bluuebunny/crossref_metadata_2025 huggingface dataset:
Raman spectroscopy in crop quality assessment: focusing on sensing secondary metabolites: a review
Authors: Park Miri , Somborn Annette , Schlehuber Dennis , Keuter Volkmar , Deerberg Görge
Published: April 2023

As a crop quality sensor, Raman spectroscopy has been consistently proposed as one of the most promising and non-destructive methods for qualitative and quantitative analysis of plant substances, because it can measure molecular structures in a short time without requiring pretreatment along with simple usage. The sensitivity of the Raman spectrum to target chemicals depends largely on the wavelength, intensity of the laser power, and exposure time. Especially for plant samples, it is very likely that the peak of the target material is covered by strong fluorescence effects. Therefore, methods using lasers with low energy causing less fluorescence, such as 785 nm or near-infrared, are vigorously discussed. Furthermore, advanced techniques for obtaining more sensitive and clear spectra, like surface-enhanced Raman spectroscopy, time-gated Raman spectroscopy or combination with thin-layer chromatography, are being investigated. Numerous interpretations of plant quality can be represented not only by the measurement conditions but also by the spectral analysis methods. Up to date, there have been attempted to optimize and generalize analysis methods. This review summarizes the state of the art of micro-Raman spectroscopy in crop quality assessment focusing on secondary metabolites, from in vitro to in vivo and even in situ, and suggests future research to achieve universal application.
Profiles of Web-based Portal Users with Inflammatory Bowel Disease
Authors: Noureldin Mohamed , Newman Kira L , Higgins Peter D R , Piette John D , Resnicow Kenneth , Louissaint Jeremy , Kenney Brooke , Berinstein Jeffrey , Waljee Akbar K , Zhu Ji , Cohen-Mekelburg Shirley
Published: April 2023

Background

Web-based portals can enhance communication between patients and providers to support IBD self-management and improve care. We aimed to identify portal use patterns of patients with inflammatory bowel disease (IBD) to inform future web portal-based interventions and portal design.

Methods

Patients with IBD receiving care at the University of Michigan between 2012 and 2021 were identified. Meta-data from electronic logs of each patient’s most recent year of portal use were abstracted. Portal engagement was characterized in terms of intensity (ie, frequency of use); comprehensiveness (ie, number of portal functions used); and duration (ie, quarters per year of portal use). We used k-means clustering, a machine-learning technique, to identify groupings of portal users defined in terms of engagement features.

Results

We found 5605 patients with IBD who had accessed their portal account at least once. The average age was 41.2 years (SD 16.7), 3035 (54.2%) were female, and 2214 (39.5%) received immune-targeted therapies. We identified 3 patterns of portal engagement: (1) low intensity users (29.5%); (2) moderate intensity, comprehensive, and sustained users (63.3%); and (3) high intensity, comprehensive, sustained users (7.2%). Patients with more intense, comprehensive, and sustained use of the portal were older, female, with more comorbidities, and were more likely to receive immune-targeted therapies.

Conclusion

Understanding distinct patterns of portal use can inform portal-based interventions and portal design. Patient portals may be particularly helpful in delivering assistance to those with comorbidities and those receiving immune-targeted therapies—many of whom demonstrate more intense, comprehensive, and sustained portal use.
Systematic Review and Meta-analysis: The Association Between Serum Ustekinumab Trough Concentrations and Treatment Response in Inflammatory Bowel Disease
Authors: Vasudevan Abhinav , Tharayil Vivek , Raffals Laura H , Bruining David H , Becker Michelle , Murad Mohammad Hassan , Loftus Edward V
Published: April 2023

Background

Optimizing therapy and monitoring response are integral aspects of inflammatory bowel disease treatment. We conducted a systematic review and meta-analysis to determine whether serum ustekinumab trough concentrations during maintenance therapy were associated with ustekinumab treatment response in patients with inflammatory bowel disease.

Methods

A systematic review was performed to March 21, 2022, to identify studies using MEDLINE, EMBASE, and the Cochrane library. We included studies that reported the association between serum ustekinumab trough concentrations with clinical or endoscopic remission. Outcome measures were combined across studies using the random-effects model with an odds ratio (OR) for binary outcomes of endoscopic and clinical remission.

Results

We identified 14 observational studies that were included in the analysis for clinical remission (919 patients, 63% with Crohn’s disease) or endoscopic remission (290 patients, all with Crohn’s disease). Median ustekinumab trough concentrations were higher amongst individuals achieving clinical remission compared with those not achieving remission (mean difference, 1.6 ug/mL; 95% confidence interval [CI], 0.21-3.01 ug/mL). Furthermore, individuals with median serum trough concentration in the fourth quartile were significantly more likely to achieve clinical (OR, 3.61; 95% CI, 2.11-6.20) but not endoscopic remission (OR, 4.67; 95% CI, 0.86-25.19) compared with those with first quartile median trough concentrations.

Conclusion

Based on the results of this meta-analysis primarily relating to patients with Crohn’s disease on maintenance ustekinumab treatment, it appears that there is an association between higher ustekinumab trough concentration and clinical outcomes. Prospective studies are required to determine whether proactive dose adjustments of ustekinumab therapy provides additional clinical benefit.
Best Practices to Promote Field Science Safety
Authors: Yarincik Kristen , Kelly Anne , McGlynn Terry , Verble Robin M
Published: April 2023

Synopsis

Interventions are necessary to address the ongoing epidemic of sexual harassment and assault in field settings. An evidence-based approach to identifying specific interventions will be most effective at promoting the safety of scientists. We present the results of a workshop conducted by experts in field biology and the study of sexual harassment and assault that identified a comprehensive set of best practices for individuals and organizations. These recommendations are grounded in peer-reviewed scholarship and are separated into four topics: culture change, accountability, policy development, and reporting. The resulting report of the workshop recommends 44 practices, categorized by the resources required for implementation, the time frame of implementation, and the level of organization responsible for implementation. The best practices that we present are designed to support individuals and organizations in the development of field safety plans.
Research on optimal scheduling of integrated energy system in low-carbon parks based on demand response
Authors: Xu Wei , Han Wei , Jin Huaizhang , Bai Yong , Liu Huan
Published: April 2023

The comprehensive energy system of the park is one of the effective ways to solve the problems of low utilization efficiency of comprehensive energy and difficulty in absorbing renewable energy. By coordinating the output of each unit to optimize the scheduling of the system, the operating cost of the system can be reduced to a certain extent, and the space for new energy generation to be connected to the Internet can be increased. Aiming at the characteristics of electric, heat and gas load demand of the integrated energy system of industrial low-carbon parks and the overall needs of low-carbon development, a research on the optimal scheduling of integrated energy systems in low-carbon parks based on demand response is proposed. By analyzing the structure and components of the integrated energy system of the low-carbon park, different types of demand response are modeled. On this basis, based on the comprehensive demand response of electricity and heat, the optimal dispatch model of the integrated energy system of the low-carbon park is constructed, and the model is solved to realize the optimal dispatch of the integrated energy system of the low-carbon park. The experimental resu lts show that the proposed method has lower operating cost of the integrated energy system, better economy of the integrated energy system and can effectively improve the power supply reliability and energy saving rate of the integrated energy system. The average system load rate of the proposed method is up to 98.7%, the average comprehensive energy utilization rate is up to 97.9% and the system operation cost is only 10343.1 yuan.
Prevalence of pretreatment drug resistance in persons initiating and reinitiating antiretroviral therapy in Sri Lanka: results from a national representative survey
Authors: Elwitigala J , Rajapaksa L , Inzaule S C , Ariyaratne K A M , Jayasena S , Kurle S , Patil A , Kale D , Siriwardna L , Samaraweera G , Perera H , Jayakody C
Published: April 2023

Background

We conducted a nationwide cross-sectional study to estimate pretreatment drug resistance (PDR) prevalence in adults initiating ART in Sri Lanka following the WHO’s recommendations.

Methods

HIV drug resistance was determined on dried blood spots (DBSs) using population-based sequencing of the protease and reverse transcriptase genes and interpretation was based on Stanford HIVdb v9.0. Analyses were weighted to adjust for multistage sampling and genotypic failure rate. We used logistic regression to assess differences between groups.

Results

Overall, in 10% (15 of 150) of patients initiating ART, HIV drug resistance mutations were detected. The prevalence of resistance to NNRTI drugs efavirenz/nevirapine was 8.4% (95% CI 4.6–15.0) but differed among those reporting having prior antiretroviral (ARV) exposure (24.4%, 95% CI 13.8–39.5) compared with 4.6% (95% CI 1.6–12.8) for those reporting as being ARV naive (OR 4.6, 95% CI 1.3–16.6, P = 0.021). PDR to efavirenz/nevirapine was also nearly twice as high among women (14.1%, 95% CI 6.1–29.4) compared with men (7.0%, 95% CI 3.1–14.7) (P = 0.340) and three times high among heterosexuals (10.4%, 95% CI 2.4–35.4) compared with MSM (3.8%, 95% CI 1.1–12.7) (P = 0.028). NRTI PDR prevalence was 3.8% (95% CI 1.1–12.1) and no PI PDR was observed in the study.

Conclusions

A high prevalence of efavirenz/nevirapine PDR was reported, especially in patients with prior ARV exposure, in women and those reporting being heterosexual. These findings highlight the need to fast-track the transition to the WHO-recommended dolutegravir-based first-line ART.
The alginate polymer OligoG alters susceptibility of biofilm-embedded non-typeableHaemophilus influenzaeto ampicillin and ciprofloxacin
Authors: Marienborg Kaja , Ambur Ole Herman , Økstad Ole Andreas Løchen , Skaare Dagfinn
Published: April 2023

Objectives

Treatment of respiratory infections with non-typeable Haemophilus influenzae (NTHi) in COPD patients is complicated by biofilm formation, protecting the bacteria against the hosts’ immune response and antibiotics. We investigated the antibiofilm and antibacterial effects of the alginate polymer OligoG, alone or combined with ampicillin or ciprofloxacin, on mature NTHi biofilms.

Materials and methods

Two unrelated COPD strains with PBP3-mediated β-lactam resistance, with additional TEM-1 β-lactamase (Hi-022) or quinolone resistance due to altered GyrA and ParC (Hi-072) were used. Antibiofilm and antibacterial effects were assessed macroscopically, by measurement of biofilm biomass (OD), and by viable cell counts, with determination of minimum biofilm inhibitory concentration (MBIC) and the novel parameter ‘minimum concentration for 2 log10 drop in viable cells in biofilm’ (MB2LDC). Drug interactions between OligoG and antibiotics were assessed by comparing expected and observed inhibitory effects (percent inhibition of no-treatment control) of combined treatment.

Results

OligoG had dose-dependent biofilm disruptive abilities and a weak inhibitory effect on viable cells. Combination with OligoG (64 g/L) significantly lowered MBIC for ampicillin (both strains) and MB2LDC for ciprofloxacin (Hi-022). For Hi-022, there was significant synergism between OligoG and both antibiotics. For Hi-072, interactions were subtle, but a tendency in direction of antagonism was significant at two concentrations of ciprofloxacin.

Conclusions

OligoG shows promise as a potential adjuvant to antibiotics in NTHi infections, but strain-specific factors appear to affect drug interactions and may lead to antagonism. More research is needed to clarify the mechanisms of action of OligoG and interactions with antibiotics.
Spamming the regulator: exploring a new lobbying strategy in EU competition procedures
Authors: Jugl Marlene , Pagel William A M , Garcia Jimenez Maria Camilla , Salendres Jean Pierre , Lowe Will , Malikova Helena , Bryson Joanna J
Published: April 2023

Regulation plays a central role in modern governance; yet, we have limited knowledge of how subjects of regulation—particularly, private actors—act in the face of potentially adverse regulatory decisions. Here, we document and examine a novel lobbying strategy in the context of competition regulation, a strategy that exploits the regulator’s finite administrative capacities. Companies with merger cases under scrutiny by the European Commission’s Directorate General for Competition appear to be employing a strategy of ‘spamming the regulator,’ through the strategic and cumulative submission of economic expert assessments. Procedural pressures may result in an undeservedly favourable assessment of the merger. Based on quantitative and qualitative analyses of an original dataset of all complex merger cases in the European Union 2005–2020, we present evidence of this new strategy and a possible learning process among private actors. We suggest remedies to ensure regulatory effectiveness in the face of this novel strategy.
An Antiviral Drug—Peramivir: Degradation and Identification of Impurities and the Endorsement of an HPLC–MS Method
Authors: Alumuri Thulaseedhar , Merugu Karuna Sree , Namburi L A Amarababu , Kurnool Aravınd , SaravanaVadivu Arunachalam , Balasubramanian Selvakumar
Published: April 2023

Background

Peramivir is a neuraminidase inhibitor that serves as a transition state analogue for influenza neuraminidase, inhibiting the formation of new viruses in infected cells, and has been approved for intravenous administration.

Objective

To validate an HPLC method used to identify the degraded products of the antiviral drug peramivir.

Methods

Herein, we report the identification of compounds formed after the degradation of peramivir through acid, alkali, peroxide, thermal, and photolytic degradation. At the level of toxicology, a technique was devised for the isolation and measurement of peramivir.

Results

A sensitive and reliable LC–tandem mass spectrometry technique for the quantitative measurement of Peramivir and its impurities was developed and verified in order to comply with the recommendations made by the International Council for Harmonisation (ICH). The proposed protocol was in the 50–750 µg/mL range. Relative Standard Deviation values of less than 2.0% indicated good recovery in the range of 98.36–102.57%. Within the studied range, the calibration curves demonstrated good linearity and, in addition, the fitting of correlation coefficient was more than 0.999 for every impurity. Quantitative analysis of contaminants revealed the high efficiency at a low level.

Conclusion

Given its ability to separate degradation products, quantitative analysis is used to detect and quantify known and unknown impurities and degradants in the peramivir drug substance during routine analysis and stability studies. No significant degradation was found in peroxide and photolytic degradation studies.

Highlights

An HPLC method was developed and put to the test in order to analyze the behavior of the impurities of peramivir as they degraded when subjected to the stress conditions suggested by the ICH. Peramivir was found to be stable under peroxide and photolysis conditions but not stable or degradable when exposed to the acid, base, and thermal stress conditions. The method developed was extremely precise, linear, accurate, robust, and rugged. As a result, this technology has the potential to be used in the medication production process for regular impurity analysis as well as for the stability analysis of peramivir.
Boosting, sorting and complexity—urban scaling of innovation around the world
Authors: Broekel Tom , Knuepling Louis , Mewes Lars
Published: April 2023

It is widely understood that innovations tend to be concentrated in cities, which is evidenced by innovative output increasing disproportionately with city size. Yet, given the heterogeneity of countries and technologies, few studies explore the relationship between population and innovation numbers. For instance, in the USA, innovative output scaling is substantial and is particularly pronounced for complex technologies. Whether this is a universal pattern of complex technologies and a potential facilitator of scaling, is unknown. Our analysis compared urban scaling in urban areas across 33 countries and 569 technologies. Considerable variation was identified between countries, which is rooted in two fundamental mechanisms (sorting and boosting). The sorting of innovation-intensive technologies is found to drive larger innovation counts among cities. Among most countries, this mechanism contributes to scaling more than city size boosting innovation within specific technologies. While complex technologies are concentrated in large cities and benefit from the advantages of urbanization, their contribution to the urban scaling of innovations is limited.
Characterization of potential Cu-Au mineralization using electrical resistivity and induced polarization methods: a case study in Eastern Labo, Bicol, Philippines
Authors: Casulla Mel Anthony A , Mizunaga Hideki
Published: April 2023

Electrical resistivity and induced polarization (ER-IP) surveys were carried out in Eastern Labo, Bicol, Philippines, to assess the potential Cu-Au mineralization in pyroclastic-covered areas. An electrical resistivity tomography method with a dipole–dipole array was used, and the L1 norm (robust) inversion approach was employed to generate the 16 2D ER-IP models. The analysis of the resistivity and chargeability classified the underlying lithology into eight zones. Zones from C to F are the potential mineralized zones, while Zones A and B (Labo Volcanic Complex) and Zones G and H (Tumbaga Formation and Tamisan Diorite) are the non-mineralized zones. Zone C, represented by low chargeability (<15 mV V−1) and intermediate resistivity (15–100 Ω-m) values, is characterized by a high concentration of disseminated sulfide minerals (e.g. chalcopyrite). Zone D has a chargeability range comparable to Zone C but higher resistivity (>100 Ω-m), which might be due to silicification. Zone E corresponds to the oxide zone with concentrated sulfide minerals along clayey, weathered, fractured areas; it has moderate to high chargeability (>15 mV V−1) and low resistivity (<15 Ω-m) signatures. Zone F has a similar resistivity range to Zone E but has lower chargeability (<15 mV V−1) values. The interpreted underlying lithological units were confirmed using borehole data. Because of the extensive occurrence of high chargeability zones with moderate resistivity anomalies, potentially mineralized areas for further investigation (e.g. drilling) were identified in the north-eastern portion of the study area.
Improving Deciduous Forest Inventory Plot Center Measurement Using Unoccupied Aerial Systems Imagery
Authors: Carpenter Joshua , Rentauskas Daniel , Makkar Nikhil , Jung Jinha , Fei Songlin
Published: April 2023

Field-based forest inventory plots are fundamental for many forest studies. These on-the-ground measurements of small samples of forested areas provide foresters with key information such as the size, abundance, health, and value of their forests. Recently, forest inventory plots have begun to be used as ground validation for tree features automatically extracted from remotely sensed data sets. Additionally, machine learning methods for feature extraction rely heavily on large quantities of training data and require these field forest inventory measurement datasets for algorithm training. Undermining the usefulness of forest inventory plot data as validation or training data is the positional uncertainty of plot location measurements. Because global navigation satellite systems (GNSS) cannot reliably measure plot center coordinates under thick tree canopy, plot center coordinates usually contain multiple meters of horizontal error. We present a method for reliably measuring plot center coordinates in which plot centers are individually marked with low-cost targets, allowing plot centers to be manually measured from orthoimagery captured during the leaf-off season. Our plot center measurements are shown to have less than 10 cm of horizontal error, an improvement of an order of magnitude over traditional GNSS methods.
Assessment of knowledge, behaviour and awareness towards antibiotic use and resistance: a cross sectional study from south Jordanian society
Authors: Al-Btoush Hayat A , Aleidi Shereen M , Al-Odinat Hind A , Qaisi Nisreen T
Published: April 2023

Objectives

This study aims to evaluate public knowledge about antibiotic use and resistance among the population in southern Jordan (a deprived region).

Methods

A cross-sectional study was carried out and 435 participants completed the questionnaire that contained four sections: socio-demographic information, participants’ knowledge and behaviour about antibiotic use, the roles of physicians and pharmacists in antibiotic misuse and the level of participants’ awareness regarding antibiotic resistance. The data were analysed using the statistical package for social science. The Chi-square test of independence was used to compare the categorical variables.

Key findings

Approximately 53% of the participants exhibited negative behaviour towards antibiotic use. The highest proportion was among those with an education level of middle school (73.3%), non-medical field employees (58%) and non-employee participants (60.8%). About 48.0% of the participants have a high level of knowledge and awareness about antibiotic resistance. This was more evident among those of the age group between 17 and 27 years old, who have bachelor’s degrees or work in both the medical and non-medical fields. Nearly 57.5% of the participants were not asked by the physician for diagnostic tests before prescribing antibiotics, and 66.9% obtain antibiotics from the pharmacy without a prescription.

Conclusions

Good awareness about antibiotic resistance in the community of southern Jordan does not prevent negative behaviour of antibiotic use. Physicians and pharmacists are strong contributors to antibiotic resistance. This demonstrates the need for regulatory actions to limit the access to and overuse of antibiotics.
Encapsulating peritoneal sclerosis post liver transplant and peritoneal dialysis: case report and literature review
Authors: Piltcher-da-Silva Rodrigo , Petry João Francisco , de Araujo Freitas Ana Laura , Rhoden Guilherme Vieceli , Jasinski Gabriel , Piltcher-Recuero Mariana , Bettini Luiz Francisco Cravo , Aguilera Yan Sacha Hass , Leme Juliana El Ghoz , da Costa Marco Aurélio Raeder , Coelho Júlio Cezar Uili
Published: April 2023

Encapsulating peritoneal sclerosis (EPS) is a rare and debilitating condition. A fibrocollagenous membrane, which promotes encasement of the small intestine leaving a cocoon-like appearance, takes place. It is mainly associated with peritoneal infections, medications, peritoneal dialysis and systemic inflammatory diseases. Diagnosis is based on clinical history, intestinal obstruction and imaging exam. We report a case of EPS in a 68-year-old man with a medical history of liver transplantation and peritoneal dialysis, complaining of obstructive bowel symptoms.
Understanding aspirations to stay: Relative endowment within a time–space perspective
Authors: Vezzoli Simona
Published: April 2023

This article explores the factors and mechanisms that underpin aspirations to stay in situations where migration could be beneficial. To do so, this article proposes a spatial–temporal comparative framework and explains aspirations to stay through the notion of relative endowment, which reveals a positive assessment of what people have, despite the awareness of social inequalities. Empirically, the article focuses on a rural town in northern Brazil that has experienced a stagnating economy since the 1990s, where young adults express aspirations to stay. Non-economic factors such as closeness to nature, family, and friends not only encourage staying, but make young people feel endowed in relation to a perceived stressful work-centered urban life. The proposed framework reveals that the overall negative perspectives on the town’s present are congruous with aspirations to stay because of young people’s positive feelings about the town’s past and future. In fact, hope plays an important role in shaping aspirations to stay. This article shows the value of considering people’s perceptions of past, present, and future and how they influence aspirations to stay, and migrate.
Hypercritical accretion during common envelopes in triples leading to binary black holes in the pair-instability-supernova mass gap
Authors: Moreno Méndez Enrique , De Colle Fabio , López-Cámara Diego , Vigna-Gómez Alejandro
Published: April 2023

Hydrodynamic studies of stellar-mass compact objects (COs) in a common envelope (CE) have shown that the accretion rate onto the CO is a few orders of magnitude below the Bondi–Hoyle–Lyttleton (BHL) estimate. This is several orders of magnitude above the Eddington limit and above the limit for neutrino-cooled accretion (i.e. hypercritical accretion or HCA). Considering that a binary system inside the CE of a third star accretes material at nearly the same rate as a single object of the same total mass, we propose stellar-evolution channels which form binary black hole (BBH) systems with its component masses within the pair-instability supernova (PISN) mass gap. Our model is based on HCA onto the BBH system engulfed into the CE of a massive tertiary star. Furthermore, we propose a mass transfer mode which allows to store mass lost by the binary onto a third star. Through the use of population synthesis simulations for the evolution of BBHs and standard binary-evolution principles for the interaction with a tertiary star, we are able to produce BBHs masses consistent with those estimated for GW190521. We also discuss the massive binary system Mk34 as a possible progenitor of BBHs in the PISN gap.
Multiband gravitational wave observations of stellar binary black holes at the low to middle and high frequencies
Authors: Zhao Yuetong , Lu Youjun , Yan Changshuo , Chen Zhiwei , Ni Wei-Tou
Published: April 2023

The ground-based gravitational wave (GW) observatories discover a population of merging stellar binary black holes (BBHs), which are promising targets for multiband observations by the low-, middle-, and high-frequency GW detectors. In this paper, we investigate the multiband GW detections of BBHs and demonstrate the advantages of such observations in improving the localization and parameter estimates of the sources. We generate mock samples of BBHs by considering different formation models as well as the merger rate density constrained by the current observations (GWTC-3). We specifically consider the astrodynamical middle-frequency interferometer GW observatory (AMIGO) in the middle-frequency band and estimate that it may detect 21–91 BBHs with signal-to-noise ratio ϱ ≥ 8 in a 4-yr observation period. The multiband observations by the low-frequency detectors [Laser Interferometer Space Antenna (LISA) and Taiji] and AMIGO may detect 5–33 BBHs with ϱLT ≥ 5 and ϱAMI ≥ 5, which can evolve to the high-frequency band within 4 yr and can be detected by the Cosmic Explorer (CE) and Einstein Telescope (ET). The joint observations of LISA-Taiji-AMIGO-ET-CE may localize the majority of the detectable BBHs in sky areas of 7 × 10−7 to 2 × 10−3 deg2, which is improved by a factor of ∼120, ∼2.4 × 105, ∼1.8 × 104, or ∼1.2 × 104, comparing with those by only adopting CE-ET, AMIGO, LISA-Taiji, or LISA-Taiji-AMIGO. These joint observations can also lead to an improvement of the measurement precision of the chirp mass (symmetric mass ratio) by a factor of ∼5.5 × 104 (33), ∼16 (8), ∼120 (90), or ∼5 (5), comparing with those by CE-ET, AMIGO, LISA-Taiji, or LISA-Taiji-AMIGO.
Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features
Authors: Czernecki Dariusz , Nourisson Antonin , Legrand Pierre , Delarue Marc
Published: April 2023

Family A DNA polymerases (PolAs) form an important and well-studied class of extant polymerases participating in DNA replication and repair. Nonetheless, despite the characterization of multiple subfamilies in independent, dedicated works, their comprehensive classification thus far is missing. We therefore re-examine all presently available PolA sequences, converting their pairwise similarities into positions in Euclidean space, separating them into 19 major clusters. While 11 of them correspond to known subfamilies, eight had not been characterized before. For every group, we compile their general characteristics, examine their phylogenetic relationships and perform conservation analysis in the essential sequence motifs. While most subfamilies are linked to a particular domain of life (including phages), one subfamily appears in Bacteria, Archaea and Eukaryota. We also show that two new bacterial subfamilies contain functional enzymes. We use AlphaFold2 to generate high-confidence prediction models for all clusters lacking an experimentally determined structure. We identify new, conserved features involving structural alterations, ordered insertions and an apparent structural incorporation of a uracil-DNA glycosylase (UDG) domain. Finally, genetic and structural analyses of a subset of T7-like phages indicate a splitting of the 3′–5′ exo and pol domains into two separate genes, observed in PolAs for the first time.
RNA-dependent interactome allows network-based assignment of RNA-binding protein function
Authors: Fradera-Sola Albert , Nischwitz Emily , Bayer Marie Elisabeth , Luck Katja , Butter Falk
Published: April 2023

RNA-binding proteins (RBPs) form highly diverse and dynamic ribonucleoprotein complexes, whose functions determine the molecular fate of the bound RNA. In the model organism Sacchromyces cerevisiae, the number of proteins identified as RBPs has greatly increased over the last decade. However, the cellular function of most of these novel RBPs remains largely unexplored. We used mass spectrometry-based quantitative proteomics to systematically identify protein–protein interactions (PPIs) and RNA-dependent interactions (RDIs) to create a novel dataset for 40 RBPs that are associated with the mRNA life cycle. Domain, functional and pathway enrichment analyses revealed an over-representation of RNA functionalities among the enriched interactors. Using our extensive PPI and RDI networks, we revealed putative new members of RNA-associated pathways, and highlighted potential new roles for several RBPs. Our RBP interactome resource is available through an online interactive platform as a community tool to guide further in-depth functional studies and RBP network analysis (https://www.butterlab.org/RINE).
Reconstructing the landscape of gut microbial species across 29,000 diverse individuals
Authors: Segota Igor , Watrous Jeramie D , Kantz Edward D , Nallamshetty Shriram , Tiwari Saumya , Cheng Susan , Jain Mohit , Long Tao
Published: April 2023

The human gut microbiome has been linked to health and disease. Investigation of the human microbiome has largely employed 16S amplicon sequencing, with limited ability to distinguish microbes at the species level. Herein, we describe the development of Reference-based Exact Mapping (RExMap) of microbial amplicon variants that enables mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures ∼75% of microbial species identified by whole-genome shotgun sequencing, despite hundreds-fold less sequencing depth. RExMap re-analysis of existing 16S data from 29,349 individuals across 16 regions from around the world reveals a detailed landscape of gut microbial species across populations and geography. Moreover, RExMap identifies a core set of fifteen gut microbes shared by humans. Core microbes are established soon after birth and closely associate with BMI across multiple independent studies. RExMap and the human microbiome dataset are presented as resources with which to explore the role of the human microbiome.
The RNA export factor TbMex67 connects transcription and RNA export in Trypanosoma brucei and sets boundaries for RNA polymerase I
Authors: Pozzi Berta , Naguleswaran Arunasalam , Florini Francesca , Rezaei Zahra , Roditi Isabel
Published: April 2023

TbMex67 is the major mRNA export factor known to date in trypanosomes, forming part of the docking platform within the nuclear pore. To explore its role in co-transcriptional mRNA export, recently reported in Trypanosoma brucei, pulse labelling of nascent RNAs with 5-ethynyl uridine (5-EU) was performed with cells depleted of TbMex67 and complemented with a dominant-negative mutant (TbMex67-DN). RNA polymerase (Pol) II transcription was unaffected, but the procyclin loci, which encode mRNAs transcribed by Pol I from internal sites on chromosomes 6 and 10, showed increased levels of 5-EU incorporation. This was due to Pol I readthrough transcription, which proceeded beyond the procyclin and procyclin-associated genes up to the Pol II transcription start site on the opposite strand. Complementation by TbMex67-DN also increased Pol I-dependent formation of R-loops and γ-histone 2A foci. The DN mutant exhibited reduced nuclear localisation and binding to chromatin compared to wild-type TbMex67. Together with its interaction with chromatin remodelling factor TbRRM1 and Pol II, and transcription-dependent association of Pol II with nucleoporins, our findings support a role for TbMex67 in connecting transcription and export in T. brucei. In addition, TbMex67 stalls readthrough by Pol I in specific contexts, thereby limiting R-loop formation and replication stress.
A novel Cas9 fusion protein promotes targeted genome editing with reduced mutational burden in primary human cells
Authors: Carusillo Antonio , Haider Sibtain , Schäfer Raul , Rhiel Manuel , Türk Daniel , Chmielewski Kay O , Klermund Julia , Mosti Laura , Andrieux Geoffroy , Schäfer Richard , Cornu Tatjana I , Cathomen Toni , Mussolino Claudio
Published: April 2023

Precise genome editing requires the resolution of nuclease-induced DNA double strand breaks (DSBs) via the homology-directed repair (HDR) pathway. In mammals, this is typically outcompeted by non-homologous end-joining (NHEJ) that can generate potentially genotoxic insertion/deletion mutations at DSB sites. Because of higher efficacy, clinical genome editing has been restricted to imperfect but efficient NHEJ-based approaches. Hence, strategies that promote DSB resolution via HDR are essential to facilitate clinical transition of HDR-based editing strategies and increase safety. Here we describe a novel platform that consists of a Cas9 fused to DNA repair factors to synergistically inhibit NHEJ and favor HDR for precise repairing of Cas-induced DSBs. Compared to canonical CRISPR/Cas9, the increase in error-free editing ranges from 1.5-fold to 7-fold in multiple cell lines and in primary human cells. This novel CRISPR/Cas9 platform accepts clinically relevant repair templates, such as oligodeoxynucleotides (ODNs) and adeno-associated virus (AAV)-based vectors, and has a lower propensity to induce chromosomal translocations as compared to benchmark CRISPR/Cas9. The observed reduced mutational burden, resulting from diminished indel formation at on- and off-target sites, provides a remarkable gain in safety and advocates this novel CRISPR system as an attractive tool for therapeutic applications depending on precision genome editing.
An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening
Authors: Xiang Manli , Xia Kaijiang , Chen Bingyi , Luo Zhiteng , Yu Ying , Jiang Lili , Zhou Huihao
Published: April 2023

Tryptophanyl-tRNA synthetase (TrpRS) links tryptophan to tRNATrp, thereby playing an indispensable role in protein translation. Unlike most class I aminoacyl-tRNA synthetases (AARSs), TrpRS functions as a homodimer. Herein, we captured an ‘open-closed’ asymmetric structure of Escherichia coli TrpRS (EcTrpRS) with one active site occupied by a copurified intermediate product and the other remaining empty, providing structural evidence for the long-discussed half-of-the-sites reactivity of bacterial TrpRS. In contrast to its human counterpart, bacterial TrpRS may rely on this asymmetric conformation to functionally bind with substrate tRNA. As this asymmetric conformation is probably a dominant form of TrpRS purified from bacterial cells, we performed fragment screening against asymmetric EcTrpRS to support antibacterial discovery. Nineteen fragment hits were identified, and 8 of them were successfully cocrystallized with EcTrpRS. While a fragment named niraparib bound to the L-Trp binding site of the ‘open’ subunit, the other 7 fragments all bound to an unprecedented pocket at the interface between two TrpRS subunits. Binding of these fragments relies on residues specific to bacterial TrpRS, avoiding undesired interactions with human TrpRS. These findings improve our understanding of the catalytic mechanism of this important enzyme and will also facilitate the discovery of bacterial TrpRS inhibitors with therapeutic potential.
AlloReverse: multiscale understanding among hierarchical allosteric regulations
Authors: Zha Jinyin , Li Qian , Liu Xinyi , Lin Weidong , Wang Tingting , Wei Jiacheng , Zhang Ziliang , Lu Xun , Wu Jing , Ni Duan , Song Kun , Zhang Liang , Lu Xuefeng , Lu Shaoyong , Zhang Jian
Published: April 2023

Increasing data in allostery are requiring analysis of coupling relationships among different allosteric sites on a single protein. Here, based on our previous efforts on reversed allosteric communication theory, we have developed AlloReverse, a web server for multiscale analysis of multiple allosteric regulations. AlloReverse integrates protein dynamics and machine learning to discover allosteric residues, allosteric sites and regulation pathways. Especially, AlloReverse could reveal hierarchical relationships between different pathways and couplings among allosteric sites, offering a whole map of allostery. The web server shows a good performance in re-emerging known allostery. Moreover, we applied AlloReverse to explore global allostery on CDC42 and SIRT3. AlloReverse predicted novel allosteric sites and allosteric residues in both systems, and the functionality of sites was validated experimentally. It also suggests a possible scheme for combined therapy or bivalent drugs on SIRT3. Taken together, AlloReverse is a novel workflow providing a complete regulation map and is believed to aid target identification, drug design and understanding of biological mechanisms. AlloReverse is freely available to all users at https://mdl.shsmu.edu.cn/AlloReverse/ or http://www.allostery.net/AlloReverse/.
Helper-embedded satellites from an integrase clade that repeatedly targets prophage late genes
Authors: Tommasini Dario , Mageeney Catherine M , Williams Kelly P
Published: April 2023

Satellites such as phage-induced chromosomal islands (PICIs) are mobile genetic elements relying on helper phages for their mobilization, through trans-regulatory interactions. We discovered a PICI with a more intimate cis-regulatory configuration, integrated within a late gene of its helper prophage. This helper-embedded PICI (HE-PICI) configuration delays expression of the interrupted helper late gene until the satellite excises and provides passive helper-driven components to both HE-PICI replication and late transcription. Upon induction of a helper-satellite composite, precise excision of the entire composite was observed, followed by composite replication, then satellite excision. We mapped 491 additional HE-PICIs to one of 14 sites in cognates of phage lambda late genes. Associated integrases form a single phylogenetic clade with subclades respecting the 14 site groups, exhibiting repeated tropism for prophage late genes as new integration sites evolve. Four ordered zones in a general gram-negative PICI genome organization are: an integration zone encoding integrase and AlpA, a dynamic zone encoding members of the Bro-N network of domain-swapping DNA-interactive proteins and immunity repressor RNAs, a replication zone, and a dynamic late zone in which clusters as large as 17 consecutive helper prophage late genes have been captured. Helper-embedded satellites present new dimensions in satellite/helper relationships.
Justified Epistemic Exclusions in Mathematics
Authors: Rittberg Colin Jakob
Published: April 2023

Who gets to contribute to knowledge production of an epistemic community? Scholarship has focussed on unjustified forms of exclusion. Here I study justified forms of exclusion by investigating the phenomenon of so-called ‘cranks’ in mathematics. I argue that workload-management concerns justify the exclusion of these outsiders from mathematical knowledge-making practices. My discussion reveals three insights. There are reasons other than incorrect mathematical argument that justify exclusions from mathematical practices. There are instances in which mathematicians are justified in rejecting even correct mathematical arguments. Finally, the way mathematicians spot mathematical crankery does not support the pejorative connotations of the ‘crank’ terminology.
Advances in osseointegration of biomimetic mineralized collagen and inorganic metal elements of natural bone for bone repair
Authors: Zhu Wenbo , Li Chao , Yao Mengxuan , Wang Xiumei , Wang Juan , Zhang Wei , Chen Wei , Lv Hongzhi
Published: April 2023

At this stage, bone defects caused by trauma, infection, tumor, or congenital diseases are generally filled with autologous bone or allogeneic bone transplantation, but this treatment method has limited sources, potential disease transmission and other problems. Ideal bone-graft materials remain continuously explored, and bone defect reconstruction remains a significant challenge. Mineralized collagen prepared by bionic mineralization combining organic polymer collagen with inorganic mineral calcium phosphate can effectively imitate the composition and hierarchical structure of natural bone and has good application value in bone repair materials. Magnesium, strontium, zinc and other inorganic components not only can activate relevant signaling pathways to induce differentiation of osteogenic precursor cells but also stimulate other core biological processes of bone tissue growth and play an important role in natural bone growth, and bone repair and reconstruction. This study reviewed the advances in hydroxyapatite/collagen composite scaffolds and osseointegration with natural bone inorganic components, such as magnesium, strontium and zinc.
House Price Dynamics, Optimal LTV Limits and the Liquidity Trap
Authors: Ferrero Andrea , Harrison Richard , Nelson Benjamin
Published: April 2023

This paper studies the optimal design of a macro-prudential instrument, a loan-to-value (LTV) limit, and its implications for monetary policy in a model with nominal rigidities and financial frictions. The analysis accounts for both an effective lower bound on the nominal interest rate and an upper bound on the ability of LTV limits to stimulate credit demand. The welfare-based loss function features a role for macro-prudential policy to enhance risk-sharing. Optimal LTV limits are strongly countercyclical. In a house price boom-bust episode, the active use of LTV limits alleviates debt-deleveraging dynamics and prevents the economy from falling into a liquidity trap.
When Do Low-Frequency Measures Really Measure Effective Spreads? Evidence from Equity and Foreign Exchange Markets
Authors: Jahan-Parvar Mohammad R , Zikes Filip
Published: April 2023

We present evidence that several popular low-frequency measures of effective spread suffer from a volatility-induced bias and that volatility is the primary driver of the variation of these liquidity proxies. Using data for U.S. equities and major foreign exchange rates, we show that the bias arises when the effective spread is small relative to volatility. We document that the bias has become more acute over time and show that volatility-biased measures fail to replicate some well-known results in empirical finance. We conclude by providing guidance on the choice of low-frequency measures in empirical applications.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Genome-Wide Association Mapping of Bacterial Leaf Streak Resistance in Two Elite Barley Breeding Panels
Authors: Ritzinger Mitch , Sallam Ahmad H. , Smith Kevin P. , Case Austin J. , Wodarek Joseph , Curland Rebecca D. , Dill-Macky Ruth , Steffenson Brian J.
Published: April 2023

Bacterial leaf streak (BLS), caused chiefly by the pathogen Xanthomonas translucens pv. translucens, is becoming an increasingly important foliar disease of barley in the Upper Midwest. The deployment of resistant cultivars is the most economical and practical method of control. To identify sources of BLS resistance, we evaluated two panels of breeding lines from the University of Minnesota (UMN) and Anheuser-Busch InBev (ABI) barley improvement programs for reaction to strain CIX95 in the field at St. Paul and Crookston, MN, in 2020 and 2021. The percentage of resistant lines in the UMN and ABI panels with mid-season maturity was 1.8% (6 of 333 lines) and 5.2% (13 of 251 lines), respectively. Both panels were genotyped with the barley 50K iSelect SNP array, and then a genome-wide association study was performed. A single, highly significant association was identified for BLS resistance on chromosome 6H in the UMN panel. This association was also identified in the ABI panel. Seven other significant associations were detected in the ABI panel: two each on chromosomes 1H, 2H, and 3H and one on chromosome 5H. Of the eight associations identified in the panels, five were novel. The discovery of resistance in elite breeding lines will hasten the time needed to develop and release a BLS-resistant cultivar.