bluuebunny/crossref_metadata_2025 huggingface dataset:
The association between socioeconomic status and prevalence, awareness, treatment and control of hypertension in different ethnic groups: the Healthy Life in an Urban Setting study
Authors: Blok Sebastiaan , Haggenburg Sabine , Collard Didier , Van Der Linden Eva L. , Galenkamp Henrike , Moll van Charante Eric P. , Agyemang Charles , Van Den Born Bert-Jan H.
Published: January 2022

Background:

Socioeconomic status (SES) and ethnicity are both important determinants of hypertension prevalence and control rates but their separate contribution is unknown. We assessed the association of SES with hypertension prevalence, awareness, treatment and control, and whether this differs between ethnic groups.

Methods:

We used baseline data from the Healthy Life in an Urban Setting (HELIUS) study, a multiethnic population-based cohort study, including 18 106 participants (84% of the total cohort) of Dutch (n = 4262), African Surinamese (n = 3732), Moroccan (n = 2902), Turkish (n = 2694), South-Asian Surinamese (n = 2664) and Ghanaian (n = 1947) descent with data on SES and hypertension status.

Results:

Regardless of ethnicity, lower SES was associated with higher hypertension prevalence, especially in participants with no education compared with those with higher levels of education [OR 2.29 (2.05–2.56)]. There was an inverse association between SES and hypertension treatment with the strongest association for lower compared with higher educated participants [OR 1.63 (1.39–1.90)]. In addition, lower SES was associated with lower hypertension control with the strongest association for participants with the lowest compared with the highest occupational level [OR 0.76 (0.60–0.95)]. The association between educational level and treatment but not the other SES- or hypertension-indicators, was influenced by ethnicity, with lower educated Dutch and African Surinamese having higher ORs for hypertensive treatment [Dutch OR 1.98 (1.43–2.76); African Surinamese OR 1.44 (1.10–1.89)].

Conclusion:

SES, in particular education, impacts hypertension treatment in the Netherlands, whereas the association of specific SES parameters with hypertension indicators differ across ethnic groups. Further exploration is needed on how sociocultural beliefs and behaviours may differentially affect blood pressure control across ethnic minority populations.
Analysis of symptomatic recurrences of common bile ducts stones after endoscopic removal
Authors: Han Soo Jeong , Chang Jae Hyuck , Gweon Tae-Geun , Kim Tae Ho , Kim Hyung-Keun , Kim Chang Whan
Published: January 2022

Early or multiple recurrences of symptomatic common bile duct (CBD) stones are troublesome late complications after endoscopic stone removal. We aimed to determine the factors related to early or multiple recurrences of CBD stones.

We retrospectively analyzed patients who underwent endoscopic CBD stone extraction in a single institute between January 2006 and December 2015. Patients were divided into 2 groups according to the number and interval of CBD stone recurrences: single versus multiple (≥2) and early (<1.5 years) versus late (≥1.5 years) recurrence.

After exclusion, 78 patients were enrolled and followed up for a median of 1974 (IQR: 938–3239) days. Twenty-seven (34.6%) patients experienced multiple recurrences (≥2 times), and 26 (33.3%) patients experienced early first recurrence (<1.5 years). In the multivariate analysis, CBD angulation was independently related to multiple CBD stone recurrence (OR: 4.689, P = .016), and endoscopic papillary large balloon dilation was independently related to late first CBD stone recurrence (OR: 3.783, P = .025). The mean CBD angles were more angulated with increasing instances of recurrence (0, 1, 2, 3, and ≥4 times) with corresponding values of 150.3°, 148.2°, 143.6°, 142.2°, and 126.7°, respectively (P = .011). The period between the initial treatment and first recurrence was significantly longer than the period between the first and second recurrence (P = .048).

In conclusion, greater CBD angulation is associated with the increased number of CBD stone recurrence, and EPLBD delays the recurrence of CBD stones after endoscopic CBD stone removal.
Combined Central and Peripheral Demyelination in a Case With Sjogren Syndrome
Authors: Sokmen Okan , Gocmen Rahsan , Nurlu Gulay , Karabudak Rana
Published: January 2022

Introduction:

Combined central and peripheral demyelination (CCPD) is a rare entity in which central and peripheral nervous system demyelination coexist. Herein, we present a patient with coexistence of Sjögren syndrome (SS) and CCPD.

Case Report:

A 58-year-old female patient was admitted to our neurology clinic with paraparesis, difficulty walking, imbalance, and paresthesia. Neurological examination showed paraparesis, absence of lower extremity deep tendon reflex, sensory deficit at the T8 level, loss of deep sensory position, and vibration. Spinal magnetic resonance imaging revealed multiple focal T2-hyperintense and contrast-enhancing cord lesions. Fat-suppressed imaging disclosed T2 hyperintensity in lumbar nerve roots, diffuse linear enhancement of the cauda equina, and diffuse increased enhancement in lumbar nerve roots. Electrodiagnostic findings fulfilled the diagnostic criteria for chronic inflammatory demyelinating polyneuropathy. Extensive laboratory workup excluded all possible pathologies. The Schirmer test detected positive in both eyes and minor salivary gland biopsy resulted in grade 3. These results were consistent with SS. The patient received intravenous methylprednisolone, azathioprine hydroxychloroquine. Approximately 2 years later, her complaints had completely disappeared, except for mild sensory complaints.

Conclusion:

It is unclear whether the association of central nervous system and peripheral nervous system demyelination and SS is a coincidence or a consequence. Our patient shows that patients with SS can have CCPD, and a significant clinical response can be obtained with early treatment. We hope that this unique case sheds light on the pathophysiology of CCPD.
Clinical Review of Smartphone Applications in Parkinson’s Disease
Authors: Tripathi Susmit , Malhotra Ashwin , Qazi Murtaza , Chou Jingyuan , Wang Fei , Barkan Samantha , Hellmers Natalie , Henchcliffe Claire , Sarva Harini
Published: January 2022

Background:

Parkinson’s disease (PD) is the second leading neurodegenerative disease worldwide. Important advances in monitoring and treatment have been made in recent years. This article reviews literature on utility of smartphone applications in monitoring PD symptoms that may ultimately facilitate improved patient care, and on movement modulation as a potential therapeutic.

Review Summary:

Novel mobile phone applications can provide one-time and/or continuous data to monitor PD motor symptoms in person or remotely, that may support precise therapeutic adjustments and management decisions. Apps have also been developed for medication management and treatment.

Conclusions:

Smartphone applications provide a wide array of platforms allowing for meaningful short-term and long-term data collection and are also being tested for intervention. However, the variability of the applications and the need to translate complicated sensor data may hinder immediate clinical applicability. Future studies should involve stake-holders early in the design process to promote usability and streamline the interface between patients, clinicians, and PD apps.
Posterior Circulation Alberta Stroke Program Early Computed Tomography Score (pc-ASPECT) for the Evaluation of Cerebellar Infarcts
Authors: Altiparmak Taylan , Nazliel Bijen , Batur Caglayan Hale , Tokgoz Nil , Akyol Gurses Asli , Ucar Murat
Published: January 2022

Background:

Patients with cerebellar ischemic stroke may be misdiagnosed and may exhibit a delayed time to acute stroke treatment compared with patients with anterior circulation ischemic stroke. The posterior circulation Alberta stroke program early computed tomography score (pc-ASPECT) score has been used to evaluate hyperacute stroke, much as the ASPECT in anterior circulation stroke recently. Our main objective was to evaluate the associations of the clinical and etiological characteristics of ischemic cerebellar infarction patients on admission with their pc-ASPECT scores, as well as the correlations of the pc-ASPECT score with morbidity and mortality rates.

Materials and Methods:

We include 114 patients with cerebellar infarction who underwent 1 year of follow-up into the study.

Results:

Patients with a pc-ASPECT score <7 were more likely to present with impaired consciousness (P<0.001), multiple posterior circulation infarcts (P<0.001), hydrocephalus (P<0.001), lesions of the vermis (P=0.028), and peduncle (P=0.024), perfusion deficits in the total of posterior inferior cerebellar artery, anterior inferior cerebellar artery, superior cerebellar artery (P<0.05), and basilar artery stenosis (P=0.005), ischemia in additional anatomical structures in the posterior circulation (P<0.001) compared with those with a score ≥7.

Conclusions:

Although the pc-ASPECT score alone is insufficient in some cases like vertebral artery dissection, using it together with the National Institutes of Health Stroke Scale (NIHSS) score and clinical findings may be beneficial during the hyperacute period of cerebellar ischemia. Presentation with impaired consciousness, basilar artery pathologies, vermian ischemia, and ischemia in additional anatomical structures in the posterior circulation other than the cerebellum appeared as important clinical and radiologic parameters predicting long-term prognosis.
Topical Review: An Update of Diagnostic and Management Algorithms for Acquired Blepharoptosis
Authors: Nichols Kelly K. , Malloy Kelly A. , Karpecki Paul M. , Bacharach Jason , Douglas Raymond S. , Foster Shane , Gromacki Susan J. , Whitley Walter O.
Published: January 2022

SIGNIFICANCE

Acquired ptosis is a condition of the upper eyelid that has negative cosmetic and functional effects but is likely underdiagnosed and undertreated. Given the evolving understanding of the condition and expanding therapeutic options, this review reappraised published evidence and clinical experience regarding diagnosis and treatment of acquired ptosis.

The authors met over two structured virtual working sessions to review current evidence and develop timely recommendations for acquired ptosis identification, differential diagnosis, characterization, and treatment selection. Diagnostic algorithms, plus management and referral guidelines, are presented. Eyelid evaluation and, when needed, ptosis diagnostic workup are essential in the comprehensive eye examination. Acquired ptosis can be efficiently identified via patient questionnaire, history, and photograph review combined with assessment of eyelid position and symmetry using established methods. When ptosis is present, it is essential to evaluate onset, symptoms, pupil diameter, and extraocular muscle function to identify or rule out serious underlying conditions. If signs of serious underlying etiology are present, immediate referral/follow-up testing is required. After ruling out serious underlying causes, masquerade conditions, and pseudoptosis, pharmacologic or surgical treatment should be selected based on the clinical evidence. Effectively managing acquired ptosis requires practice-wide commitment to thorough eyelid evaluation, accurate diagnosis, and adoption of new treatment modalities. Aided by evolving pharmacologic therapeutic options, shifting from a “detect and refer” to a “diagnose and manage” approach can support identification and treatment of more patients with acquired ptosis, particularly mild-to-moderate cases.
Pediatric Carbon Monoxide Poisoning
Authors: Bağci Zafer , Arslan Abdullah , Neşelioğlu Salim
Published: January 2022

Objectives

Carbon monoxide (CO) poisoning remains the foremost cause of poisoning worldwide. This study aimed to investigate the effects of hyperbaric oxygen therapy (HBOT) and normobaric oxygen therapy (NBOT) on thiol/disulfide homeostasis in children with CO intoxication.

Methods

Eighty-one children aged 0 to 18 years with CO intoxication were included in this cross-sectional study. No changes were made in the routine clinical evaluation and treatment practices of the patients. Thirty-two children who received HBOT and 49 children who received NBOT were compared for serum native thiol, disulfide, and total thiol levels, as well as for the changes in disulfide/native thiol, disulfide/total thiol, and native thiol/total thiol ratios before and after treatment.

Results

Antioxidant levels, such as native thiol and total thiol, were significantly decreased in patients who received HBOT and increased in those who received NBOT (P = 0.02 and P = 0.01, respectively). There was no statistically significant difference between the 2 groups concerning the change of native thiol/total thiol ratios (P = 0.07). In addition, there was no significant difference regarding changes in disulfide, disulfide/native thiol, and disulfide/total thiol levels before and after treatment (P = 0.39, P = 0.07, and P = 0.07, respectively).

Conclusions

Although thiol-disulfide balance is maintained in patients treated with HBOT, antioxidant levels decrease significantly compared with NBOT. Despite efficiency of HBOT in CO intoxication, oxidative stress and reperfusion injury due to hyperoxygenation should be considered in the treatment of HBOT.
How We Incorporate Venetoclax in Treatment Regimens for Acute Myeloid Leukemia
Authors: Maiti Abhishek , Konopleva Marina Y.
Published: January 2022

Venetoclax has transformed the therapeutic landscape of acute myeloid leukemia (AML). Hypomethylating agents with venetoclax (HMA-VEN) have significantly improved outcomes and have become the standard therapy for older/unfit patients with newly diagnosed AML and are comparable to intensive chemotherapy in salvage setting. Venetoclax with intensive chemotherapy have shown high response rates in both frontline and salvage setting in younger patients, and triplet combinations with HMA-VEN and FLT3 inhibitors have shown encouraging results in FLT3
mut AML. While patients with NPM1
mut, IDH1/2
mut experience favorable outcomes, those with TP53
mut and secondary AML may experience minimal benefit from the addition of venetoclax. Despite improved outcomes, severe cytopenias and infectious complications are common with venetoclax-based regimens. Early response evaluation, dose reductions, venetoclax interruptions, use of growth factors, and prophylactic antimicrobials may minimize such myelosuppression and risk of infections. Outcomes after failure of frontline HMA-VEN are dismal, and novel approaches are needed to abrogate primary and acquired resistance.
What Are the Prospects for Treating TP53 Mutated Myelodysplastic Syndromes and Acute Myeloid Leukemia?
Authors: Wang Chen , Sallman David A.
Published: January 2022

TP53 is a key tumor suppressor gene involved in fundamental biological processes of genomic stability and is recurrently mutated in a subgroup of myelodysplastic syndromes and acute myeloid leukemia. These patients have unique clinical and molecular features resulting in dismal outcomes despite standard cytotoxic chemotherapy, and long-term survival is seldom achieved with allogeneic stem cell transplant. Upfront use of hypomethylating agents with or without venetoclax has resulted in a favorable initial response over intensive cytotoxic chemotherapy, albeit responses are nondurable, and the median overall survival is typically less than 6 to 8 months. In this review, we examine the evidence of conventional treatments and focus on the emerging novel therapeutic options, including targeted molecular and immunotherapies for this challenging molecular subgroup. Together, there are still significant unmet needs to improve outcomes of patients with TP53 mutated myelodysplastic syndromes and acute myeloid leukemia, and enrollment in clinical trials should be highly favored whenever they are available.
Improving the Diagnosis of Menstrual Dysfunction through Quality Improvement
Authors: Daniel Kayla , Fischer Anastasia , Welty Michael , Valasek Amy E.
Published: January 2022

Introduction:

Prevalence of menstrual dysfunction (MD) in high school athletes ranges from 7% to 54%. Early recognition and intervention are crucial to prevent future consequences. The purpose of this Quality Improvement project was to optimize the institution’s Epic Best Practice Advisory (BPA) screening tool and synthesize new patient questionnaires to diagnose MD in athletes greater than 12 years of age presenting to a pediatric sports medicine clinic.

Methods:

Using Quality Improvement methodology, we evaluated clinic flow, the Epic BPA tool, and actions by the physician following the appropriate triggering of the BPA. Diagnoses targeted were primary amenorrhea, oligomenorrhea, or irregular menstruation unspecified. Areas for intervention were global staff education, patient education, and provider alert fatigue. Our team implemented interventions using monthly Plan-Do-Study-Act cycles to address our key drivers. Proper implementation of questionnaire data and restructuring of the Epic BPA promoted identification and diagnosis of MD. The clinician discussed the diagnosis with the patient and family and provided an educational handout on MD.

Results:

The rate of appropriate diagnosis of MD in athletes greater than 12 years of age seen at a pediatric sports medicine clinic increased from a baseline of 2.1% to 30% over ten months. Identification of three key drivers ultimately drove the success and achievement of our aim.

Conclusions:

Using Quality Improvement methodology, we optimized the EPIC BPA and subsequently increased the rate of appropriate diagnosis of MD. Identification of the proper diagnosis improves our patient education. Ultimately, this project provided the framework for applicable discussion, interventions, and work-up for at-risk athletes.
Quality Improvement Methodology Facilitates Adherence to Echocardiogram Protocol Measurements
Authors: Siddiqui Saira , Hahn Eunice , Hill Garick D. , Brown James , Lehmkuhl Katherine , Statile Christopher
Published: January 2022

Introduction:

Local institutional echocardiogram protocols reflect standard measurements as per national guidelines, but adherence to measurements was inconsistent. This inconsistency led to variability in reporting and impacted the use of serial measurements for clinical decision-making. Therefore, we aimed to improve complete adherence to universal and protocol-specific measures for echocardiograms performed for first-time or cardiomyopathy studies from 60% to 90% from July 2019 to February 2020.

Methods:

We included all sonographer-performed echocardiograms for first-time or cardiomyopathy protocol studies. We reviewed universal measures and protocol-specific measures for all included studies. We created a scoring system reflecting measurement completion. We used a control chart to measure compliance and established a baseline over 2 months. PDSA cycles over 5 months included interventions such as sonographer education, technical improvements to the measurement toolbar, and group and individual performance feedback.

Results:

We reviewed over 4000 studies—the reporting of complete universal measures improved significantly from a median score of 60% to 93%. Protocol-specific measures for first-time studies also showed significant improvement from 62% to 90% adherence. Cardiomyopathy-specific measures demonstrated 87% adherence at baseline, which improved to 95% but then returned to baseline. Sonographer education and toolbar adjustment prompted special cause variation with further improvement following performance feedback. The universal and first-time protocol measures reached 90% adherence with sustained improvement for over 9 months.

Conclusions:

We employed quality improvement methodology to improve complete adherence to echocardiographic protocol measurements, thereby facilitating echocardiographic quality and reporting consistency. We plan to spread these interventions to improve adherence to other protocols.
Improving Care for Children with Bloody Diarrhea at Risk for Hemolytic Uremic Syndrome
Authors: Burns Carson S. , Rubin Jason , Sardesai Tara , Klein Eileen J. , Vora Surabhi B. , Kearney Ryan , Rutman Lori
Published: January 2022

Introduction:

Children with infectious bloody diarrhea are at an increased risk for developing hemolytic uremic syndrome (HUS). Early intervention may improve outcomes. This study evaluated the impact of a clinical pathway designed to identify those at risk for HUS, guide initial management, and provide decision support regarding patient disposition.

Methods:

We performed a retrospective cohort study of children 4 months to 19 years of age who presented with the acute onset of bloody diarrhea or other HUS risk factors to the pediatric emergency department (ED) from September 2015 through July 2020. A rapid stool polymerase chain reaction (PCR) test became available in May 2017. The clinical pathway was implemented in January 2018. We used Fisher’s exact tests and statistical process control charts to analyze patient- and system-level changes following pathway implementation.

Results:

Three hundred five patients were included. Postimplementation, stool PCR use increased (78%–91%), hospitalization decreased (49%–30%), and mean total charges decreased ($7715–$6797). There were increases in length of stay (226–288 minutes) and charges ($2651–$3524) for patients discharged from the ED. All changes met rules for special cause variation. There was no change in early IV fluid administration, inpatient length of stay, ED return visits, hospital readmissions, or patients with Shiga toxin-producing Escherichia coli (STEC), acute kidney injury (AKI) or HUS.

Conclusions:

For children presenting to the ED with bloody diarrhea, introduction of a rapid stool PCR test and clinical pathway correlated with decreased hospitalizations and overall costs without adverse clinical outcomes.
Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)
Authors: Legein Marie , Wittouck Stijn , Lebeer Sarah
Published: January 2022

Thirteen Gram-positive, catalase-positive, rod-shaped single colonies were obtained after culturing a strawberry leaf on de Man–Rogosa–Sharpe agar. Based on 16S rRNA gene and rpoA gene sequence similarities, ranging between 99.0–100% and 96.5–100%, respectively, the 13 isolates were found to be closely related to each other. Two of the independent isolates, AMBP162T and AMBP252, were whole-genome sequenced, and showed to be undistinguishable with an average nucleotide identity (ANI) value of 100 %. Compared to the reference genomes for all species in the family

Lactobacillaceae

, the AMBP162T genome was most similar to the reference strain of

Latilactobacillus curvatus

with ANI of only 89.5 %, indicating they were a different species. Based on genotypic and phenotypic data, a novel

Latilactobacillus

species, Latilactobacillus fragifolii sp. nov., with the type strain AMBP162T (=LMG 32285T=CECT 30357T) is proposed.
Hymenobacter piscis sp. nov., isolated from a fish pond
Authors: Sheu Shih-Yi , Yang Che-Chia , Kwon Soon-Wo , Chen Wen-Ming
Published: January 2022

Bacterial strain NST-14T, isolated from a freshwater fish pond in Taiwan, was characterized using a polyphasic taxonomy approach. The strain was Gram-stain-negative, strictly aerobic, non-motile, rod-shaped and formed pink colonies. Optimal growth occurred at 30 °C, pH 7 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain NST-14T formed a phylogenetic lineage in the genus

Hymenobacter

. Analysis of 16S rRNA gene sequences showed that strain NST-14T had the highest similarity to

Hymenobacter actinosclerus

CCUG 39621T (97.7%),

Hymenobacter amundsenii

P5136T (97.3%) and

Hymenobacter humicola

P6312T (96.9%). Strain NST-14T showed 75.1–85.3 % average nucleotide identity, 73.7–89.8 % average amino acid identity and 14.5–26.0 % digital DNA–DNA hybridization with the type strains of other closely related

Hymenobacter

species. Strain NST-14T contained iso-C15 : 0, C16 : 1
 ω5c and summed feature 3 (C16 : 1
 ω7c and/or C16 : 1
 ω6c) as the predominant fatty acids. The major hydroxyl fatty acids were iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The polar lipids were phosphatidylethanolamine, one unidentified glycolipid, four unidentified aminophospholipids, one unidentified aminolipid, two unidentified phospholipids and three unidentified lipids. The major polyamine was homospermidine. The major isoprenoid quinone was MK-7. The DNA G+C content of the genomic DNA was 62.4 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain NST-14T should be classified as a novel species of the genus

Hymenobacter

, for which the name Hymenobacter piscis sp. nov. is proposed. The type strain is NST-14T (=BCRC 81249T=LMG 31686T).
Identification of replication fork-associated proteins in Drosophila embryos and cultured cells using iPOND coupled to quantitative mass spectrometry
Authors: Munden Alexander , Wright Madison T. , Han Dongsheng , Tirgar Reyhaneh , Plate Lars , Nordman Jared T.
Published: January 2022

Replication of the eukaryotic genome requires the formation of thousands of replication forks that must work in concert to accurately replicate the genetic and epigenetic information. Defining replication fork-associated proteins is a key step in understanding how genomes are replicated and repaired in the context of chromatin to maintain genome stability. To identify replication fork-associated proteins, we performed iPOND (Isolation of Proteins on Nascent DNA) coupled to quantitative mass spectrometry in Drosophila embryos and cultured cells. We identified 76 and 278 fork-associated proteins in post-MZT embryos and Drosophila cultured S2 cells, respectively. By performing a targeted screen of a subset of these proteins, we demonstrate that BRWD3, a targeting specificity factor for the DDB1/Cul4 ubiquitin ligase complex (CRL4), functions at replication forks to promote fork progression and maintain genome stability. Altogether, our work provides a valuable resource for those interested in the DNA replication, repair and chromatin assembly during development.
SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation
Authors: Choi Jung-Hyun , Zhang Xu , Zhang Christine , Dai David L. , Luo Jun , Ladak Reese , Li Qian , Wiebe Shane , Liu Alex C.H. , Ran Xiaozhuo , Yang Jiaqi , Naeli Parisa , Garzia Aitor , Zhou Lele , Mahmood Niaz , Deng Qiyun , Elaish Mohamed , Lin Rongtuan , Hobman Tom , Pelletier Jerry , Alain Tommy , Vidal Silvia , Duchaine Thomas , Mazhab-Jafari Mohammad T. , Mao Xiaojuan , Jafarnejad Seyed Mehdi , Sonenberg Nahum
Published: January 2022

Viruses evade the innate immune response by suppressing the production or activity of cytokines such as type I interferons (IFNs). Here we report the discovery of a novel mechanism by which the SARS-CoV-2 virus co-opts an intrinsic cellular machinery to suppress the production of the key immunostimulatory cytokine IFN-β. We reveal that the SARS-CoV-2 encoded Non-Structural Protein 2 (NSP2) directly interacts with the cellular GIGYF2 protein. This interaction enhances the binding of GIGYF2 to the mRNA cap-binding protein 4EHP, thereby repressing the translation of the Ifnb1 mRNA. Depletion of GIGYF2 or 4EHP significantly enhances IFN-β production, leading to reduced viral infection. Our findings reveal a new target for rescuing the antiviral innate immune response to SARS-CoV-2 and other RNA viruses.
End-to-end orientation estimation from 2D cryo-EM images
Authors: Lian Ruyi , Huang Bingyao , Wang Liguo , Liu Qun , Lin Yuewei , Ling Haibin
Published: January 2022

Cryo-electron microscopy (cryo-EM) is a Nobel Prize-winning technique for determining high-resolution 3D structures of biological macromolecules. A 3D structure is reconstructed from hundreds of thousands of noisy 2D projection images. However, existing 3D reconstruction methods are still time-consuming, and one of the major computational bottlenecks is recovering the unknown orientation of the particle in each 2D image. The dominant methods typically exploit an expensive global search on each image to estimate the missing orientations. Here, a novel end-to-end supervised learning method is introduced to directly recover the missing orientations from 2D cryo-EM images. A neural network is used to approximate the mapping from images to orientations. A robust loss function is proposed for optimizing the parameters of the network, which can handle both asymmetric and symmetric 3D structures. Experiments on synthetic data sets with various symmetry types confirm that the neural network is capable of recovering orientations from 2D cryo-EM images, and the results on a real cryo-EM data set further demonstrate its potential under more challenging imaging conditions.
Detecting ice artefacts in processed macromolecular diffraction data with machine learning
Authors: Nolte Kristopher , Gao Yunyun , Stäb Sabrina , Kollmannsberger Philip , Thorn Andrea
Published: January 2022

Contamination with diffraction from ice crystals can negatively affect, or even impede, macromolecular structure determination, and therefore detecting the resulting artefacts in diffraction data is crucial. However, once the data have been processed it can be very difficult to automatically recognize this problem. To address this, a set of convolutional neural networks named Helcaraxe has been developed which can detect ice-diffraction artefacts in processed diffraction data from macromolecular crystals. The networks outperform previous algorithms and will be available as part of the AUSPEX web server and the CCP4-distributed software.
Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization
Authors: Prangé Thierry , Carpentier Philippe , Dhaussy Anne-Claire , van der Linden Peter , Girard Eric , Colloc'h Nathalie
Published: January 2022

The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.
Severity of US sanctions against foreign firms: evidence from the FCPA enforcements
Authors: Kuvvet Emre
Published: January 2022

Purpose

The purpose of this study is to examine whether foreign firms pay disproportionately higher monetary penalties after controlling for factors that affect the sanctioning of the firm.

Design/methodology/approach

In this paper, a cross-sectional data analysis has been used to examine the enforcement actions of the Foreign Corrupt Practices Act (FCPA) against all private and public companies from 1978 to 2019.

Findings

The findings indicate that that foreign firms pay disproportionately higher monetary penalties than domestic firms after controlling for factors that affect the sanctioning of firms. On average, foreign firms pay $43.3m more to the US government than US firms pay. This is a considerable difference in monetary penalties and equal to 68.95% of the average monetary penalty.

Originality/value

This paper shows that the US government treats US firms more favorably than foreign firms in monetary sanctions. Because the FCPA is not applied equally, this is contrary to US government guidelines and to the rule of law. The government needs to reconsider the consequences of imposing disproportionately higher penalties on foreign firms. Given the lack of judicial scrutiny of the FCPA settlement amounts against foreign firms, prosecutorial harshness against them can be remedied by amending the FCPA to eliminate the unequal treatment of foreign entities.
A bi-level optimization framework for charging station design problem considering heterogeneous charging modes
Authors: Zhang Le , Zeng Ziling , Gao Kun
Published: January 2022

Purpose

The purpose of this paper is to optimize the design of charging station deployed at the terminal station for electric transit, with explicit consideration of heterogenous charging modes.

Design/methodology/approach

The authors proposed a bi-level model to optimize the decision-making at both tactical and operational levels simultaneously. Specifically, at the operational level (i.e. lower level), the service schedule and recharging plan of electric buses are optimized under specific design of charging station. The objective of lower-level model is to minimize total daily operational cost. This model is solved by a tailored column generation-based heuristic algorithm. At the tactical level (i.e. upper level), the design of charging station is optimized based upon the results obtained at the lower level. A tabu search algorithm is proposed subsequently to solve the upper-level model.

Findings

This study conducted numerical cases to validate the applicability of the proposed model. Some managerial insights stemmed from numerical case studies are revealed and discussed, which can help transit agencies design charging station scientifically.

Originality/value

The joint consideration of heterogeneous charging modes in charging station would further lower the operational cost of electric transit and speed up the market penetration of battery electric buses.
Machine learning for predictive maintenance scheduling of distribution transformers
Authors: Alvarez Quiñones Laura Isabel , Lozano-Moncada Carlos Arturo , Bravo Montenegro Diego Alberto
Published: January 2022

Purpose

The purpose of this paper is to describe a methodology that has been set up to schedule predictive maintenance of distribution transformers at Cauca Department (Colombia) using machine learning.

Design/methodology/approach

The proposed methodology relies on classification predictive model that finds the minimal number of distribution transformers prone to failure. To verify this, the model was implemented and tested with real data in Cauca Department Colombia.

Findings

The implementation of the methodology allows a saving of 13% in corrective maintenance expenses for the year 2020.

Originality/value

The proposed model is an effective decision-making tool that provides an ideal solution for preventive maintenance scheduling problems for distribution transformers.
YouTube and the protocological control of platform organisations
Authors: Xiang Yu
Published: January 2022

Purpose

This paper aims to examine the recommendation system of the video-sharing website YouTube to study how control of users is effected on online platforms.

Design/methodology/approach

This paper conceptualises algorithmic systems as protocols – technological and social infrastructures that both facilitate and govern interactions between autonomous actors (Galloway and Thacker, 2004, 2007). It adopts a netnographic approach (Kozinets, 2002) to study not only the formal, technological systems of the platform but also the systems as they were made sense of, understood and enacted upon by actors. It relies both on information as revealed by the organisation itself, as well as discussions between lay users in online forums and press coverage.

Findings

The results of this study indicate that the ways in which platforms selectively facilitate interactions between users constitute a form of control. While maintaining the appearance of an open and neutral marketplace, interactions on the platform are in fact highly structured. The system relies on the surveillance of user interactions to rapidly identify and propagate marketable contents, so as to maximise user “engagement” and ad revenue. The systems place few demands or restrictions on individual users, instead control is effected in a probabilistic fashion, over the population of users as a whole, so as to, in aggregate, accomplish organisational goal.

Originality/value

This paper contributes to the literature on accounting and control practices in online spaces, by extending the notion of control beyond overt rankings and evaluations, to the underlying technical and social infrastructures that facilitate and shape interactions.
Accounting for past patient composition in evaluations of quality reporting
Authors: Tierney Katherine I. , Fishman Samuel
Published: January 2022

Objective

To investigate whether accounting for past patient composition in evaluations of the association between public quality reports and patient selectivity changes findings and conclusions.

Data Sources

Secondary data analysis of public reports of Assisted Reproductive Technology Clinic success rates between 2011 and 2018.

Study Design

Two sets of fixed effects models, (1) a standard fixed‐effects model (FE) and (2) a dynamic panel model using structural equation modeling estimated with maximum‐likelihood (ML‐SEM) with one‐ and two‐year lagged patient characteristics, are compared. The outcome variables are patient composition features associated with success rates, including two age categories and eight diagnoses of infertility. Two‐year lagged success rates for any live birth and a singleton live birth are central predictor variables.

Data Collection/Extraction Methods

Clinics with complete records for the 2011–2018 period were included (N = 303).

Principal Findings

For live birth success rates, the two models show increases in the two‐year lagged success rate is associated with a reduction in (1) the transformed percentage of patients with endometriosis (FE: β = −0.006, SE = 0.002, p < 0.01; ML‐SEM: β = −0.005, SE = 0.002, p < 0.01) and (2) the percentage of patients with tubal diagnoses (FE: β = −0.090, SE = 0.017, p < 0.001; ML‐SEM: β = −0.064, SE = 0.027, p < 0.05). For singleton birth success rates, the models show positive associations between the two‐year lagged success rate and the percent of patients over 35 years old (FE: β = 0.219, SE = 0.033, p < 0.001; ML‐SEM: β = 0.095, SE = 0.047, p < 0.05). Overall, the FE models show numerous significant associations with the two‐year lagged success rate not observed in the ML‐SEM models. Thus, the preferred and theoretically appropriate model (ML‐SEM) and the more commonly used model (FE) yield different results.

Conclusions

Researchers and policymakers should use models that account for past patient composition when evaluating the associations between quality reports and patient selectivity.
Understanding nutritive need inHarmonia axyridislarvae: Insights from nutritional geometry
Authors: Sun Shao‐Lei , Abudisilimu Nibijiang , Yi Hao , Li Sali , Liu Tong‐Xian , Jing Xiangfeng
Published: January 2022

The multicolored Asian lady beetle,Harmonia axyridis(Pallas) (Coleoptera: Coccinellidae), is an important natural enemy in agricultural ecosystems. In spite of being a carnivore consuming protein‐rich preys, the lady beetles often consume carbohydrate‐rich food like nectar or honeydew. However, most studies on nutrition regulation of carnivores mainly focus on protein and lipid, two major macronutrients in preys. In this study, nutrition regulation of protein and carbohydrate has been investigated in the 4th instar larvae ofH. axyridisusing Geometric Framework. We provided the insects two pairs of foods, one a protein‐biased one and the second carbohydrate‐biased, to determine the intake target. We then confined them to nutritionally imbalanced foods to examine how they regulated food intake to achieve maximal performance. The larvae performed well on the 2 foods that containing the closest P : C ratios to the intake target, but, surprisingly, the lipid content was much lower than that in the choice experiment. The lady beetles seemed to maintain the optimal lipid content by consuming carbohydrate‐rich food. Moreover, consuming the carbohydrate‐rich food was less metabolically expensive than the protein‐rich food. Therefore, switching behavior between plant and animal foods actually reflects their nutritive needs. These findings extended our understanding of predator forage behavior and its influence on food web in ecosystems, and shed light on the role of agri‐environment schemes in meeting the nutritional need of predators in field.
When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships
Authors: Sipiczki Matthias
Published: January 2022

DNA barcoding is based on the premise that the barcode sequences can distinguish individuals (strains) of different species because their sequence variation between species exceeds that within species. The primary barcodes used in fungal and yeast taxonomy are the ITS segments and the LSU (large subunit) D1/D2 domain of the homogenized multicopy rDNA repeats. The secondary barcodes are conserved segments of protein‐encoding genes, which usually have single copies in haploid genomes. This study shows that the analysis of barcode sequences fails to reconstruct accurate species trees and differentiate species when the organisms have chimeric genomes composed of admixed mosaics of different origins. It is shown that the type strains of 10 species of the pulcherrima clade of the ascomycetous yeast genus Metschnikowia cannot be differentiated with standard barcodes because their intragenomic diversity is comparable to or even higher than the interstrain diversity. The analysis of a large group of genes of the sequenced genomes of the clade and the viability and segregation of the hybrids of ex‐type strains indicate that the high intragenomic barcode differences can be attributed to admixed genome structures. Because of the mosaic structures of the genomes, the rDNA repeats do not form continuous arrays and thus cannot be homogenized. Since the highly diverse ITS and D1/D2 sequences of the type strains form a continuous pool including pseudogenes, the evolution of their rDNA appears to involve reticulation. The secondary barcode sequences and the nonbarcode genes included in the analysis show incongruent phylogenetic relationships among the type strains, which can also be attributed to differences in the phylogenetic histories of the genes.
Comparative evaluation of chemiluminescent immunoassay and enzyme‐linked immunosorbent assays for the diagnosis of West Nile virus infections
Authors: Gómez‐Vicente Esther , Garcia Rafael , Calatrava Elizabeth , Olivares Duran María Jose , Gutiérrez‐Bautista Juan Francisco , Rodriguez‐Granger Javier , Cobo Fernando , Navarro Mari Jose Maria , Sampedro‐Martinez Antonio
Published: January 2022

In August 2020, anew West Nile virus (WNV) outbreak affected 71 people with meningoencephalitis in Andalusia (Spain). Samples from these individuals were received in our laboratory, a regional Virus Referral Centre. The aim of this study was to compare the agreement, sensitivity and specificity of findings between the WNV VIRCLIA IgG and IgM assay (Vircell, Spain) and the WNV ELISA IgM and IgG assay (Euroimmun, Germany) and to compare the performance of WNV VIRCLIA IgM and Euroimmun ELISA for cerebrospinal fluid (CSF) diagnosis. The study included 24 CSF samples (paired with serum samples) and 247 serum samples from 217 patients with suspected WNV infection (1 or 2 per patient). The agreement between ELISA and CLIA tests for IgM and Ig G detection in serum was 93% (kappa index = 0.85) and 96% (kappa index = 0.89) respectively. Sensitivity values of ELISA and CLIA tests for IgM in serum samples were 96.7% and 98.9%, respectively, and specificity values were 96.4% and 95.4% respectively. Sensitivity values of ELISA and CLIA test for IgG in serum samples were 91.1% and 97%, respectively, and specificity values were 100% and 98.8% respectively. Results obtained with ELISA and CLIA tests in CSF samples showed 75% agreement between them (kappa index = 0.51). According to these findings, the WNV VIRCLIA IgM and IgG monotest offers an accurate qualitative detection of WNV in serum and CSF specimens.
Body shape variation in the Characid Psalidodon rivularis from São Francisco river, Southeast Brazil (Characiformes: Stethaprioninae)
Authors: Rodrigues‐Oliveira Igor Henrique , Kavalco Karine Frehner , Pasa Rubens
Published: January 2022

Psalidodon rivularis is a species of tetra endemic to the São Francisco River basin and, based on cytogenetic and molecular studies, represents a complex of species. The objective of the present work was to identify morphological differences in the body shape of seven populations of P. rivularis from the Upper and Middle São Francisco River basin through geometric morphometry. In all, we photographed 174 individuals on the right side of the body and 17 landmarks were digitized on each image. To study the effects of allometry on the shape, we performed regression analysis and, to study shape modulation at different collection points and sub‐basins, the canonical variation analyses. We found differences in shape between collection points and sub‐basins associated with relative body height and sub‐orbital plate recoil, in addition to a significant influence of size on specimen shape (allometry) associated with the ventral skull, orbits and sub‐orbital plate. We do not envision differences in body shape between males and females. Several works with fish relate body height with water velocity, while the sub‐orbital plate recoil shows a taxonomic or ecological potential, marking the main difference between the populations of the Upper and Middle São Francisco River.
Hypokalaemia in patients treated with intravenous flucloxacillin: Incidence and risk factors
Authors: Leegwater Emiel , Westgeest Annette C. , Schippers Emile F. , Wilms Erik B. , van Nieuwkoop Cees , Visser Loes E.
Published: January 2022

Introduction

Hypokalaemia is a potentially life‐threatening adverse event of flucloxacillin with unknown incidence. The risk of flucloxacillin‐induced hypokalaemia has recently been suggested to be increased among females compared to males. The aim of this study is to describe the incidence and to determine the influence of sex and other risk factors on flucloxacillin‐induced hypokalaemia.

Methods

A retrospective single‐centre cohort study was performed. Patients treated with intravenous flucloxacillin for >24 hours between January 2017 and October 2020, a baseline potassium level of ≥3.5 mmol/L and potassium measurement during treatment were included. The primary endpoint was incidence of hypokalaemia defined as the percentage of patients with a potassium measurement <3.5 mmol/L during flucloxacillin treatment. Logistic regression modelling was used to establish risk factors for hypokalaemia.

Results

A total of 835 patients were included, 58.2% male and median age 71.0 years (interquartile range 61.0‐81.0). The incidence of hypokalaemia was 23.7% (28.4% in females vs 20.4% in males). A dose‐dependent relation between sex and the incidence of hypokalaemia was found. The risk of hypokalaemia was 4.41 (95% confidence interval 1.47‐13.24) times higher in females compared to males when receiving a flucloxacillin dose of >8 g/24 h. No sex differences were found for lower daily doses. Other risk factors for hypokalaemia were older age, concomitant antibiotic use, lower bodyweight, lower baseline plasma potassium concentration and longer treatment duration.

Conclusion

Hypokalaemia is a frequent complication in patients treated with intravenous flucloxacillin. Females receiving >8 g intravenous flucloxacillin per day are more prone to develop hypokalaemia compared to males.