bluuebunny/crossref_metadata_2025 huggingface dataset:
Nuclear–plastid discordance indicates past introgression inEpidendrumspecies (Laeliinae: Orchidaceae) with highly variable chromosome numbers
Authors: Pessoa Edlley M , Nollet Felipe , Magalhães Rafael F , Viruel Juan , Pinheiro Fábio , Chase Mark W
Published: October 2021

Here we study a challenging group of karyotypically highly variable Epidendrum spp. using phylogenetic methods to help understand how hybridization/introgression contributes to karyotype evolution. We hypothesize that species with great chromosome number variation are a result of past hybridization/introgression. Conflicting topologies in trees constructed using separate plastid and nuclear datasets suggest past hybridization events that occurred most probably at least 3.7 Mya. A basic number x = 14 and substantial karyotype change followed by species divergence are suggested. Descending dysploidy and polyploidy were the most frequent changes estimated across the phylogenetic tree of the group. Two species, Epidendrum secundum and E. xanthinum, have probably experienced unidirectional gene flow involving their ancestors (the pollen recipients) and ancestors of E. puniceoluteum and E. denticulatum/E. flammeum, respectively, the pollen donors. However, it is not possible to say whether hybridization participated in the origin of E. secundum and E. xanthinum or merely contributed to their genomic divergence and karyotype change through introgression as has been observed in modern hybrid zones in Epidendrum. This pattern of introgression causing karyotype disruption and divergence could help explain the enigma of some highly diverse genera, such as Epidendrum. Further studies using a wider sampling of the genus could test if gene flow and karyotype variability are associated with the increase of speciation rates.
Atypical development of Broca’s area in a large family with inherited stuttering
Authors: Thompson-Lake Daisy G Y , Scerri Thomas S , Block Susan , Turner Samantha J , Reilly Sheena , Kefalianos Elaina , Bonthrone Alexandra F , Helbig Ingo , Bahlo Melanie , Scheffer Ingrid E , Hildebrand Michael S , Liégeois Frédérique J , Morgan Angela T
Published: October 2021

Developmental stuttering is a condition of speech dysfluency, characterized by pauses, blocks, prolongations and sound or syllable repetitions. It affects around 1% of the population, with potential detrimental effects on mental health and long-term employment. Accumulating evidence points to a genetic aetiology, yet gene–brain associations remain poorly understood due to a lack of MRI studies in affected families. Here we report the first neuroimaging study of developmental stuttering in a family with autosomal dominant inheritance of persistent stuttering.

We studied a four-generation family, 16 family members were included in genotyping analysis. T1-weighted and diffusion-weighted MRI scans were conducted on seven family members (six male; aged 9–63 years) with two age and sex matched controls without stuttering (n = 14). Using Freesurfer, we analysed cortical morphology (cortical thickness, surface area and local gyrification index) and basal ganglia volumes. White matter integrity in key speech and language tracts (i.e. frontal aslant tract and arcuate fasciculus) was also analysed using MRtrix and probabilistic tractography.

We identified a significant age by group interaction effect for cortical thickness in the left hemisphere pars opercularis (Broca’s area). In affected family members this region failed to follow the typical trajectory of age-related thinning observed in controls. Surface area analysis revealed the middle frontal gyrus region was reduced bilaterally in the family (all cortical morphometry significance levels set at a vertex-wise threshold of P < 0.01, corrected for multiple comparisons). Both the left and right globus pallidus were larger in the family than in the control group (left P = 0.017; right P = 0.037), and a larger right globus pallidus was associated with more severe stuttering (rho = 0.86, P = 0.01). No white matter differences were identified. Genotyping identified novel loci on chromosomes 1 and 4 that map with the stuttering phenotype.

Our findings denote disruption within the cortico-basal ganglia-thalamo-cortical network. The lack of typical development of these structures reflects the anatomical basis of the abnormal inhibitory control network between Broca’s area and the striatum underpinning stuttering in these individuals. This is the first evidence of a neural phenotype in a family with an autosomal dominantly inherited stuttering.
Neuronal Electrical Ongoing Activity as Cortical Areas Signature: An Insight from MNI Intracerebral Recording Atlas
Authors: Armonaite Karolina , Bertoli Massimo , Paulon Luca , Gianni Eugenia , Balsi Marco , Conti Livio , Tecchio Franca
Published: October 2021

The time course of the neuronal activity in the brain network, the neurodynamics, reflects the structure and functionality of the generating neuronal pools. Here, using the intracranial stereo-electroencephalographic (sEEG) recordings of the public Montreal Neurological Institute (MNI) atlas, we investigated the neurodynamics of primary motor (M1), somatosensory (S1) and auditory (A1) cortices measuring power spectral densities (PSD) and Higuchi fractal dimension (HFD) in the same subject (M1 vs. S1 in 16 subjects, M1 vs. A1 in 9, S1 vs. A1 in 6).

We observed specific spectral features in M1, which prevailed above beta band, S1 in the alpha band, and A1 in the delta band. M1 HFD was higher than S1, both higher than A1.

A clear distinction of neurodynamics properties of specific primary cortices supports the efforts in cortical parceling based on this expression of the local cytoarchitecture and connectivity. In this perspective, we selected within the MNI intracortical database a first set of primary motor, somatosensory and auditory cortices’ representatives to query in recognizing ongoing patterns of neuronal communication.

Potential clinical impact stands primarily in exploiting such exchange patterns to enhance the efficacy of neuromodulation intervention to cure symptoms secondary to neuronal activity unbalances.
Choices in hemodialysis therapies: variants, personalized therapy and application of evidence-based medicine
Authors: Canaud Bernard , Stuard Stefano , Laukhuf Frank , Yan Grace , Canabal Maria Ines Gomez , Lim Paik Seong , Kraus Michael A
Published: October 2021

The extent of removal of the uremic toxins in hemodialysis (HD) therapies depends primarily on the dialysis membrane characteristics and the solute transport mechanisms involved. While designation of ‘flux’ of membranes as well toxicity of compounds that need to be targeted for removal remain unresolved issues, the relative role, efficiency and utilization of solute removal principles to optimize HD treatment are better delineated. Through the combination and intensity of diffusive and convective removal forces, levels of concentrations of a broad spectrum of uremic toxins can be lowered significantly and successfully. Extended clinical experience as well as data from several clinical trials attest to the benefits of convection-based HD treatment modalities. However, the mode of delivery of HD can further enhance the effectiveness of therapies. Other than treatment time, frequency and location that offer clinical benefits and increase patient well-being, treatment- and patient-specific criteria may be tailored for the therapy delivered: electrolytic composition, dialysate buffer and concentration and choice of anticoagulating agent are crucial for dialysis tolerance and efficacy. Evidence-based medicine (EBM) relies on three tenets, i.e. clinical expertise (i.e. doctor), patient-centered values (i.e. patient) and relevant scientific evidence (i.e. science), that have deviated from their initial aim and summarized to scientific evidence, leading to tyranny of randomized controlled trials. One must recognize that practice patterns as shown by Dialysis Outcomes and Practice Patterns Study and personalization of HD care are the main driving force for improving outcomes. Based on a combination of the three pillars of EBM, and particularly on bedside patient–clinician interaction, we summarize what we have learned over the last 6 decades in terms of best practices to improve outcomes in HD patients. Management of initiation of dialysis, vascular access, preservation of kidney function, selection of biocompatible dialysers and use of dialysis fluids of high microbiological purity to restrict inflammation are just some of the approaches where clinical experience is vital in the absence of definitive scientific evidence. Further, HD adequacy needs to be considered as a broad and multitarget approach covering not just the dose of dialysis provided, but meeting individual patient needs (e.g. fluid volume, acid–base, blood pressure, bone disease metabolism control) through regular assessment—and adjustment—of a series of indicators of treatment efficiency. Finally, in whichever way new technologies (i.e. artificial intelligence, connected health) are embraced in the future to improve the delivery of dialysis, the human dimension of the patient–doctor interaction is irreplaceable. Kidney medicine should remain ‘an art’ and will never be just ‘a science’.
Multiplexed Assay to Quantify the PP-Fold Family of Peptides in Human Plasma Using Microflow Liquid Chromatography–Tandem Mass Spectrometry
Authors: Reverter-Branchat Gemma , Eugster Philippe J , Kuenzli Christina , Rindlisbacher Barbara , Stauffer Thomas , Nakas Christos T , Herzig David , Grouzmann Eric , Bally Lia
Published: October 2021

Background

Peptide Tyr-Tyr (PYY1-36), pancreatic polypeptide (PP1-36) and neuropeptide Y (NPY1-36) constitute the PP-fold family of peptides that is involved in metabolic regulation. Very low plasma concentrations and cleavage into active 3–36 fragments challenge bioanalytical assays used for the quantification of these peptides.

Methods

We developed a multiplexed isotopic dilution assay to quantify PYY1-36, PP1-36, and NPY1-36 and their dipeptidyl peptidase-4 (DPP4)-derived metabolites PYY3-36, PP3-36 and NPY3-36. All peptides were immunocaptured from plasma using a monoclonal antibody and quantified by micro-ultra-HPLC-MS/MS. Blood samples from healthy volunteers were collected fasting and 30 min after nutrient stimulation. Method comparison was performed with commercial immunoassays.

Results

Linearity was shown in the measured intervals (r2 > 0.99). The lower limit of quantification (LLOQ) with a CV at 20% was 1.5 pM for PYY1-36 and PYY3-36, 3.0 pM for PP1-36 and PP3-36, 0.8 pM for NPY1-36 and 0.5 pM for NPY3-36. In all cases, intra- and inter-assay bias and imprecision were <21%. Pre-analytical stability required addition of a protease inhibitor cocktail. Physiological concentrations of PYY3-36, NPY3-36, PP1-36 and PP3-36 were above the LLOQ in 43% to 100% of the samples. PYY1-36 and NPY1-36 were above the LLOQ in 9% and 0% of the samples, respectively. Immunoassays showed higher concentrations of measurands and poor agreement when compared with micro-UHPLC-MS/MS.

Conclusions

The assay allowed for specific multiplexed analysis of the PP-fold family of peptides and their DPP4-cleaved fragments in a single sample, thereby offering new perspectives to study the role and therapeutic potential of these essential peptide hormones in health and metabolic disease.
Phenotyping patients with borderline elevated esophageal acid exposure
Authors: Reddy Chanakyaram A , Wenzke Kevin , Watts Lydia S , Armstrong Moira , Chen Vincent L , Baker Jason R , Chen Joan W
Published: October 2021

Acid exposure time (AET) <4% on ambulatory reflux monitoring definitively rules out pathologic gastroesophageal acid reflux, while AET >6% indicates pathologic reflux per the Lyon Consensus, leaving AET of 4–6% as borderline. We aimed to elucidate the borderline AET population and identify metrics that could help differentiate this group. A total of 50 subjects in each group, AET <4, 4–6, and >6% on pH-impedance monitoring between 2015 and 2019, were retrospectively reviewed. In addition to demographic and clinical information, the extracted data included mean nocturnal baseline impedance (MNBI) on reflux study and high-resolution manometry (HRM) parameters and diagnosis. After excluding patients with prior foregut surgery, major esophageal motility disorder, or unreliable impedance testing, a total of 89 subjects were included in the analysis (25 with normal AET < 4%, 38 with borderline 4–6%, 26 with abnormal >6%). MNBI in borderline AET patients was significantly lower compared to normal AET (1607.7 vs. 2524.0 ohms, P < 0.01), and higher than abnormal AET (951.5 ohms, P < 0.01). Borderline subjects had a greater frequency of ineffective esophageal motility (IEM) diagnosis per Chicago classification v3.0 (42.1 vs. 8.0%, P = 0.01), but did not demonstrate any differences compared to abnormal subjects (34.6%, P = 0.56). Patients with borderline AET had an average MNBI that was in between normal AET and abnormal AET. Borderline AET patients also commonly demonstrate IEM on HRM, similar to those with abnormal AET. Our findings can be potentially useful in assigning higher clinical significance for patients found to have borderline AET with concomitant low MNBI and IEM on manometry.
A case report of ventricular septal defect complicating transcatheter aortic valve implant for aortic regurgitation: novel complication and technical considerations
Authors: Hartnett Jack , Brandon Lisa , Waterhouse Deirdre , Murphy Ross T , Walsh Kevin P , Spence Mark S , Maree Andrew O
Published: October 2021

Background

Transcatheter aortic valve implantation (TAVI) has proven efficacy in the treatment of aortic stenosis (AS). Understandably, there is increasing enthusiasm for its use to treat aortic regurgitation (AR). However, there are significant anatomical differences between AS and AR which make TAVI for AR more complex.

Case summary

We present the case of technically challenging TAVI for severe AR, which was complicated by a traumatic ventricular septal defect (VSD) that required percutaneous closure. To our knowledge, this is the first published case of VSD post-TAVI for AR.

Discussion

This unanticipated complication highlights anatomical differences between TAVI use in AS and AR. Lack of aortic valve calcification and excessive annular compliance made stable deployment of a self-expanding valve extremely challenging. Despite device oversizing, repeated embolization of the prosthesis into the left ventricular outflow tract traumatized the interventricular septum.
Ictal syncope or isolated syncope? A case report highlighting the overlap
Authors: Fanous Yehia , Astrada Miguel A , Mirsattari Seyed , Khan Habib R
Published: October 2021

Background

Ictal bradyarrhythmia is a rare condition defined by temporal lobe epilepsy resulting in bradycardia or asystole and can result in syncope. This needs to be differentiated from isolated syncope in patients with seizure disorder, as treatment strategies differ.

Case summary

A 50-year-old female with well-controlled temporal epilepsy and a 20-year seizure-free period presented to her neurologist with abrupt onset of sudden drop attacks thought to be ictal events with potential underlying ictal bradyarrhythmia and was initially treated with escalation of anticonvulsant therapy. However, her workup was consistent with a diagnosis of cardiac syncope. She subsequently underwent successful insertion of a pacemaker, with no recurrence of her presenting episodes at a 13-month follow-up.

Discussion

Ictal syncope and isolated syncope may share a common terminal pathway and may have similar presenting symptoms. In patients with known seizure disorder, loss of consciousness may be attributable to epileptic events, ictal syncope, or isolated syncope—which can be difficult to differentiate. This case highlights the ambiguous nature of such episodes and the importance of simultaneous electroencephalogram/electrocardiogram monitoring, as this can have implications on treatment.
Sedentary Behavior and Happiness: The Mediation Effects of Social Capital
Authors: Yasunaga Akitomo , Koohsari Mohammad Javad , Shibata Ai , Ishii Kaori , Miyawaki Rina , Araki Kuniko , Oka Koichiro
Published: October 2021

Background and Objectives

This study aimed to examine the associations between time spent in 6 different domains of sedentary behavior and happiness and whether social capital mediated such associations among adults and older adults living in a rural area of Japan.

Research Design and Methods

Cross-sectional data from 3,357 participants (mean age: 60 ± 16 years) were used. 6 domains of sedentary behavior, happiness, and social capital were assessed using a self-report questionnaire. Age-stratified multivariable linear regression models adjusted for covariates were used to examine the associations between 6 domains of sedentary behavior and happiness. For relationships where the direct effect was significant, we tested the mediating effects of 2 social capital measures.

Results

Among both adults and older adults, more time spent viewing television was significantly associated with lower happiness scores, and more time spent engaging in other leisure activities was significantly associated with higher happiness scores. In addition, more time spent using cell phones and computers was significantly associated with lower happiness scores among the adults. Engaging in activities with neighbors significantly mediated the relationship between other leisure activities and happiness in the adults and older adults, and between television viewing and happiness in the older adults.

Discussion and Implications

Our findings indicated that less television viewing and more mentally active sedentary behavior (e.g., talking with others and engaging in hobbies) were associated with greater happiness. One aspect of social capital, engaging in activities with neighbors, acts as a potential mediator for relationships between sedentary behavior and happiness.
Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase
Authors: Maruyama Shun , Sawano Kota , Amaki Satoko , Suzuki Takehiro , Narita Satoru , Kimura Kenta , Arakawa Takatoshi , Yamada Chihaya , Ito Yukishige , Dohmae Naoshi , Fujita Kiyotaka , Ishiwata Akihiro , Fushinobu Shinya
Published: October 2021

β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-β-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, β-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas α-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the β-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.
Altered Polarization and Impaired Phagocytic Activity of Lung Macrophages in People With Human Immunodeficiency Virus and Chronic Obstructive Pulmonary Disease
Authors: Akata Kentaro , Leung Janice M , Yamasaki Kei , Leitao Filho Fernando S , Yang Julia , Xi Yang Chen , Takiguchi Hiroto , Shaipanich Tawimas , Sahin Basak , Whalen Beth A , Yang Cheng Wei Tony , Sin Don D , van Eeden Stephan F
Published: October 2021

Background

People with human immunodeficiency virus (PWH) have an increased risk of developing chronic obstructive pulmonary disease (COPD).

Methods

We phenotyped lung macrophages in 4 subgroups—M1 (CD40+CD163−), M2 (CD40−CD163+), double positives (CD40+CD163+), and double negatives and (CD40−CD163−)—and we determined their phagocytic capacity in PWH with and without COPD.

Results

People with human immunodeficiency virus with COPD have more double-negative macrophages (84.1%) versus PWH without (54.3%) versus controls (23.9%) (P=.004) and reduced phagocytosis (P=.012). Double-negative macrophages had the worst phagocytic capacity (P<.001).

Conclusions

People with human immunodeficiency virus with COPD have an abundance of nonpolarized macrophages, which have poor phagocytic capacity and therefore predispose PWH to increased risk of disease progression.
Oral and Anal Carriage of Streptococcus pneumoniae Among Sexually Active Men With HIV Who Have Sex With Men
Authors: Tinggaard Michaela , Slotved Hans-Christian , Fuursted Kurt , Storgaard Merete , Dröse Sandra , Somuncu Johansen Isik , Thorsteinsson Kristina , Kronborg Gitte , Lebech Anne-Mette , Benfield Thomas
Published: October 2021

People with HIV are at increased risk of pneumococcal disease. We investigate oral and anal carriage rates of Streptococcus pneumoniae by molecular methods among 82 men with HIV who have sex with men (MSM). A questionnaire, oral wash, and anal swab samples were obtained at baseline and 12 months. Oral carriage rates were 32.9% (27/82) at baseline and 41.7% (30/72) at follow-up. Anal carriage rates were 2.4% (2/82) at baseline and 2.9% (2/70) at follow-up. Genogroup 24 was predominant. Results suggest high oral carriage rates of S. pneumoniae among MSM living with HIV. A minority were anal carriers.
Transmission and molecular characteristics of blaNDM-producing Escherichia coli between companion animals and their healthcare providers in Guangzhou, China
Authors: Wang Min-Ge , Fang Chang , Liu Kai-Di , Wang Lin-Lin , Sun Ruan-Yang , Zhang Rong-Min , Fang Liang-Xing , Sun Jian , Liu Ya-Hong , Liao Xiao-Ping
Published: October 2021

Objectives

To determine the transmission and molecular characteristics of blaNDM-producing Escherichia coli between companion animals and their healthcare providers at veterinary clinics in Guangzhou, China.

Methods

A total of 359 samples from companion animals and their healthcare providers were collected at 14 veterinary clinics in Guangzhou, China. Genomic characteristics and clonal relationships for blaNDM-positive E. coli and complete plasmid sequences were characterized based on WGS data from combined Illumina and MinION platform reads.

Results

Forty-five blaNDM-positive bacteria were recovered from companion animals (n = 43) and their healthcare providers (n = 2) at 10 veterinary clinics. Overall, E. coli (73.3%, 33/45) and Klebsiella pneumoniae (13.3%, 6/45) were the most prevalent species among the seven species of blaNDM-positive bacteria. Four blaNDM variants (blaNDM-1, blaNDM-4, blaNDM-5 and blaNDM-7) were identified in 45 blaNDM-positive bacteria and blaNDM-5 was the most prevalent (77.8%, 35/45). WGS indicated that the most prevalent STs were ST405 (8/33), ST453 (6/33), ST457 (6/33) and ST410 (5/33) among the 33 blaNDM-positive E. coli isolates. Phylogenomics and PFGE analysis revealed that clonal spread of blaNDM-positive ST453 E. coli isolates between companion animals and their healthcare providers was evident. In addition, two novel IncFIB plasmids carrying blaNDM-4 (pF765_FIB and pG908_FIB) were found in this study and indicated that IS26 may promote the horizontal transmission of blaNDM between different plasmid types.

Conclusions

In this study we conducted a large-scale investigation on the prevalence of blaNDM-positive E. coli isolates from companion animals and their healthcare providers and revealed the clonal spread of blaNDM-positive E. coli isolates between these two groups.
Acceptability of innovative culture-based antibiotic prophylaxis strategies: a multi-method study on experiences regarding transrectal prostate biopsy
Authors: Tops Sofie C M , Huis Anita M P , Trompers Willeke , Oerlemans Anke J M , Sedelaar J P Michiel , Kolwijck Eva , Wertheim Heiman F L , Hulscher Marlies E J L
Published: October 2021

Background

The acceptability of innovative medical strategies among healthcare providers and patients affects their uptake in daily clinical practice.

Objectives

To explore experiences of healthcare providers and patients with culture-based antibiotic prophylaxis in transrectal prostate biopsy with three swab-screening scenarios: self-sampling at home, self-sampling in the hospital and sampling by a healthcare provider.

Methods

We performed focus group interviews with urologists and medical microbiologists from 11 hospitals and six connected clinical microbiological laboratories. We used Flottorp’s comprehensive checklist for identifying determinants of practice to guide data collection and analysis. The experiences of 10 laboratory technicians from five laboratories and 452 patients from nine hospitals were assessed using a questionnaire.

Results

Overall, culture-based prophylaxis strategies were experienced as feasible in daily clinical practice. None of the three swab-screening scenarios performed better. For urologists (n = 5), implementation depended on the effectiveness of the strategy. In addition, it was important to them that the speed of existing oncology care pathways is preserved. Medical microbiologists (n = 5) and laboratory technicians (n = 8) expected the strategy to be fairly easy to implement. Patients (n = 430; response rate 95.1%) were generally satisfied with the screening scenario presented to them. To meet the various patients’ needs and preferences, multiple scenarios within a hospital are probably needed.

Conclusions

This multi-method study has increased our understanding of the acceptability of culture-based prophylaxis strategies in prostate biopsy, which can help healthcare providers to offer high-quality patient-centred care. The strategy seems relatively straightforward to implement as overall acceptance appears to be high.
Validation of the Thermo Scientific SureTect™ Escherichia coli O157:H7 and STEC Screening PCR Assay and SureTect™ Escherichia coli STEC Identification PCR Assay for the Detection of Escherichia coli O157:H7 and the Escherichia coli STEC Serotypes (O26, O45, O103, O111, O121, O145) from Fresh Raw Spinach, Fresh Baby Leaves, Fresh Cut Tomatoes, Frozen Raw Beef, Raw Beef Trim, and Beef Carcass Sponges: AOAC Performance Tested MethodSM 012102
Authors: Faulds Nikki , Evans Katharine , Williams Jessica , Leonte Ana-Maria , Crabtree David , Church Katherine , Leak Dean , Sohier Daniele , Palomäki Jukka-Pekka , Heikkinen Pauliina , Manthe Craig , Koch Kateland , Bastin Benjamin , Benzinger M Joseph , Agin James
Published: October 2021

Background

The Thermo Scientific SureTect™ Escherichia coli O157:H7 and STEC Screening PCR Assay and SureTect Escherichia coli STEC Identification PCR Assay are real-time PCR kits for the rapid detection of E. coli O157:H7 and non-E. coli O157 Shiga toxin-producing E. coli (STEC) serotypes (O26, O45, O103, O111, O121, O145) from fresh raw spinach, fresh baby leaves, fresh cut tomatoes, frozen raw beef, raw beef trim, and beef carcass sponges.

Objective

Both assays were evaluated for AOAC®Performance Tested MethodsSM certification.

Methods

Detection and confirmation inclusivity/exclusivity, matrix, product consistency and stability, and robustness studies were conducted. In the matrix studies, the candidate method was validated against United States and international reference methods for STEC serotypes.

Results

Matrix studies showed no statistically significant differences between the candidate and reference method results when analyzed by probability of detection. For each inclusivity/exclusivity study, all inclusivity strains and no exclusivity strains were detected by either kit. Robustness testing demonstrated that the identification assay performed reliably despite method deviations; however, although not statistically significant, the screening assay performance was impacted. Product consistency and stability testing demonstrated no statistically significant differences between kit lots and storage time points.

Conclusion

The data presented show that both assays constitute a rapid and reliable workflow for the detection and confirmation of E. coli O157:H7 and stipulated non-E. coli O157:H7 STEC serotypes from the tested matrixes.

Highlights

Results are obtained in 80 min post-enrichment with both assays run simultaneously, allowing for the detection and confirmation of STEC within a single workflow.
Validation of the Thermo Scientific™ SureTect™Staphylococcus aureus PCR Assay for the Detection of Staphylococcus aureus in Dairy Matrixes: AOAC Performance Tested MethodSM 052101
Authors: Evans Katharine , Faulds Nikki , Crabtree David , Hughes Annette , Sohier Daniele , Manthe Craig , Hahs Matthew , Heikkinen Pauliina , Hurskainen Emmi , Koch Kateland , Thompson Wesley , Bastin Benjamin , Benzinger M Joseph
Published: October 2021

Background

The Thermo Scientific™ SureTect™Staphylococcus aureus PCR Assay is a real-time PCR assay for the detection of Staphylococcus aureus in dairy samples.

Objective

The Thermo Scientific SureTect Staphylococcus aureus PCR Assay was evaluated for AOAC Performance Tested MethodSM certification.

Methods

Inclusivity/exclusivity, matrix studies, product consistency and stability, and robustness testing were conducted to assess the method’s performance. For the matrix study, the method was validated on the Applied Biosystems™ QuantStudio™ 5 Real-Time PCR instrument and the Applied Biosystems 7500 Fast Real-Time PCR instrument against the ISO 6888-3:2003 Microbiology of food and animal feeding stuffs—Horizontal method for the enumeration of coagulase-positive staphylococci (Staphylococcus aureus and other species)—Part 3: Detection and MPN technique for low numbers, and the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Ch. 12, Staphylococcus aureus, 2016, reference methods.

Results

Matrix studies showed no statistically significant differences between the candidate and reference methods or between presumptive and confirmed results. The inclusivity/exclusivity study correctly identified/excluded all strains analyzed. Robustness testing showed no statistically significant difference in assay performance after set method parameter deviations, and product consistency and stability studies demonstrated no statistically significant differences in performance between kit lots at different expiration points.

Conclusion

The data presented show that the assay is a rapid and reliable workflow for the detection of S. aureus from dairy matrixes.

Highlights

The PCR assay allows for fast, reliable detection of S. aureus in dairy matrixes with results obtained in as little as 80 min post enrichment.
Research progress of pharmacological effects of Siraitia grosvenorii extract
Authors: Li He , Li Ruli , Jiang Wei , Zhou Liming
Published: October 2021

Objectives

To summarise the ingredients of Luo Han Guo extract and the different pharmacological activity of the different ingredients. Find and evaluate the research value of Luo Han Guo extract as a therapeutic drug.

Key findings

Siraitia grosvenorii is a fruit native to China and has many years of medicinal history. Because of its low-calorie and sugar-free properties, it is approved as a sweetener substitute in foods for obese and diabetic patients. Experiments have shown that this sweetener is non-toxic. This article summarises much literature on S. grosvenorii extracts, briefly introduces their chemical composition and metabolic distribution and summarises the possible pharmacological effects of each S. grosvenorii extract. Siraitia grosvenorii extract has anti-diabetic, anti-tumour, anti-inflammatory, antioxidant, neuroprotective and lipogenic inhibitory effects. These pharmacological activities suggest the medicinal value of S. grosvenorii.

Luo Han Guo extract is a low-calorie, non-toxic substance, and its pharmacological activity and its potential medicinal properties support its further utilisation and research.
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse
Authors: Zhang Yuexin , Song Chao , Zhang Yimeng , Wang Yuezhu , Feng Chenchen , Chen Jiaxin , Wei Ling , Pan Qi , Shang Desi , Zhu Yanbing , Zhu Jiang , Fang Shuangsang , Zhao Jun , Yang Yongsan , Zhao Xilong , Xu Xiaozheng , Wang Qiuyu , Guo Jincheng , Li Chunquan
Published: October 2021

Transcription co-factors (TcoFs) play crucial roles in gene expression regulation by communicating regulatory cues from enhancers to promoters. With the rapid accumulation of TcoF associated chromatin immunoprecipitation sequencing (ChIP-seq) data, the comprehensive collection and integrative analyses of these data are urgently required. Here, we developed the TcoFBase database (http://tcof.liclab.net/TcoFbase), which aimed to document a large number of available resources for mammalian TcoFs and provided annotations and enrichment analyses of TcoFs. TcoFBase curated 2322 TcoFs and 6759 TcoFs associated ChIP-seq data from over 500 tissues/cell types in human and mouse. Importantly, TcoFBase provided detailed and abundant (epi) genetic annotations of ChIP-seq based TcoF binding regions. Furthermore, TcoFBase supported regulatory annotation information and various functional annotations for TcoFs. Meanwhile, TcoFBase embedded five types of TcoF regulatory analyses for users, including TcoF gene set enrichment, TcoF binding genomic region annotation, TcoF regulatory network analysis, TcoF-TF co-occupancy analysis and TcoF regulatory axis analysis. TcoFBase was designed to be a useful resource that will help reveal the potential biological effects of TcoFs and elucidate TcoF-related regulatory mechanisms.
Severe Lung Infection and Septicemia Caused by Paludibacterium purpuratum—A Case Report and Evaluation of Bacterial Traits
Authors: Cia Cong-Tat , Chen Jenn-Wei , Su Shu-Li , Tsai Pei-Fang , Shu Cing-Ying , Ko Wen-Chien , Chen Po Lin
Published: October 2021

Paludibacterium species are gram stain–negative rods that are facultatively anaerobic; they have been isolated from wetland soil. Clinical infection caused by this genus is rarely reported. We report the case of an 84-year-old woman with chronic renal disease and hypertension who acquired P. purpuratum lung infection and septicemia in Southern Taiwan.
What Gender-Neutral Activation? Understanding the Gender Sanction Gap in Germany’s Welfare System
Authors: Knize Veronika J
Published: October 2021

Women are half as likely to be sanctioned as men in Germany’s means-tested welfare system, despite sanctions not explicitly being a gendered activation measure. I investigate the reasons underlying the “gender sanction gap” with a decomposition analysis on a sample from registry data. Findings show differences between women and men in their distributions on family-related and human-capital-related variables explain much of the gap. Results further suggest gender differences in behavior and treatment by public employment services also contribute to the gap, with women more frequently being exempted from sanctions due to childcare responsibilities.
Binding the Acoustic Features of an Auditory Source through Temporal Coherence
Authors: Rezaeizadeh Mohsen , Shamma Shihab
Published: October 2021

Numerous studies have suggested that the perception of a target sound stream (or source) can only be segregated from a complex acoustic background mixture if the acoustic features underlying its perceptual attributes (e.g., pitch, location, and timbre) induce temporally modulated responses that are mutually correlated (or coherent), and that are uncorrelated (incoherent) from those of other sources in the mixture. This “temporal coherence” hypothesis asserts that attentive listening to one acoustic feature of a target enhances brain responses to that feature but would also concomitantly (1) induce mutually excitatory influences with other coherently responding neurons, thus enhancing (or binding) them all as they respond to the attended source; by contrast, (2) suppressive interactions are hypothesized to build up among neurons driven by temporally incoherent sound features, thus relatively reducing their activity. In this study, we report on EEG measurements in human subjects engaged in various sound segregation tasks that demonstrate rapid binding among the temporally coherent features of the attended source regardless of their identity (pure tone components, tone complexes, or noise), harmonic relationship, or frequency separation, thus confirming the key role temporal coherence plays in the analysis and organization of auditory scenes.
Contrasting selection pressure on body and weapon size in a polygynous megaherbivore
Authors: Shannon Graeme , Sadler Phoebe , Smith Joanna , Roylance-Casson Eleanor , Cordes Line S.
Published: October 2021

Sexual size dimorphism (SSD) is a common morphological trait in ungulates, with polygyny considered the leading driver of larger male body mass and weapon size. However, not all polygynous species exhibit SSD, while molecular evidence has revealed a more complex relationship between paternity and mating system than originally predicted. SSD is, therefore, likely to be shaped by a range of social, ecological and physiological factors. We present the first definitive analysis of SSD in the common hippopotamus (Hippopotamus amphibius) using a unique morphological dataset collected from 2994 aged individuals. The results confirm that hippos exhibit SSD, but the mean body mass differed by only 5% between the sexes, which is rather limited compared with many other polygynous ungulates. However, jaw and canine mass are significantly greater in males than females (44% and 81% heavier, respectively), highlighting the considerable selection pressure for acquiring larger weapons. A predominantly aquatic lifestyle coupled with the physiological limitations of their foregut fermenting morphology likely restricts body size differences between the sexes. Indeed, hippos appear to be a rare example among ungulates whereby sexual selection favours increased weapon size over body mass, underlining the important role that species-specific ecology and physiology have in shaping SSD.
Do I stay or do I go? Shifts in perch use by lizards during morning twilight suggest anticipatory behaviour
Authors: Chen Chih-Wei , Whiting Martin J. , Yang En-Cheng , Lin Si-Min
Published: October 2021

Anticipatory behaviour is the expectation of a near-future event based on information processed in the past and influences an animal's tactical decisions, particularly when there are significant fitness consequences. The grass lizard (Takydromus viridipunctatus) perches on blades of grass at night which likely reduces the probability of predation by terrestrial predators such as snakes, rodents and shrews. During twilight (starting 30 min before sunrise), they move from above the grass to within grass clumps and this is thought to afford the lizard protection while reducing detection by avian predators. Here, we examined how lizards shift their behaviour as a function of visual detectability to their primary predator, the cattle egret (Bubulcus ibis). We show that the lizards shift from their perch site during twilight at the earliest time at which egrets depart communal roosts. At the same time, visual modelling shows a dramatic increase in the detectability of the lizards to the visual system of egrets. Therefore, anticipatory behaviour in response to environmental cues acts to reduce predation risk as lizards become more conspicuous and predators become more active. Grass lizard anticipatory behaviour appears to be finely tuned by natural selection to adjust to temporal changes in predation risk.
Novel generic models for differentiating stem cells reveal oscillatory mechanisms
Authors: Farjami Saeed , Camargo Sosa Karen , Dawes Jonathan H. P. , Kelsh Robert N. , Rocco Andrea
Published: October 2021

Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically motivated mathematical models for cell differentiation that generically generate oscillations and hence suggest alternatives to the standard framework based on Waddington’s epigenetic landscape. The models allow us to suggest two generic dynamical scenarios that describe the differentiation process. In the first scenario, gradual variation of a single control parameter is responsible for both entering and exiting the oscillatory regime. In the second scenario, two control parameters vary: one responsible for entering, and the other for exiting the oscillatory regime. We analyse the standard repressilator and four variants of it and show the dynamical behaviours associated with each scenario. We present a thorough analysis of the associated bifurcations and argue that gene regulatory networks with these repressilator-like characteristics are promising candidates to describe cell fate selection through an oscillatory process.
A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage
Authors: AbuOun Manal , Jones Hannah , Stubberfield Emma , Gilson Daniel , Shaw Liam P. , Hubbard Alasdair T. M. , Chau Kevin K. , Sebra Robert , Peto Tim E. A. , Crook Derrick W. , Read Daniel S. , Gweon H. Soon , Walker A. Sarah , Stoesser Nicole , Smith Richard P. , Anjum Muna F. ,   on behalf of the REHAB consortium
Published: October 2021

Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain to humans, thereby increasing the AMR burden and affecting our ability to tackle infections. In this study 168 isolates from four genera of the order

Enterobacterales

, primarily

Escherichia coli

, were purified from livestock (cattle, pigs and sheep) faeces from 14 farms in the United Kingdom. Their genomes were resolved using long- and short-read sequencing to analyse AMR genes and their genetic context, as well as to explore the relationship between AMR burden and on-farm antimicrobial usage (AMU), in the three months prior to sampling. Although

E. coli

isolates were genomically diverse, phylogenetic analysis using a core-genome SNP tree indicated pig isolates to generally be distinct from sheep isolates, with cattle isolates being intermediates. Approximately 28 % of isolates harboured AMR genes, with the greatest proportion detected in pigs, followed by cattle then sheep; pig isolates also harboured the highest number of AMR genes per isolate. Although 90 % of sequenced isolates harboured diverse plasmids, only 11 % of plasmids (n=58 out of 522) identified contained AMR genes, with 91 % of AMR plasmids being from pig, 9 % from cattle and none from sheep isolates; these results indicated that pigs were a principle reservoir of AMR genes harboured by plasmids and likely to be involved in their horizontal transfer. Significant associations were observed between AMU (mg kg−1) and AMR. As both the total and the numbers of different antimicrobial classes used on-farm increased, the risk of multi-drug resistance (MDR) in isolates rose. However, even when AMU on pig farms was comparatively low, pig isolates had increased likelihood of being MDR; harbouring relatively more resistances than those from other livestock species. Therefore, our results indicate that AMR prevalence in livestock is not only influenced by recent AMU on-farm but also livestock-related factors, which can influence the AMR burden in these reservoirs and its plasmid mediated transmission.
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations
Authors: Gerlin Léo , Cottret Ludovic , Escourrou Antoine , Genin Stéphane , Baroukh Caroline
Published: October 2021

Predicting and understanding plant responses to perturbations requires integrating the interactions between nutritional sources, genes, cell metabolism and physiology in the same model. This can be achieved using metabolic modeling calibrated by experimental data. In this study, we developed a multi-organ metabolic model of a tomato plant during vegetative growth, named VYTOP (Virtual Young TOmato Plant) that combines genome-scale metabolic models of leaf, stem and root and integrates experimental data acquired from metabolomics and high-throughput phenotyping of tomato plants. It is composed of 6689 reactions and 6326 metabolites. We validated VYTOP predictions on five independent use cases. The model correctly predicted that glutamine is the main organic nutrient of xylem sap. The model estimated quantitatively how stem photosynthetic contribution impact exchanges between the different organs. The model was also able to predict how nitrogen limitation affects the plant vegetative growth, and to predict the metabolic behavior of transgenic tomato lines with altered expressions of core metabolic enzymes. The integration of different components such as a metabolic model, physiological constraints and experimental data generates a powerful predictive tool to study plant behavior, which will be useful for several other applications such as plant metabolic engineering or plant nutrition.

One sentence summary

A multi-organ metabolic model of tomato gives biological insights into the functioning of a plant such as xylem composition, the role of the stem and the response to environmental or genetic perturbation.
Hi-C detects genomic structural variants in peripheral blood of pediatric leukemia patients
Authors: Mallard Claire , Johnston Michael J , Bobyn Anna , Nikolic Ana , Argiropoulos Bob , Chan Jennifer A , Guilcher Gregory MT , Gallo Marco
Published: October 2021

B-cell acute lymphoblastic leukemia (B-ALL) is often driven by chromosome translocations that result in recurrent and well-studied gene fusions. Currently, fluorescent in-situ hybridization probes are employed to detect candidate translocations in bone marrow samples from B-ALL patients. Recently Hi-C, a sequencing-based technique originally designed to reconstruct the three-dimensional architecture of the nuclear genome, was shown to effectively recognize structural variants. Here, we demonstrate that Hi-C can be used as a genome-wide assay to detect translocations and other structural variants of potential clinical interest. Structural variants were identified in both bone marrow and peripheral blood samples, including an ETV6-RUNX1 translocation present in one pediatric B-ALL patient. Our report provides proof-of-principle that Hi-C could be an effective strategy to globally detect driver structural variants in B-ALL peripheral blood specimens, reducing the need for invasive bone marrow biopsies and candidate-based clinical tests.