bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of clinically relevant antibiotic resistant bacteria in shared fomites, waste water, and municipal solid wastes disposed in vicinity of residential areas of Nigerian Urban City
Authors: Yusuf Ibrahim , Muhammad Zainab Damji , Muhammad Amin Binta , Shuaibu Maryam Danladi , Hamza Nafisatu , Isah Hajara Dauda , Abdullahi Nasir Bako , Ene Patience James , Shuaibu Sameera Salisu , Doguwa Nasir , Pedro Shamsudeen Lekan , Muhammad Maryam Adamu
Published: October 2023

SStudies investigating environmental hotspots of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in Nigeria are limited. This study was designed to assess various environmental sources and commonly touched surfaces as potential carriers of ARB and ARGs with implications for public health. A total of 392 samples, including sewage (36), sludge (36), diapers (20), plastics (20), water sachet polythene bags (20), food wastes (20), soil beneath dump sites (20), and frequently touched surfaces like restroom floors (80), corridors (24), door handles (56), and room floors and walls (60), were collected and screened for the presence of resistant bacteria carrying genes such as blaKPC, blaNDM-1, blaCMY-2, blaIMP, blaOXA66, and MecA. Additionally, we employed standard techniques to detect methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase-producing Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. We also evaluated the effectiveness of routine disinfection procedures in eliminating ARB from restroom floors. Our findings revealed that sewage, sludge, diapers, food wastes, and restroom floors are frequently contaminated with highly and moderately resistant strains of E. coli, K. pneumoniae, P. aeruginosa, and MRSA. Notably, we identified two variants of the blaOXA51-like gene (blaOXA-66 & blaOXA-180) in A. baumannii isolated from these environmental sources. Furthermore, we detected seven ESBL-K. pneumoniae, five ESBL-A. baumannii, two ESBL-E. coli, and one ESBL-P. aeruginosa, all carrying one or more ARGs (blaKPC, blaNDM-1, blaCMY-2), in isolates recovered from sewage, sludge, restroom floors, and plastics. It is worth noting that ARB persisted on restroom floors even after disinfection procedures. In conclusion, this study highlights that environmental wastes indiscriminately discarded in residential areas and shared surfaces among individuals are heavily colonized by ARB carrying ARGs of significant public health importance.
Osteoarticular tuberculosis of the ankle, a rare localization: a case report
Authors: Malihy Zakaria , Benaissa Elmostafa , Ben Lahlou Yassine , Maleb Adil , Elouennass Mostafa
Published: October 2023

Tuberculosis is a real scourge, posing a real public health problem in countries where the disease is endemic. Osteoarticular tuberculosis represents 3% to 5% of all tuberculosis cases and 10% to 15% of extra-pulmonary tuberculosis cases. Involvement of the foot and ankle is rarer. We report the case of osteoarticular tuberculosis of the ankle in a 71-year-old patient with type 2 diabetes and hypertension who presented to the trauma department of the Mohammed V Military Hospital with a painful swelling of the ankle. Standard X-rays and CT scan of the ankle showed inflammatory involvement of the bone and joints. Antitubercular therapy was instituted. Given the context of endemicity, any atypical presentation of lingering bone lesions should raise the suspicion of an osteoarticular tuberculosis in order to ensure early therapeutic management.
Galbibacter pacificus sp. nov., isolated from surface seawater of the western Pacific Ocean and transfer of Joostella marina to the genus Galbibacter as Galbibacter orientalis nom. nov. and emended description of the genus Galbibacter
Authors: Wei Lin , Wang Jianning , Liu Xiupian , Lai Qiliang , Li Guizhen , Fu Xiaoteng , Li Guangyu , Shao Zongze , Dong Chunming
Published: October 2023

Two Gram-stain-negative, non-motile, non-spore-forming, strictly aerobic and rod-shaped bacterial strains, CMA-7T and CAA-3, were isolated from surface seawater samples collected from the western Pacific Ocean. Phylogeny of 16S rRNA gene sequences indicated they were related to the genera

Galbibacter

and

Joostella

and shared 95.1, 90.9 and 90.8% sequence similarity with

G. mesophilus

Mok-17T,

J. marina

DSM 19592T and

G. marinus

ck-I2-15T, respectively. Phylogenomic analysis showed that the two strains, together with the members of the genera

Galbibacter

and

Joostella

, formed a monophyletic clade that could also be considered a monophyletic taxon. This distinctiveness was supported by amino acid identity and percentage of conserved proteins indices, phenotypic and chemotaxonomic characteristics and comparative genomics analysis. Digital DNA‒DNA hybridization values and average nucleotide identities between the two strains and their closest relatives were 18.0–20.8 % and 77.7–79.3 %, respectively. The principal fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, Summed Feature 3 (C16 : 1
 ω7c/C16 : 1
 ω6c or C16 : 1
 ω6c/C16 : 1
 ω7c), Summed Feature 9 (iso-C17 : 1
 ω9c or C16 : 0 10-methyl), and C15 : 0 3-OH. The predominant respiratory quinone was MK-6. The polar lipids were phosphatidylethanolamine, aminolipid, aminophospholipid, phospholipid, phosphoglycolipid, glycolipid and unknown polar lipid. The genomic DNA G+C content of strains CMA-7T and CAA-3 was both 38.4 mol%. Genomic analysis indicated they have the potential to degrade cellulose and chitin. Based on the polyphasic evidence presented in this study, the two strains represent a novel species within the genus

Galbibacter

, for which the name Galbibacter pacificus sp. nov. is proposed. The type strain is CMA-7T (=MCCC M28999T = KCTC 92588T). Moreover, the transfer of

Joostella marina

to the genus

Galbibacter

as Galbibacter orientalis nom. nov. (type strain En5T = KCTC 12518T = DSM 19592T=CGMCC 1.6973T) is also proposed.
Danxiaibacter flavus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from forest soil on Danxia Mountain
Authors: Zheng Zhuo-Huan , Lu Chun-Yan , Lian Wen-Hui , Han Jia-Rui , Chen Fang , Zhou Ting , Li Shuai , Dong Lei , Li Wen-Jun
Published: October 2023

A Gram-stain-negative, aerobic, short rod-shaped, yellow bacterium, designated SYSU DXS3180T, was isolated from forest soil of Danxia Mountain in PR China. Growth occurred at 15–37 °C (optimum, 28–30 °C), pH 6.0–10.0 (optimum, pH 7.0–8.0) and with 0–2.0 % NaCl (optimum, 0–0.5 %, w/v). Strain SYSU DXS3180T was positive for hydrolysis of Tween 20, Tween 60, Tween 80 and starch, but negative for urease, H2S production, nitrate reduction, Tween 40 and gelatin. Phylogenetic analysis based on 16S rRNA gene and genome sequences showed that SYSU DXS3180T belonged to the family

Chitinophagaceae

. The closely related members were Foetidibacter luteolus YG09T (94.2 %),

Limnovirga soli

KCS-6T (93.9 %) and

Filimonas endophytica

SR 2-06T (93.7 %). The genome of strain SYSU DXS3180T was 7287640 bp with 5782 protein-coding genes, and the genomic DNA G+C content was 41.4 mol%. The main respiratory quinone was MK-7 and the major fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The major polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain SYSU DXS3180T is proposed to represent a novel species of a novel genus named Danxiaibacter flavus gen. nov., sp. nov., within the family

Chitinophagaceae

. The type strain is SYSU DXS3180T (=KCTC 92895T=GDMCC 1.3825 T).
Human immunodeficiency virus 1 5′-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations
Authors: Nouhin Janin , Tzou Philip Lei , Rhee Soo-Yon , Sahoo Malaya K. , Pinsky Benjamin A. , Krupkin Miri , Puglisi Joseph D. , Puglisi Elisabetta V. , Shafer Robert W.
Published: October 2023

Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) initiation depends on interaction between viral 5′-leader RNA, RT and host tRNA3Lys. Therefore, we sought to identify co-evolutionary changes between the 5′-leader and RT in viruses developing RT-inhibitor resistance mutations. We sequenced 5′-leader positions 37–356 of paired plasma virus samples from 29 individuals developing the nucleoside RT inhibitor (NRTI)-resistance mutation M184V, 19 developing a non-nucleoside RT inhibitor (NNRTI)-resistance mutation and 32 untreated controls. 5′-Leader variants were defined as positions where ≥20 % of next-generation sequencing (NGS) reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing a ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20 % of NGS reads. Among 80 baseline sequences, 87 positions (27.2 %) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs 0/32; P=0.0006) or NNRTI-resistance (4/19 vs 0/32; P=0.02; Fisher’s exact test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0 and 28.8 %, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analysed 5′-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six National Center for Biotechnology Information (NCBI) BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5′-leader positions. Although we did not convincingly document co-evolutionary changes between RT and 5′-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201 immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.
Rapid response of a public health reference laboratory to the COVID-19 pandemic
Authors: Pinhata Juliana Maira Watanabe , Brandao Angela Pires , Leite Daniela , Oliveira Rosangela Siqueira de , Fukasawa Lucila Okuyama , Gonçalves Maria Gisele , Guerra Juliana Mariotti , Araujo Leonardo José Tadeu de , Mansueli Gina Ploeger , Santos Lilian Beserra , Borghesan Tarcilla Corrente , Kimura Lidia Midori , Takahashi Juliana Possatto Fernandes , Garcia Juliana Alves , Piza Ana Rita de Toledo , Ferreira Camila Santos da Silva , Polatto Ricardo , Guerra Maria Luiza Leopoldo e Silva , Fazioli Raquel dos Anjos , Zanella Rosemeire Cobo , Blanco Roberta Morozetti ,   IAL-2 Working Group†
Published: October 2023

Introduction. Brazil was one of the most affected countries by the COVID-19 pandemic. Instituto Adolfo Lutz (IAL) is the reference laboratory for COVID-19 in São Paulo, the most populous state in Brazil. In April 2020, a secondary diagnostic pole named IAL-2 was created to enhance IAL’s capacity for COVID-19 diagnosis.

Hypothesis/Gap Statement. Public health laboratories must be prepared to rapidly respond to emerging epidemics or pandemics.

Aim. To describe the design of IAL-2 and correlate the results of RT-qPCR tests for COVID-19 with secondary data on suspected cases of SARS-CoV-2 infection in the São Paulo state.

Methodology. This is a retrospective study based on the analysis of secondary data from patients suspected of infection by SARS-CoV-2 whose clinical samples were submitted to real-time PCR after reverse transcription (RT-qPCR) at IAL-2, between 1 April 2020 and 8 March 2022. RT-qPCR Ct results of the different kits used were also analysed.

Results. IAL-2 was implemented in April 2020, just over a month after the detection of the first COVID-19 case in Brazil. The laboratory performed 304,250 RT-qPCR tests during the study period, of which 98 319 (32.3 %) were positive, 205827 (67.7 %) negative, and 104 (0.03 %) inconclusive for SARS-CoV-2. RT-qPCR Ct values≤30 for E/N genes of SARS-CoV-2 were presented by 79.7 % of all the samples included in the study.

Conclusion. IAL was able to rapidly implement a new laboratory structure to support the processing of an enormous number of samples for diagnosis of COVID-19, outlining strategies to carry out work with quality, using different RT-qPCR protocols.
An Exploratory Study to Detect the Effects of the Combined Intake of Gamma-aminobutyric Acid (GABA) and L-theanine on Sleep by Wearable Device
Authors: Konno Hiroyuki , Murotani Rikuto , Kamada Yukikazu
Published: October 2023

Objectives

Sleep disorders are a global issue, and supplements for sleep and new devices for daily sleep status assessment are becoming widely available. Gamma-aminobutyric acid (GABA) and L-theanine are commonly used dietary supplements to improve sleep. This study examined whether the combined GABA (700 mg/day) and L-theanine (200 mg/day) intake improve sleep in adults with sleep problems and whether the Fitbit Charge 5 can detect sleep status changes the supplements induced.

Methods

Participants received the supplements for four weeks, and changes in sleep quality measured using the Pittsburgh Sleep Quality Index (PSQI) and sleep-related data measured by the Fitbit Charge 5 were evaluated before and after the intake of the supplements.

Results

Results obtained from 19 participants indicated significant improvement in the total PSQI score (9.42 ± 1.80 to 6.26 ± 1.66 (mean ± standard deviation), p<0.001). Sleep score improvement was insignificant for the Fitbit data(N=17). However, sleep recovery scores improved significantly (p=0.042). In addition, heart rate during sleep decreased with a significant difference of 1.3 bpm decrease in the first week of intake (p = 0.045).

Conclusions

The simultaneous intake of GABA and L-theanine improved sleep in adults, and the Fitbit Charge 5 could detect improvements in objective information regarding sleep status.
Evaluating the comparability of osteoporosis treatments using propensity score and negative control outcome methods in UK and Denmark electronic health record databases
Authors: Rathod-Mistry Trishna , Tan Eng Hooi , Strauss Victoria Y , O’Kelly James , Giorgianni Francesco , Baxter Richard , Brunetti Vanessa C , Pedersen Alma Becic , Ehrenstein Vera , Prieto-Alhambra Daniel
Published: October 2023

Evidence on the comparative effectiveness of osteoporosis treatments is heterogeneous. This may be attributed to different populations and clinical practice, but also to differing methodologies ensuring comparability of treatment groups before treatment effect estimation and the amount of residual confounding by indication. This study assessed the comparability of denosumab vs oral bisphosphonate (OBP) groups using propensity score (PS) methods and negative control outcome (NCO) analysis. A total of 280,288 women aged ≥50 years initiating denosumab or OBP in 2011-2018 were included from the UK Clinical Practice Research Datalink (CPRD) and the Danish National Registries (DNR). Balance of observed covariates was assessed using absolute standardised mean difference (ASMD) before and after PS weighting, matching, and stratification, with ASMD >0.1 indicating imbalance. Residual confounding was assessed using NCOs with ≥100 events. Hazard ratio (HR) and 95% confidence interval (CI) between treatment and NCO was estimated using Cox models. Presence of residual confounding was evaluated with two approaches: (1) >5% of NCOs with 95% CI excluding 1, (2) >5% of NCOs with an upper CI <0.75 or lower CI >1.3. The number of imbalanced covariates before adjustment (CPRD 22/87; DNR 18/83) decreased, with 2-11% imbalance remaining after weighting, matching or stratification. Using approach 1, residual confounding was present for all PS methods in both databases (≥8% of NCOs). Using approach 2, residual confounding was present in CPRD with PS matching (5.3%) and stratification (6.4%), but not with weighting (4.3%). Within DNR, no NCOs had HR estimates with upper or lower CI limits beyond the specified bounds indicating residual confounding for any PS method. Achievement of covariate balance and determination of residual bias were dependent upon several factors including the population under study, PS method, prevalence of NCO, and the threshold indicating residual confounding.
Interest of tri-axial rubidium and helium optically pumped magnetometers for on-scalp magnetoencephalography recording of interictal epileptiform discharges
Authors: Feys Odile , Corvilain Pierre , Labyt Etienne , Mahmoudzadeh Mahdi , Routier Laura , Sculier Claudine , Holmes Niall , Brookes Matthew , Goldman Serge , Romain Rudy , Mitryukovskiy Sergey , Palacios-Laloy Agustin , Schwartz Denis , Betrouni Nacim , Derambure Philippe , Wallois Fabrice , Wens Vincent , De Tiège Xavier
Published: October 2023

Cryogenic magnetoencephalography (MEG) enhances the presurgical assessment of refractory focal epilepsy (RFE). Optically pumped magnetometers (OPMs) are cryogen-free sensors that enable on-scalp MEG recordings. Here, we investigate the interest of tri-axial OPMs (87Rb (Rb-OPM) and4He gas (He-OPM)) for the detection of interictal epileptiform discharges (IEDs).

IEDs were recorded simultaneously with 4 tri-axial Rb- and 4 tri-axial He-OPMs in a child with RFE. IEDs were identified visually, isolated from magnetic background noise using independent component analysis (ICA), and the orientation of magnetic field generated by the IEDs was reconstructed at each sensor location.

Most IEDs (>1,000) were detectable by both He- and Rb-OPM recordings. IEDs were isolated by ICA and the resulting magnetic field oriented mostly tangential to the scalp in Rb-OPMs and radial in He-OPMs. Likely due to differences in sensor locations, the IED amplitude was higher with Rb-OPMs.

This case study shows comparable ability of Rb-OPMs and He-OPMs to detect IEDs and the substantial benefits of triaxial OPMs to detect IEDs from different sensor locations. Tri-axial OPMs allow to maximize spatial brain sampling for IEDs detection with a limited number of sensors.
District Level Variation in Hypertension Epidemiology in India and Influence of Social Determinants: National Family Health Survey-5
Authors: Gupta Rajeev , Gaur Kiran , Sharma Suresh C , Khedar Raghubir S , Dhamija Rajinder K
Published: October 2023

BACKGROUND

Enumeration of state and district-level variation in hypertension prevalence in India and to evaluate the influence of social determinants.

METHODS

We used data from the Fifth National Family Health Survey (NFHS-5) from 707 districts and 825,954 participants (women 724,115, men 101,839 men) on prevalence of hypertension defined according to standard criteria. Data on multiple social determinants were also obtained from NFHS-5 report.

RESULTS

Age-standardized prevalence of hypertension was 22.4% (women 21.3%, men 24.0%) with the highest prevalence in women and men, respectively, in Sikkim (34.5 and 41.6%) and Punjab (31.2 and 37.7%) and lowest in Rajasthan (15.4 and 17.9%) and Ladakh (15.7 and 17.4%). Prevalence was more in western and southern Indian districts. High prevalence of hypertension in the young (<30y) was observed in northeastern and northern states. District-level hypertension prevalence correlated negatively with multi-dimensional poverty index (R2women 0.299, men 0.245) and positively with female literacy (women 0.165, men 0.134). Among women, districts with the highest availability of electricity, clean water, sanitation, clean cooking fuels, healthcare service delivery and better nutrition were associated with more hypertension on univariate and multivariate analyses (p<0.05).

CONCLUSIONS

The study shows significant geographical variation in hypertension prevalence in India. Hypertension is more in men with high prevalence of premature hypertension. Better district-level development (less poverty, more literacy) and healthcare services are associated with greater hypertension prevalence in women.

SUMMARY TABLE

What is known about the topic

Significant state-level variation in hypertension prevalence in India has been reported but district-level variation is not known.

Social determinants are important in hypertension but not well studied, especially in women.

What this study adds

The study shows a significant district-level variation with greater hypertension prevalence in southern and western India.

Hypertension among the young, <30 years, is more in less developed districts.

Social determinants of hypertension in women are less poverty, more literacy and availability of healthcare services.
Rolling 2D Bioelectronic film into 1D: a Suturable Long-term Implantable Soft Microfiber
Authors: Xie Ruijie , Yu Qianhengyuan , Li Dong , Han Xu , Xu Xiaolong , Huang Jianping , Yan Wei , Zhou Xiaomeng , Deng Xinping , Tian Qiong , Li Qingsong , Li Hanfei , Zheng Hairong , Li Guanglin , Han Fei , Xu Tiantian , Liu Zhiyuan
Published: October 2023

Long-term implantable bioelectronics can efficiently evaluate the function of the nervous system. 1D fiber-shaped devices require small surgical incisions significantly benefiting long-term biocompatibility. We report a strategy of rolling to reduce the dimension of bioelectronic devices from 2D film to 1D microfiber. The soft and stretchable multifunctional microfiber accommodates more than 60-channel longitudinally-distributed electrodes for bio-electric and -mechanical monitoring. It can be sutured into muscle with tiny incision for 8-month bio-electrical monitoring in rats. Importantly, after 13-month implantation, the fibroblast encapsulation around the fiber is negligible. Moreover, it can wander inside a brain under magnetic field. This strategy not only opens up the study of multi-channel and -function soft and stretchable fiber-shaped sensors but offers a platform for minimally-invasive implantable bioelectronics.

One-Sentence Summary

The rolling enables stretchable electrode array along one single microfiber and multimodal long-termin-vivomonitoring.
Reconstructing the Phylogeny ofCalliandrasect.Androcallis(Fabaceae): Insights from the Inclusion of Colombian Species, with a Focus on the Enigmatic TaxonCalliandra medellinensis
Authors: Arias Tatiana , Saldarriaga Juan David , Arenas-Castro Henry , Idárraga-Piedrahita Álvaro , López-Alvarez Norberto , Luque Eduardo Tovar , Torres-Morales Germán , Gonzalez Mailyn A. , Soto-Calderón Iván Darío
Published: October 2023

Phylogenetic relationships for the genusCalliandrasectionAndrocallis(Fabaceae) were reconstructed, including previously sequenced species from Central and South America and unexamined species from Colombia, one ofCalliandramain diversity centers. Here, we generated novel DNA sequences ofCalliandraspecies from Colombia for the nuclear Internal Transcribed Spacer (ITS)and the chloroplasttrnLandtrnL-Fintergenic spacer. By incorporating a broader taxonomic sampling, the relationships among main clades inAndrocalliswere clarified, providing a systematics framework in which to test evolutionary hypotheses. Phylogenetic analysis recovered five well-supported clades withinAndrocallis. Most species within each clade had similar geographical distributions and relationships between the five major clades are strongly supported for the first time. However, coreAndrocallisrelationships, including most species from Colombia sequenced here, remain unclear. A second goal of this study was to determine the taxonomic status ofCalliandra medellinensis. This enigmatic taxon emblematic of Medellín, Colombia, is found in limited numbers within the Aburrá Valley and has been proposed to be a hybrid taxon. Here,C. medellinensis,C. magdalenaeandC. haematocephalawere not monophyletic within the coreAndrocallisclade. This suggests thatC. medellinensiscould potentially be an interspecific hybrid betweenC. magdalenaeandC. haematocephala, thus challenging the taxonomic status of this species; however, more informative molecular markers should be used in future studies. Specifically, genomic studies should assess interspecific hybridization demographic models. Such insights can illuminate theC. medellinensisorigin, guiding conservation strategies and providing valuable evolutionary overviews.
Long-term engraftment of adult hematopoietic progenitors in a novel model of humanized mice
Authors: Yu Chun I , Maser Rick , Marches Florentina , Banchereau Jacques , Palucka Karolina
Published: October 2023

Pre-clinical use of humanized mice transplanted with CD34+hematopoietic progenitor cells (HPCs) is limited by insufficient engraftment with adult HPCs. Here, we developed a novel immunodeficient mice based in NOD-SCID-Il2γc-/-(NSG) mice to support long-term engraftment with human adult HPCs and tissue colonization with human myeloid cells. As both Flt3L and IL-6 are critical for many aspects of hematopoiesis, we knock-out mouseFlt3and knock-in humanIL6gene. The resulting mice showed an increase in the availability of mouse Flt3L to human cells, and a dose-dependent production of human IL-6 upon activation. Upon transplantation with low number of human HPCs from adult bone marrow, these humanized mice demonstrated a significantly higher engraftment with multilineage differentiation of human lymphoid and myeloid cells. Furthermore, higher frequencies of human lymphoid and myeloid cells were detected in tissues at one year after adult HPC transplant. Thus, these mice enable studies of human hematopoiesis and tissue colonization over time.

Pre-clinical use of humanized mice is limited by insufficient engraftment with adult hematopoietic progenitor cells (HPCs). Here, we developed a novel immunodeficient mice which support long-term engraftment with adult bone marrow HPCs and facilitate building autologous models for immuno-oncology studies.
Host glutathione is required forRickettsia parkerito properly septate, avoid ubiquitylation, and survive in macrophages
Authors: Sun Han , Luu Anh Phuong , Danielson Meggie , Vo Thaomy T. , Burke Thomas P.
Published: October 2023

Spotted fever groupRickettsiaobligately reside in the cytosol where they parasitize over fifty metabolites from their hosts. However, the role for metabolite acquisition in pathogenesis remains unclear. Here, we find that depletion of the abundant low molecular weight thiol glutathione led to an impaired ability ofRickettsia parkerito form plaques. Super-resolution microscopy revealed that glutathione depletion with buthionine sulfoximine (BSO) in endothelial or epithelial cells led to the formation of bacterial chains that increased in length over time. Chained bacteria had fewer actin-tails and were impeded for their ability to spread from cell to cell. Glutathione depletion also caused an increased frequency of colocalization between the bacterial surface and polyubiquitin.R. parkeriwas significantly more restricted upon glutathione depletion in primary macrophages than in epithelial cells in a mechanism that avoided activating the inflammasome and the production of type I interferon. Together, these data suggest that host glutathione is critical for rickettsial septation, actin-based motility, avoiding ubiquitylation, and survival in immune cells.
Robotic System for Organoid Assembly in a Multi-Well Microfluidic Chip
Authors: Sachs David M , Costa Kevin D
Published: October 2023

While many cell culture systems are sensitive to the conditions in which cells are introduced into the system, we find that in situ differentiated tube-shaped microfluidic organoids have a particularly high sensitivity. Preliminary experiments using conventional seeding techniques revealed that biases in initial cell number and distribution dramatically impacted organoid shape and behavior downstream. Residual flows during seeding further complicated the process, dispersing cells to undesirable locations within the chip. To address this problem, a a robotic seeding system for controlling the process of inserting cells into microfluidic chips was developed. Environmental control of temperature, CO2, and humidity was implemented by modifying a commercial Arduino-controlled incubator. An eight-channel syringe pump controlled flow to eight cell dispensers, while a vertical leadscrew stage raised and lowered them, and a set of stackable flexure micromanipulators individually controlled the X and Y position of each cell dispenser. The flexure manipulators were 3D printed, driven by low-cost motors and electronics, and required little assembly and no alignment, resulting in a cheap and scalable method of controlling a dense array of micromanipulators. A dual objective microscope on a motorized gantry used an oblique lighting system to observe the seeding process, allowing for real-time interventions or passive observation of automated protocols. The robotic cell seeding system provided a platform for optimizing a sensitive process towards increasing the repeatability and physiological relevance of tube-shaped microfluidic organoids.
Finding and Following: A deep learning-based pipeline for tracking platelets during thrombus formationin vivoandex vivo
Authors: McGovern Abigail S. , Larsson Pia , Tarlac Volga , Setiabakti Natasha , Mashcool Leila Shabani , Hamilton Justin R. , Boknäs Niklas , Nunez-Iglesias Juan
Published: October 2023

The last decade has seen increasing use of advanced imaging techniques in platelet research. However, there has been a lag in the development of image analysis methods, leaving much of the information trapped in images. Herein, we present a robust analytical pipeline for finding and following individual platelets over time in growing thrombi. Our pipeline covers four steps: detection, tracking, estimation of tracking accuracy, and quantification of platelet metrics. We detect platelets using a deep learning network for image segmentation, which we validated with proofreading by multiple experts. We then track platelets using a standard particle tracking algorithm and validate the tracks with custom image sampling — essential when following platelets within a dense thrombus. We show that our pipeline is more accurate than previously described methods. To demonstrate the utility of our analytical platform, we use it to show thatin vivothrombus formation is much faster than thatex vivo. Furthermore, plateletsin vivoexhibit less passive movement in the direction of blood flow. Our tools are free and open source and written in the popular and user-friendly Python programming language. They empower researchers to accurately find and follow platelets in fluorescence microscopy experiments.x

Plain language summary

In this paper we describe computational tools to find and follow individual platelets in blood clots recorded with fluorescence microscopy. Our tools work in a diverse range of conditions, both in living animals and in artificial flow chamber models of thrombosis. Our work uses deep learning methods to achieve excellent accuracy. We also provide tools for visualising data and estimating error rates, so you don’t have to just trust the output. Our workflow measures platelet density, shape, and speed, which we use to demonstrate differences in the kinetics of clotting in living vessels versus a synthetic environment. The tools we wrote are open source, written in the popular Python programming language, and freely available to all. We hope they will be of use to other platelet researchers.
Inhibition of Lactate Dehydrogenase A (LDH-A) by Diclofenac Sodium Induces Apoptosis in HeLa Cells by Activation of AMPK
Authors: Malla Avirup , Gupta Suvroma , Sur Runa
Published: October 2023

Cancer cells exhibit a unique metabolic preference for choosing the glycolytic pathway over oxidative phosphorylation for maintaining the tumor microenvironment. Lactate dehydrogenase-A (LDH-A) is a key enzyme that facilitates glycolysis by converting pyruvate to lactate and has been shown to be upregulated in multiple cancers due to the hypoxic tumor microenvironment. Diclofenac (DCF), a non-steroidal anti-inflammatory drug, has been shown to exhibit anti-cancer effects by interfering with the glucose metabolism pathway. However, the specific targets remain unknown. Usingin-silico, biochemical, and biophysical studies, we show that DCF binds to LDH-A adjacent to the substrate binding site and dose-dependently inhibits its activity in an allosteric manner in HeLa cells. Thus, DCF inhibits the hypoxic microenvironment and induces apoptosis-mediated cell death. DCF fails to induce cytotoxicity in LDH-A knocked-down HeLa cells, confirming that DCF renders its anti-mitotic effects via LDH-A inhibition. DCF-induced LDH-A inhibition alters pyruvate, lactate, NAD+, and ATP production in cells, and this could be a possible mechanism by which DCF inhibits glucose uptake in cancer cells. DCF-induced ATP deprivation leads to mitochondria-mediated oxidative stress, which results in DNA damage, lipid peroxidation, and apoptosis-mediated cell death. Reduction in intracellular ATP levels additionally activates AMPK, a sensor kinase, which further downregulates p-S6K, leading to apoptosis-mediated cell death. We find that in LDH-A knocked-down cells, intracellular ATP levels were depleted, resulting in the inhibition of p-S6K, implying the involvement of DCF-induced LDH-A inhibition in the activation of the AMPK/S6K signaling pathway.
Cheminformatics identification of phenolics as modulators of penicillin binding protein (PBP) 2x ofStreptococcus pneumoniaetowards interventive antibacterial therapy
Authors: Aribisala Jamiu Olaseni , S’thebe Nosipho Wendy , Sabiu Saheed
Published: October 2023

Infections caused by multidrug-resistantStreptococcus pneumoniaeremain the leading cause of pneumonia-related deaths in children < 5 years globally, and mutations in penicillin-binding protein (PBP) 2x have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (−19.23 kcal/mol), allosteric site (−33.75 Kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (−38.41 kcal/mol) and allosteric (−50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of < 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused byS. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatoryin vitroresearch.
United States Marijuana Legalization and Opioid Mortality Trends Before and During the First Year of the COVID-19 Pandemic
Authors: Bleyer Archie , Barnes Brian , Finn Kenneth
Published: October 2023

To determine if marijuana legalization reduced opioid mortality, the U.S. opioid and fentanyl subset death trends during the 2010-2019 decade were compared in states and District of Columbia (D.C.) (jurisdictions) that had implemented marijuana legalization with states that had not. Acceleration of opioid mortality during 2020, first year of the COVID-19 pandemic, was also compared in recreational and medicinal-only legalizing jurisdictions. Joinpoint methodology was applied to Centers for Disease Control and Prevention WONDER data. Trends in legalizing jurisdictions were cumulative aggregates. The overall opioid and fentanyl death rates and percentage of opioid deaths due to fentanyl increased more during 2010-2019 in jurisdictions that legalized marijuana than in those that did not (pairwise comparison p = 0.007, 0.05, and 0.006, respectively). By 2019, the opioid and fentanyl death rates were 44% and 50% greater in the legalizing than non-legalizing jurisdictions, respectively. When the COVID-19 pandemic hit in 2020, jurisdictions that implemented recreational marijuana legalization before 2019 had significantly greater increases in both overall opioid and fentanyl death rates than jurisdictions with medicinal-only legalization. For all opioids, the mean (95% confidence interval [CI]) 2019-to-2020 increases were 46.5% (95% CI, 36.6% to 56.3%) and 29.1% (95% CI 20.2% to 37.9%), respectively (p = 0.02). For fentanyl, they were 115.6% (95% CI, 80.2% to 151.6%) and 55.4% (95% CI, 31.6% to 79.2%), respectively (p = 0.01). Marijuana legalization is correlated with worsening of the U.S. opioid epidemic, and especially during the COVID-19 pandemic with recreational legalization.
Segzoo: a turnkey system that summarizes genome annotations
Authors: Mendez Mickaël , Liu Yushan , Asenjo Ponce de León Marc , Hoffman Michael M.
Published: October 2023

Segmentation and automated genome annotation (SAGA) techniques, such as Segway and ChromHMM, assign labels to every part of the genome, identifying similar patterns across multiple genomic input signals. Inferring biological meaning in these patterns remains challenging. Doing so requires a time-consuming process of manually downloading reference data, running multiple analysis methods, and interpreting many individual results.

To simplify these tasks, we developed the turnkey system Segzoo. As input, Segzoo only requires a genome annotation file in browser extensible data (BED) format. It automatically downloads the rest of the data required for comparisons. Segzoo performs analyses using these data and summarizes results in a single visualization.

Availability and Implementation

Source code for Python ≥3.7 on Linux freely available for download athttps://github.com/hoffmangroup/segzoounder the GNU General Public License (GPL) version 2. Segzoo is also available in the Bioconda package segzoo:https://anaconda.org/bioconda/segzoo.
Pax Protein Depletion in Proximal Tubules Triggers Conserved Mechanisms of Resistance to Acute Ischemic Kidney Injury and Prevents Transition to Chronic Kidney Disease
Authors: Beamish Jeffrey A. , Telang Asha C. , McElliott Madison C. , Al-Suraimi Anas , Chowdhury Mahboob , Ference-Salo Jenna T. , Otto Edgar A. , Menon Rajasree , Soofi Abdul , Weinberg Joel M. , Patel Sanjeevkumar R. , Dressler Gregory R.
Published: October 2023

Acute kidney injury (AKI) is a common condition that lacks effective treatments. In part this shortcoming is due to an incomplete understanding of the genetic mechanisms that control pathogenesis and recovery. Pax2 and Pax8 are homologous transcription factors with overlapping functions that are critical for kidney development and are re-activated in AKI. In this report, we examined the role of Pax2 and Pax8 in recovery from ischemic AKI. We found that Pax2 and Pax8 are upregulated after severe AKI and correlate with chronic injury. Surprisingly, we then discovered that proximal-tubule-selective deletion of Pax2 and Pax8 resulted in a less severe chronic injury phenotype. This effect was mediated by protection against the acute insult, similar to preconditioning. Prior to injury, Pax2 and Pax8 mutant mice develop a unique subpopulation of S3 proximal tubule cells that display features usually seen only in acute or chronic injury. The expression signature of these cells was strongly enriched with genes associated with other mechanisms of protection against ischemic AKI including caloric restriction, hypoxic preconditioning, and female sex. Taken together, our results identify a novel role for Pax2 and Pax8 in mature proximal tubules that regulates critical genes and pathways involved in both injury response and protection from ischemic AKI.

TRANSLATIONAL STATEMENT

Identifying the molecular and genetic regulators unique to the nephron that dictate vulnerability to injury and regenerative potential could lead to new therapeutic targets to treat ischemic kidney injury. Pax2 and Pax8 are two homologous nephron-specific transcription factors that are critical for kidney development and physiology. Here we report that proximal-tubule-selective depletion of Pax2 and Pax8 protects against both acute and chronic injury and induces an expression profile in the S3 proximal tubule with common features shared among diverse conditions that protect against ischemia. These findings highlight a new role for Pax proteins as potential therapeutic targets to treat AKI.
SC-Track: a robust cell tracking algorithm for generating accurate single-cell lineages from diverse cell segmentations
Authors: Li Chengxin , Xie Shuang Shuang , Wang Jiaqi , Sharvia Septavera , Chan Kuan Yoow
Published: October 2023

Computational analysis of fluorescent timelapse microscopy images at the single-cell level is a powerful approach to study cellular changes that dictate important cell fate decisions. Core to this approach is the need to generate reliable cell segmentations and classifications necessary for accurate quantitative analysis. Deep learning-based convolutional neural networks (CNNs) have emerged as a promising solution to these challenges. However, current CNNs are prone to produce noisy cell segmentations and classifications, which is a significant barrier to constructing accurate single-cell lineages. To address this, we developed a novel algorithm called Single Cell Track (SC-Track), which employs a hierarchical probabilistic cache cascade model based on biological observations of cell division and movement dynamics. Our results show that SC-Track performs better than a panel of publicly available cell trackers on a diverse set of cell segmentation types. This cell-tracking performance was achieved without any parameter adjustments, making SC-Track an excellent generalised algorithm that can maintain robust cell-tracking performance in varying cell segmentation qualities, cell morphological appearances and imaging conditions. Furthermore, SC-Track is equipped with a cell class correction function to improve the accuracy of cell classifications in multi-class cell segmentation time series. These features together make SC-Track a robust cell-tracking algorithm that works well with noisy cell instance segmentation and classification predictions from CNNs to generate accurate single-cell lineages and classifications.
Towards quantitative DNA Metabarcoding: A method to overcome PCR amplification bias
Authors: Moinard Sylvain , Piau Didier , Laporte Frédéric , Rioux Delphine , Taberlet Pierre , Gonindard-Melodelima Christelle , Coissac Eric
Published: October 2023

Metabarcoding analyses have recently undergone significant development due to the power of this technique in biodiversity monitoring. However, it is still difficult to draw accurate quantitative conclusions about the ecosystems studied, mainly because of biases inherent in the environmental DNA or introduced during the experimental process. These biases alter the relationship between the amount of DNA observed and the biomass or number of individuals of the species detected. Two of the biases inherent in metabarcoding have been measured: the ratio between total DNA and target DNA concentrations, and the PCR amplification bias. A method for their correction is proposed. All experimental tests were performed on mock alpine plant communities using the markerSper01, which is expected to have low amplification bias due to its highly conserved priming sites. Our approach combines standard quantitative PCR techniques (qPCR and digital droplet PCR) with a realistic stochastic model of PCR dynamics that accounts for PCR saturation. The model was used to estimate PCR efficiencies for each species and to infer the true species proportions of the mock communities from the read relative frequencies. The corrections are easy to implement and can be applied to previously generated DNA metabarcoding data. This work demonstrates the relative importance of the two biases considered and is an open door to quantitative metabarcoding data, although many other biases remain to be considered.
Prognostic implications and biological roles of EMT-related lncRNAs in lung squamous cell carcinoma: an in-depth analysis utilizing a novel prognostic signature and classification system
Authors: Zhang Jinming , Zheng Baihong , Zhang Xiuying , Liu Ying , Guo Ying , Zhao Jia , Liu Jiamei , Xue Hui
Published: October 2023

Background

Lung squamous cell carcinoma (LUSC) represents a major subtype of non-small cell lung cancer (NSCLC), a leading contributor to cancer-related mortality. Epithelial-mesenchymal transition (EMT)-associated genes have been implicated in poor survival and metastatic gene expression in LUSC. Long non-coding RNAs (lncRNAs) are known to facilitate tumor progression and metastasis via EMT regulation. However, the prognostic significance and biological functions of EMT-associated lncRNAs in LUSC remain to be elucidated.

Methods

In this study, we aimed to develop an EMT-related lncRNA prognostic signature (EMT-LPS) utilizing RNA transcription data from LUSC patients in The Cancer Genome Atlas (TCGA) database, along with corresponding clinical characteristics. Kaplan-Meier analysis, receiver operating characteristic (ROC) curves, and Cox regression were employed to validate and assess the model. Furthermore, we confirmed the independent prognostic value of key genes in EMT-LPS using Gene Expression Profiling Interactive Analysis (GEPIA). Additionally, we proposed a novel LUSC classification system based on EMT-related lncRNA expression patterns, evaluating the prognostic profile, tumor microenvironment, and immunotherapy sensitivity of each subtype.

Results

A prognostic signature comprising twelve genes was constructed, and patients were stratified into high and low-risk groups according to their risk scores. Cox regression analysis revealed that the risk score served as an independent prognostic factor. A nomogram was generated to predict LUSC patient survival rates. Distinct subtypes exhibited varying tumor purity, immunogenicity, and immunotherapy drug sensitivity.

Conclusions

Our findings underscore the relevance of EMT-related lncRNAs in LUSC and their potential utility in guiding immunotherapy strategies. The EMT-LPS and novel LUSC typing scheme provide a new perspective for understanding the biological functions and prognostic role of EMT-related lncRNAs in LUSC.