthcare professional cannot be expected to repair the system that has precipitated his or her condition. The approach to changing the culture of medicine may be multifaceted, but ultimately, we should rethink professionalism and the definition of duty of care putting emphasis on the well-being of those delivering the care as the way to assure best possible care.
Blended analysis of occupational safety hazards and digital transformation of risk assessment in construction industries
Authors: Qiu Changcui , Li Xinming
Published: June 2022

Occupational safety hazards and risk management in construction industries are major worldwide concerns due to the unique dynamic nature of their working environment. Safety-related documentations such as injury reports, physical demand analyses (PDAs), and standard operating procedures (SOPs) contain valuable information to support the risk prevention algorithms. This paper presents a blended study on occupational risk assessment, in perspective with both attribute-based and data mining approaches. The study explored a strategy of attribute-based identification and degree of risk classification by applying distinctive quantitative analysis on the level of injuries. Data mining analysis further exposed the causality links of potentially hazardous activities and injuries. A conceptual digital transformation framework is proposed to assess digital mapping and future predictive measurements for up-to-date risk factor evaluation. The blended analysis is expected to help the construction industry identify relationships on causes of safety hazards, key safety attributes, as well as their corresponding risk controls.
QCD chiral condensate and pseudoscalar-meson properties in the nuclear medium at finite temperature
Authors: Hutauruk Parada T. P. , Nam Seung-il
Published: June 2022

The pion and kaon properties in a nuclear medium at nonvanishing temperature as well as the quantum chromodynamics (QCD) chiral condensate in the presence of a magnetic field for various baryon densities are studied in the Nambu–Jona–Lasinio (NJL) model with the help of the proper-time regularization (PTR) scheme, simulating a QCD confinement. The density dependence of the quark mass in symmetric nuclear matter is obtained from the quark-meson coupling (QMC) model, which shares the same covariant feature with the NJL model, at quark level. We then analyze the QCD chiral condensates and dynamical masses for various baryon densities at finite temperature and magnetic field as well as the pion and kaon masses, pion and kaon weak-decay constants, pion- and kaon-quark coupling constants, and wave function renormalization factors for various baryon densities at finite temperature. We find that the QCD chiral condensates suppress with increasing temperature and baryon density and enhance under the presence of a magnetic field, which are consistent with other model predictions. Interestingly, the wave function renormalization factors for the pion and kaon increase with respect to temperature and reduce as the baryon density increases are found.
Dynamical noncommutative graphene
Authors: Haouam Ilyas , Alavi S. A.
Published: June 2022

We study graphene in a two-dimensional dynamical noncommutative (NC) space in the presence of a constant magnetic field. The model is solved using perturbation theory and to the second-order of perturbation. The energy levels of the system are calculated and the corresponding eigenstates are obtained. For all cases, the energy shift depends on the dynamical NC (DNC) parameter [Formula: see text]. Using the accuracy of energy measurement, we put an upper bound on the noncommutativity parameter [Formula: see text]. In addition, we investigate some of the thermodynamic quantities of the system at zero temperature limit and extreme relativistic case, which reveals interesting differences between nondynamical and DNC spaces.
Non-Abelian lattice theories: Consistent measures and strata
Authors: Mendes R. Vilela
Published: June 2022

The role of consistent measures in the rigorous construction of non-Abelian lattice theories is analyzed. General conditions that measure must fulfill to insure consistency, positivity and a mass gap are obtained. The impact of nongeneric strata on the nature of the Hamiltonian lattice potential is also discussed.
SFCDecomp: Multicriteria Optimized Tool Path Planning in 3D Printing using Space-Filling Curve Based Domain Decomposition
Authors: Gupta Prashant , Guo Yiran , Boddeti Narasimha , Krishnamoorthy Bala
Published: June 2022

We explore efficient optimization of toolpaths based on multiple criteria for large instances of 3D printing problems. We first show that the minimum turn cost 3D printing problem is NP-hard, even when the region is a simple polygon. We develop SFCDecomp, a space filling curve based decomposition framework to solve large instances of 3D printing problems efficiently by solving these optimization subproblems independently. For the Buddha model, our framework builds toolpaths over a total of 799,716 nodes across 169 layers, and for the Bunny model it builds toolpaths over 812,733 nodes across 360 layers. Building on SFCDecomp, we develop a multicriteria optimization approach for toolpath planning. We demonstrate the utility of our framework by maximizing or minimizing tool path edge overlap between adjacent layers, while jointly minimizing turn costs. Strength testing of a tensile test specimen printed with tool paths that maximize or minimize adjacent layer edge overlaps reveal significant differences in tensile strength between the two classes of prints.
Statistically Efficient, Polynomial-Time Algorithms for Combinatorial Semi-Bandits
Authors: Cuvelier Thibaut , Combes Richard , Gourdin Eric
Published: June 2022

We consider combinatorial semi-bandits over a set X ⊂ (0,1)d where rewards are uncorrelated across items. For this problem, the algorithm ESCB yields the smallest known regret bound R(T) = O ( d (łn m)2 (łn T) øver Δmin) after T rounds, where m = maxx ∈ X 1Tx. However, ESCB has computational complexity O(|X|), which is typically exponential in d, and cannot be used in large dimensions. We propose the first algorithm that is both computationally and statistically efficient for this problem with regret R(T) = O (d (łn m)2 (łn T)øver Δmin) and computational asymptotic complexity O( δT-1 poly (d)), where δT is a function which vanishes arbitrarily slowly. Our approach involves carefully designing AESCB, an approximate version of ESCB with the same regret guarantees. We show that, whenever budgeted linear maximization over X can be solved up to a given approximation ratio, AESCB is implementable in polynomial time O (δT-1 poly (d)) by repeatedly maximizing a linear function over X subject to a linear budget constraint, and showing how to solve these maximization problems efficiently. Additional algorithms, proofs and numerical experiments are given in the complete version of this work.
Achieving Zero Asymptotic Queueing Delay for Parallel Jobs
Authors: Weng Wentao , Wang Weina
Published: June 2022

Zero queueing delay is highly desirable in large-scale computing systems. Existing work has shown that it can be asymptotically achieved by using the celebrated Power-of-d-choices (Pod) policy with a probe overhead d = Ω(log N/1-λ), and it is impossible when d = O(1/1-λ), where N is the number of servers and λ is the load of the system. However, these results are based on the model where each job is an indivisible unit, which does not capture the parallel structure of jobs in today's predominant parallel computing paradigm.

This paper considers a model where each job consists of a batch of parallel tasks. Under this model, we propose a new notion of zero (asymptotic) queueing delay that requires the job delay under a policy to approach the job delay given by the max of its tasks' service times, i.e., the job delay assuming its tasks entered service right upon arrival. This notion quantifies the effect of queueing on a job level for jobs consisting of multiple tasks, and thus deviates from the conventional zero queueing delay for single-task jobs in the literature.

We show that zero queueing delay for parallel jobs can be achieved using the batch-filling policy (a variant of the celebrated Pod policy) with a probe overhead d = Ω(1/(1-λ)log k) in the sub-Halfin-Whitt heavy-traffic regime, where k is the number of tasks in each job and k properly scales with N (the number of servers). This result demonstrates that for parallel jobs, zero queueing delay can be achieved with a smaller probe overhead. We also establish an impossibility result: we show that zero queueing delay cannot be achieved if d = (o(log N/log k)). Simulation results are provided to demonstrate the consistency between numerical results and theoretical results under reasonable settings, and to investigate gaps in the theoretical analysis.
I Know What You Bought At Chipotle for $9.81 by Solving A Linear Inverse Problem
Authors: Fleder Michael , Shah Devavrat
Published: June 2022

We consider the question of identifying which set of products are purchased and at what prices in a given transaction by observing only the total amount spent in the transaction, and nothing more. The ability to solve such an inverse problem can lead to refined information about consumer spending by simply observing anonymized credit card transactions data. Indeed, when considered in isolation, it is impossible to identify the products purchased and their prices from a given transaction based on just the transaction total. However, given a large number of transactions, there may be a hope.

As the main contribution of this work, we provide a robust estimation algorithm for decomposing transaction totals into the underlying, individual product(s) purchased by utilizing a large corpus of transactions. Our method recovers a (product prices) vector $p ∈ RN>0 of unknown dimension (number of products) N as well as matrix $A ∈ ZM x N≥0 simply from M observations (transaction totals) y ∈ RM>0 such that y = A p + η with η ∈ RM representing noise (taxes, discounts, etc.). We formally establish that our algorithm identifies N, A precisely and p approximately, as long as each product is purchased individually at least once, i.e. M ≥ N and A has rank N. Computationally, the algorithm runs in polynomial time (with respect to problem parameters), and thus we provide a computationally efficient and statistically robust method for solving such inverse problems. We apply the algorithm to a large corpus of anonymized consumer credit card transactions in the period 2016-2019, with data obtained from a commercial data vendor. The transactions are associated with spending at Apple, Chipotle, Netflix, and Spotify. From just transactions data, our algorithm identifies (i) key price points (without access to the listed prices), (ii) products purchased within a transaction, (iii) product launches, and (iv) evidence of a new 'secret' product from Netflix - rumored to be in limited release.
Refining Mean-field Approximations by Dynamic State Truncation
Authors: Randone Francesca , Bortolussi Luca , Tribastone Mirco
Published: June 2022

Mean-field models are an established method to analyze large stochastic systems with N interacting objects by means of simple deterministic equations that are asymptotically correct when N tends to infinity. For finite N, mean-field equations provide an approximation whose accuracy is model- and parameter-dependent. Recent research has focused on refining the approximation by computing suitable quantities associated with expansions of order $1/N$ and $1/N^2$ to the mean-field equation. In this paper we present a new method for refining mean-field approximations. It couples the master equation governing the evolution of the probability distribution of a truncation of the original state space with a mean-field approximation of a time-inhomogeneous population process that dynamically shifts the truncation across the whole state space. We provide a result of asymptotic correctness in the limit when the truncation covers the state space; for finite truncations, the equations give a correction of the mean-field approximation. We apply our method to examples from the literature to show that, even with modest truncations, it is effective in models that cannot be refined using existing techniques due to non-differentiable drifts, and that it can outperform the state of the art in challenging models that cause instability due orbit cycles in their mean-field equations.
Where did my 256 GB go? A Measurement Analysis of Storage Consumption on Smart Mobile Devices
Authors: Bijlani Ashish , Ramachandran Umakishore , Campbell Roy
Published: June 2022

This work presents the first-ever detailed and large-scale measurement analysis of storage consumption behavior of applications (apps) on smart mobile devices. We start by carrying out a five-year longitudinal static analysis of millions of Android apps to study the increase in their sizes over time and identify various sources of app storage consumption. Our study reveals that mobile apps have evolved as large monolithic packages that are packed with features to monetize/engage users and optimized for performance at the cost of redundant storage consumption.

We also carry out a mobile storage usage study with 140 Android participants. We built and deployed a lightweight context-aware storage tracing tool, called cosmos, on each participant's device. Leveraging the traces from our user study, we show that only a small fraction of apps/features are actively used and usage is correlated to user context. Our findings suggest a high degree of app feature bloat and unused functionality, which leads to inefficient use of storage. Furthermore, we found that apps are not constrained by storage quota limits, and developers freely abuse persistent storage by frequently caching data, creating debug logs, user analytics, and downloading advertisements as needed.

Finally, drawing upon our findings, we discuss the need for efficient mobile storage management, and propose an elastic storage design to reclaim storage space when unused. We further identify research challenges and quantify expected storage savings from such a design. We believe our findings will be valuable to the storage research community as well as mobile app developers.
Chasm in Hegemony
Authors: Zhang Yiguang , Han Jessy Xinyi , Mahajan Ilica , Bengani Priyanjana , Chaintreau Augustin
Published: June 2022

In networks with a minority and a majority community, it is well-studied that minorities are under-represented at the top of the social hierarchy. However, researchers are less clear about the representation of minorities from the lower levels of the hierarchy, where other disadvantages or vulnerabilities may exist. We offer a more complete picture of social disparities at each social level with empirical evidence that the minority representation exhibits two opposite phases: at the higher rungs of the social ladder, the representation of the minority community decreases; but, lower in the ladder, which is more populous, as you ascend, the representation of the minority community improves. We refer to this opposing phenomenon between the upper-level and lower-level as the chasm effect. Previous models of network growth with homophily fail to detect and explain the presence of this chasm effect. We analyze the interactions among a few well-observed network-growing mechanisms with a simple model to reveal the sufficient and necessary conditions for both phases in the chasm effect to occur. By generalizing the simple model naturally, we present a complete bi-affiliation bipartite network-growth model that could successfully capture disparities at all social levels and reproduce real social networks. Finally, we illustrate that addressing the chasm effect can create fairer systems with two applications in advertisement and fact-checks, thereby demonstrating the potential impact of the chasm effect on the future research of minority-majority disparities and fair algorithms.
Compartmentalization of RNA Degradosomes in Bacteria Controls Accessibility to Substrates and Ensures Concerted Degradation of mRNA to Nucleotides
Authors: Carpousis Agamemnon J. , Campo Nathalie , Hadjeras Lydia , Hamouche Lina
Published: June 2022

RNA degradosomes are multienzyme complexes composed of ribonucleases, RNA helicases, and metabolic enzymes. RNase E–based degradosomes are widespread in Proteobacteria. The Escherichia coli RNA degradosome is sequestered from transcription in the nucleoid and translation in the cytoplasm by localization to the inner cytoplasmic membrane, where it forms short-lived clusters that are proposed to be sites of mRNA degradation. In Caulobacter crescentus, RNA degradosomes localize to ribonucleoprotein condensates in the interior of the cell [bacterial ribonucleoprotein-bodies (BR-bodies)], which have been proposed to drive the concerted degradation of mRNA to nucleotides. The turnover of mRNA in growing cells is important for maintaining pools of nucleotides for transcription and DNA replication.Membrane attachment of the E. coli RNA degradosome is necessary to avoid wasteful degradation of intermediates in ribosome assembly. Sequestering RNA degradosomes to C. crescentus BR-bodies, which exclude structured RNA, could have a similar role in protecting intermediates in ribosome assembly from degradation.
How Apicomplexa Parasites Secrete and Build Their Invasion Machinery
Authors: Cova Marta Mendonça , Lamarque Mauld H. , Lebrun Maryse
Published: June 2022

Apicomplexa are obligatory intracellular parasites that sense and actively invade host cells. Invasion is a conserved process that relies on the timely and spatially controlled exocytosis of unique specialized secretory organelles termed micronemes and rhoptries. Microneme exocytosis starts first and likely controls the intricate mechanism of rhoptry secretion. To assemble the invasion machinery, micronemal proteins—associated with the surface of the parasite—interact and form complexes with rhoptry proteins, which in turn are targeted into the host cell. This review covers the molecular advances regarding microneme and rhoptry exocytosis and focuses on how the proteins discharged from these two compartments work in synergy to drive a successful invasion event. Particular emphasis is given to the structure and molecular components of the rhoptry secretion apparatus, and to the current conceptual framework of rhoptry exocytosis that may constitute an unconventional eukaryotic secretory machinery closely related to the one described in ciliates.
Mechanisms Underlying Vibrio cholerae Biofilm Formation and Dispersion
Authors: Teschler Jennifer K. , Nadell Carey D. , Drescher Knut , Yildiz Fitnat H.
Published: June 2022

Biofilms are a widely observed growth mode in which microbial communities are spatially structured and embedded in a polymeric extracellular matrix. Here, we focus on the model bacterium Vibrio cholerae and summarize the current understanding of biofilm formation, including initial attachment, matrix components, community dynamics, social interactions, molecular regulation, and dispersal. The regulatory network that orchestrates the decision to form and disperse from biofilms coordinates various environmental inputs. These cues are integrated by several transcription factors, regulatory RNAs, and second-messenger molecules, including bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP). Through complex mechanisms, V. cholerae weighs the energetic cost of forming biofilms against the benefits of protection and social interaction that biofilms provide.
Metabolic Enabling and Detoxification by Mammalian Gut Microbes
Authors: Dearing M. Denise , Weinstein Sara B.
Published: June 2022

The longstanding interactions between mammals and their symbionts enable thousands of mammal species to consume herbivorous diets. The microbial communities in mammals degrade both plant fiber and toxins. Microbial toxin degradation has been repeatedly documented in domestic ruminants, but similar work in wild mammals is more limited due to constraints on sampling and manipulating the microbial communities in these species. In this review, we briefly describe the toxins commonly encountered in mammalian diets, major classes of biotransformation enzymes in microbes and mammals, and the gut chambers that house symbiotic microbes. We next examine evidence for microbial detoxification in domestic ruminants before providing case studies on microbial toxin degradation in both foregut- and hindgut-fermenting wild mammals. We end by discussing species that may be promising for future investigations, and the advantages and limitations of approaches currently available for studying degradation of toxins by mammalian gut microbes.
APOBEC3: Friend or Foe in Human Papillomavirus Infection and Oncogenesis?
Authors: Warren Cody J. , Santiago Mario L. , Pyeon Dohun
Published: June 2022

Human papillomavirus (HPV) infection is a causative agent of multiple human cancers, including cervical and head and neck cancers. In these HPV-positive tumors, somatic mutations are caused by aberrant activation of DNA mutators such as members of the apolipoprotein B messenger RNA–editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of cytidine deaminases. APOBEC3 proteins are most notable for their restriction of various viruses, including anti-HPV activity. However, the potential role of APOBEC3 proteins in HPV-induced cancer progression has recently garnered significant attention. Ongoing research stems from the observations that elevated APOBEC3 expression is driven by HPV oncogene expression and that APOBEC3 activity is likely a significant contributor to somatic mutagenesis in HPV-positive cancers. This review focuses on recent advances in the study of APOBEC3 proteins and their roles in HPV infection and HPV-driven oncogenesis. Further, we discuss critical gaps and unanswered questions in our understanding of APOBEC3 in virus-associated cancers.
Electrochemical Stability and Reversibility of Aqueous Polysulfide Electrodes Cycled Beyond the Solubility Limit
Authors: Pan Menghsuan Sam , Su Liang , Eiler Stephanie L. , Jing Linda W. , Badel Andres F. , Li Zheng , Brushett Fikile R. , Chiang Yet-Ming
Published: June 2022

Batteries which use dissolved redox-active species, such as redox flow batteries (RFBs), are often considered to be constrained in their operation and energy density by the solubility limit of the redox species. Here, we show that soluble redox active electrolytes can be reversibly cycled deeply into the precipitation regime, permitting higher effective concentrations, energy densities, and lower costs. Using aqueous sodium polysulfide negative electrolytes cycled in the nominal Na2S2 to Na2S4 capacity range as an example, we show that the effective solubility can be increased from 5 M in the fully-dissolved state to as much as 10 M using the precipitation strategy. Stable cycling was observed at 8 M concentration over more than 1600h at room temperature. We also analyze the range of polysulfide electrochemical stability, and characterize the precipitate composition. This enhanced effective concentration approach may be generalized to other redox chemistries that utilize solubilized reactants, and may be especially useful for long-duration storage applications where slow charge-discharge rates allow equilibration of precipitated species with the redox-active solution.
Review—The Oxygen Reduction Reaction on MXene-Based Catalysts: Progress and Prospects
Authors: Yoo Ray , Pranada Eugenie , Johnson Denis , Qiao Zhi , Djire Abdoulaye
Published: June 2022

The oxygen reduction reaction (ORR) is a critical, but sluggish reaction used for various applications, including fuel cells and metal-oxygen batteries. Currently, the benchmark catalysts for ORR are Pt-based catalysts. However, due to these catalysts being scarce and very expensive, alternative catalysts that are more abundant and less expensive are urgently in demand. MXenes, a new two-dimensional (2D) material based on transition metal carbides and nitrides, have advanced the performance of many existing technologies, including batteries, supercapacitors, sensors, etc. Owing to their unique electronic structure, physical and chemical properties, and tunable morphology, MXenes are expected to thrive in the ORR electro- and photo-catalytic systems. Recent studies reported better-performing ORR catalysts with MXenes as supports, which holds promise in the significant reduction of Pt loading for efficient catalysts. Furthermore, MXenes exhibit wide applicability and stability in a range of pH values, from acidic to basic. In this work, we carefully review the most pertinent works on ORR using MXenes. We first discuss the catalytic performance of MXenes in alkaline and acidic environments, followed by their application in metal-air batteries. We investigate the gaps and challenges in the field, identify key areas that need further attention, and provide directions for future research.
Suppressing Carbon Deposition by Introducing SiO3
2− in Molten CaCl2 for Efficient Electro-Deoxidation
Authors: Pang Fangzhao , Li Peng , Zhao Zhuqing , Guo Lei , Du Kaifa , Deng Bowen , Wang Dihua , Yin Huayi
Published: June 2022

Electrolysis of solid oxides in molten CaCl2 has been proven a straightforward process to extract various metals thanks to the wide electrochemical window of CaCl2 and CaO which is soluble in molten CaCl2. However, the CaO produced during the cathodic reduction of oxides not only shuttles O2−, but also captures CO2 to generate CO3
2− that can be reduced to carbon at the cathode, resulting in decreasing current efficiency and contaminating the cathodic products by carbon. To solve this problem, we employed CaSiO3 to replace CaO to suppress/avoid the formation of CO3
2− and thereafter prevent the carbon deposition. The suppression of CO3
2− formation is because SiO3
2− is thermodynamically more stable than CO3
2−, i.e., the CO2 generated on the graphite anode can not be captured by SiO3
2−. In molten CaCl2−8.0 wt% CaSiO3, Cr2O3 and SiO2 are reduced to Cr and Si with much less carbon deposition than in molten CaCl2. As a result, the current efficiency increases from 21.4% to 51.9% for the reduction of Cr2O3 and 37.1% to 72.2% for the reduction of SiO2. Although introducing SiO3
2− will slightly decrease the electrochemical window of CaCl2, it will be a promising method to avoid carbon contamination and increase current efficiency especially for Si production.
Void Formation Mechanism Related to Particles During Wafer-to-Wafer Direct Bonding
Authors: Nagano F. , Iacovo S. , Phommahaxay A. , Inoue F. , Chancerel F. , Naser H. , Beyer G. , Beyne E. , De. Gendt S.
Published: June 2022

Achieving a void-free bonding interface is an important requirement for the wafer-to-wafer direct bonding process. The two main potential mechanisms for void formation at the interface are (i) void formation induced by gas, such as condensation by-products caused by the bonding process or outgassing of trapped precursors, and (ii) void formation induced by physical obstacles, such as particles. In this work, emphasis is on the latter process. Particles were intentionally deposited on the wafer prior to bonding to study the kinetics of the physical void formation process. Void formations induced by particles deposited on different dielectrics bonding materials were analyzed using scanning acoustic microscopy and image software. The void formation mechanism is then discussed along with the wafer bonding dynamics at room temperature.
PTPα promotes fibroproliferative responses after acute lung injury
Authors: Aschner Yael , Correll Kelly A. , Beke Keriann M. , Foster Daniel G. , Roybal Helen M. , Nelson Meghan R. , Meador Carly L. , Strand Matthew , Anderson Kelsey C. , Moore Camille M. , Reynolds Paul R. , Kopf Katrina W. , Burnham Ellen L. , Downey Gregory P.
Published: June 2022

The acute respiratory distress syndrome (ARDS) is a major healthcare problem, accounting for significant mortality and long-term disability. Approximately 25% of patients with ARDS will develop an overexuberant fibrotic response, termed fibroproliferative ARDS (FP-ARDS) that portends a poor prognosis and increased mortality. The cellular pathological processes that drive FP-ARDS remain incompletely understood. We have previously shown that the transmembrane receptor-type tyrosine phosphatase protein tyrosine phosphatase-α (PTPα) promotes pulmonary fibrosis in preclinical murine models through regulation of transforming growth factor-β (TGF-β) signaling. In this study, we examine the role of PTPα in the pathogenesis of FP-ARDS in a preclinical murine model of acid (HCl)-induced acute lung injury. We demonstrate that although mice genetically deficient in PTPα ( Ptpra−/−) are susceptible to early HCl-induced lung injury, they exhibit markedly attenuated fibroproliferative responses. In addition, early profibrotic gene expression is reduced in lung tissue after acute lung injury in Ptpra−/− mice, and stimulation of naïve lung fibroblasts with the BAL fluid from these mice results in attenuated fibrotic outcomes compared with wild-type littermate controls. Transcriptomic analyses demonstrate reduced extracellular matrix (ECM) deposition and remodeling in mice genetically deficient in PTPα. Importantly, human lung fibroblasts modified with a CRISPR-targeted deletion of PTPRA exhibit reduced expression of profibrotic genes in response to TGF-β stimulation, demonstrating the importance of PTPα in human lung fibroblasts. Together, these findings demonstrate that PTPα is a key regulator of fibroproliferative processes following acute lung injury and could serve as a therapeutic target for patients at risk for poor long-term outcomes in ARDS.