bluuebunny/crossref_metadata_2025 huggingface dataset:
Acute Appendicitis in Children During the COVID-19 Pandemic
Authors: Gaitero Tristán Jara , Souto Romero Henar , Escalada Pellitero Silvia , Espiñera Clara Rico , Andina Martín David , Espinosa Góngora Rocío , Martín Diaz María José , Leónidas Espinoza Manuel
Published: January 2021

Aim

The aim of this study was to describe the incidence of complicated appendicitis during the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic lockdown.

Methods

This was a retrospective study of pediatric patients diagnosed with acute appendicitis in a single pediatric institution that assumed care responsibility for most of the pediatric emergencies during the lockdown period in Madrid (Spain). A control group was made up of the same number of patients diagnosed the previous year.

Results

One hundred fifty-one patients diagnosed with acute appendicitis were included (77 during self-quarantine and 74 during the previous year). The incidence of complicated appendicitis was 38.9% versus 28.3%, showing no significant differences. The 2 groups were homogeneous, with no differences in time elapsed between symptom onset and first emergency department visit, laboratory test results, median length of stay, intensive care admissions, or patients correctly diagnosed on their first visit.

Conclusions

COVID-19 (coronavirus disease 2019) self-quarantine has not increased the incidence of complicated appendicitis, and children who developed complicated appendicitis did not have worse clinical outcomes. Parents did not delay presenting for medical attention, and emergency department pediatricians did not fail to diagnose this condition. Reorganization of hospital resources, fast-track treatment protocols for noncomplicated appendicitis, and extended use of home-stay hospitalization for complicated appendicitis could have contributed to these favorable outcomes.
Triple-Negative Breast Cancer
Authors: Nunnery Sara E. , Mayer Ingrid A. , Balko Justin M.
Published: January 2021

Triple-negative breast cancer (TNBC) is pathologically defined by lack of expression of the estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 amplification and portends an aggressive clinical course with worse outcomes compared with other breast cancers. Until recently, standard treatment options consisted of sequential cytotoxic chemotherapies for both early and metastatic disease. Advances in sequencing technology have led to the identification of 4 main subtypes of TNBC based on recurrent genetic alterations, transcriptional patterns, and molecular features: basal-like 1 (BL1), basal-like 2 (BL2), mesenchymal (M), and luminal androgen receptor (LAR). Frequent alterations found in DNA damage response pathways, germline and somatic BRCA1/2 genes, PI3K signaling pathways, and the presence of androgen receptors and infiltrating immune cells could serve as actionable targets to optimize treatments and improve outcomes for patients with TNBC. Recent approvals for immune checkpoint inhibitors and the antibody-drug conjugate, sacituzumab govitecan-hziy, for advanced TNBC illustrate the advances in treatment that can result from these molecular discoveries. This review will explore the molecular subtypes of TNBC and their distinct characteristics, as well as highlight the molecular features and potential “drivers” that have been identified as promising targets for new treatment strategies.
Adjuvant and Neoadjuvant Treatment of Triple-Negative Breast Cancer With Chemotherapy
Authors: Marra Antonio , Curigliano Giuseppe
Published: January 2021

Triple-negative breast cancer (TNBC) accounts for 15% to 20% of all invasive breast carcinomas and is defined by the lack of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Although TNBC is characterized by high rates of disease recurrence and worse survival, it is significantly more sensitive to chemotherapy as compared with other breast cancer subtypes. Accordingly, despite great efforts in the genomic characterization of TNBC, chemotherapy still represents the cornerstone of treatment. For the majority of patients with early-stage TNBC, sequential anthracycline- and taxane-based neoadjuvant chemotherapy (NACT) represents the standard therapeutic approach, with pathological complete response that strongly correlates with long-term survival outcomes. However, some issues about the optimal neoadjuvant regimen, as well as the effective role of chemotherapy in patients with residual disease after NACT, are still debated. Herein, we will review the current evidences that guide the use of (neo)adjuvant chemotherapy in patients with early-stage TNBC. Furthermore, we will discuss current controversies, including the incorporation of platinum compounds to the neoadjuvant backbone and the optimal treatment for patients with residual disease after NACT. Lastly, we will outline potential future directions that can guide treatment escalation and de-escalation, as well as the development of new therapies. In our view, the application of multi-omics technologies, liquid biopsy assays, and machine learning algorithms are strongly warranted to pave the way toward personalized anticancer treatment for early-stage TNBC.
PARP Inhibitors in Triple-Negative Breast Cancer Including Those With BRCA Mutations
Authors: Layman Rachel M. , Arun Banu
Published: January 2021

Poly(ADP-ribose) polymerase (PARP) is involved in single-strand DNA break base excision repair. PARP inhibition causes synthetic lethality in breast cancers associated with germline BRCA1 and BRCA2 mutations and is routinely used in clinical practice for metastatic breast cancer. Breast cancers with homologous recombination deficiency or BRCAness, most commonly triple-negative breast cancers, may also benefit. Currently, PARP inhibitor use for triple-negative breast cancer with wild-type BRCA does not have definitive efficacy; however, this is an area of active research. Further clinical and translational data may identify additional patient populations that will benefit from PARP inhibitor therapy.
“Triple-Negative Breast Cancer Central Nervous System Metastases From the Laboratory to the Clinic”
Authors: Zimmer Alexandra S.
Published: January 2021

Triple-negative breast cancer (TNBC) accounts for 15% to 20% of breast cancers and has an incidence as high as 50% of brain metastases once patients develop advanced disease. The lack of targeted and effective therapies, characteristic of this subtype of breast cancer, is especially evident once central nervous system (CNS) metastases occur. Compared with other subtypes of breast cancer, TNBC patients have the shorter interval from diagnosis to development of brain metastases and the shorter overall survival once they occur, a median of 4 to 6 months. Preclinical studies of TNBC and CNS microenvironment are actively ongoing, clarifying mechanisms and orienting more effective approaches to therapy. While the first drugs have been specifically approved for use in metastatic TNBC, data on their CNS effect are still awaited.
Development and Validation of a Diagnostic Nomogram for the Preoperative Differentiation Between Follicular Thyroid Carcinoma and Follicular Thyroid Adenomas
Authors: Tang Pengzhou , Ren Caiyue , Shen Lijuan , Zhou Zhengrong
Published: January 2021

Objective

The aim of the study was to construct and validate a nomogram for differentiating follicular thyroid carcinoma (FTC) from follicular thyroid adenoma (FTA).

Methods

Two hundred patients with pathologically confirmed thyroid follicular neoplasms were retrospectively analyzed. The patients were randomly divided into a training set (n = 140) and validation set (n = 60). Baseline data including demographics, CT (computed tomography) signs, and radiomic features were analyzed. Predictive models were developed and compared to build a nomogram. The predictive effectiveness of it was evaluated by the area under receiver operating characteristic curve (AUC).

Results

The CT model, radiomic model and combination model showed excellent discrimination (AUCs [95% confidence interval] = 0.847 [0.766–0.928], 0.863 [0.746–0.932], 0.913 [0.850–0.975]). The nomogram based on the combination model showed remarkable discrimination in the training and validation sets. The calibration curves suggested good consistency between actual observation and prediction.

Conclusions

This study proposed a nomogram that can accurately and intuitively predict the malignancy potential of follicular thyroid neoplasms.
Repair, Reconstruct, or Divert
Authors: Tang Andrew , Ahmad Usman , Raja Siva , Siddiqui Hafiz U. , Sinopoli Jillian N. , O’Dell Alexander , Pande Amol , Blackstone Eugene H. , Murthy Sudish C.
Published: January 2021

Objectives:

The aim of this study was to determine differences in esophageal perforation populations undergoing different advanced interventions for perforated esophagus and identify predictors of treatment outcomes.

Summary Background Data:

Contained esophageal perforation can often be managed expectantly, but uncontained perforation is uniformly fatal without invasive intervention. Treatment options for the latter range from simple endoscopic control through advanced intervention. Clinical presentation varies greatly and directs which intervention is most appropriate.

Methods:

From 1996 to 2017, 335 patients were treated for esophageal perforation, and 166 for advanced interventions: 74 primary repair with tissue flap (repair), 26 esophagectomy and gastric pull-up (resection), and 66 esophagectomy and immediate diversion with planned delayed reconstruction (resection-diversion). Patient characteristics, clinical presentation, operative outcomes, and survival were abstracted. Pittsburgh Severity Scores (PSS) were retrospectively calculated. Random survival forest analysis was performed for 90-day mortality and competing risks for reconstruction after resection-diversion.

Results:

Repair and resection patients had lower PSS than resection-diversion patients (3 vs 3 vs 6, respectively). Ninety-day mortality for repair, resection, and resection-diversion was 11% vs 7.7% vs 23%, and 5-year survival was 71% vs 63% vs 47%. Risk of death after resection-diversion was highest within 1 year, but 52% of patients had reconstruction of the upper alimentary tract within 2 years.

Conclusions:

Several advanced interventions exist for critically ill patients with uncontained esophageal perforation. Repair and organ preservation are always preferred; however, patients at extremes of illness might best be treated with resection-diversion, with the understanding that the competing risk of death may preclude eventual reconstruction.
Methods for frailty screening and geriatric assessment in older adults with cancer
Authors: Puts Martine , Soo Wee Kheng , Szumacher Ewa , Decoster Lore
Published: January 2021

Purpose of review

This review highlights the latest development in the use of geriatric assessment(GA) and frailty assessment for older adults with cancer.

Recent findings

From 2019, there were six large randomized controlled trials (RCTs) completed of GA for older adults with cancer, as well as several studies of frailty screening tools.

The findings in this review highlight the benefits of implementing GA, followed by interventions to address the identified issues (GA -guided interventions). Four of six RCTs that implemented GA for older adults with cancer showed positive impact on various outcomes, including treatment toxicity and quality of life. GA implementation varied significantly between studies, from oncologist acting on GA summary, geriatrician comanagement, to full GA by a multidisciplinary team. However, there were several barriers reported to implementing GA for all older adults with cancer, such as access to geriatrics and resource issues. Future research needs to elucidate how to best operationalize GA in various cancer settings. The authors also reviewed frailty screening tools and latest evidence on their use and impact.
A meta-analysis of the diagnostic accuracy of chest ultrasound for the diagnosis of occult penetrating cardiac injuries in hemodynamically stable patients with penetrating thoracic trauma
Authors: Manzano-Nunez Ramiro , Gomez Alexandra , Espitia David , Sierra-Ruiz Melibea , Gonzalez Jessica , Rodriguez-Narvaez Jose G. , Castillo Andrea C. , Gonzalez Alejandro , Orjuela Jose , Orozco-Martin Viviana , Bernal Felipe , Giron Felipe , Rios Angela C. , Carranza Paola , Gonzalez-Hadad Adolfo , García-Perdomo Herney A. , García Alberto F.
Published: January 2021

BACKGROUND

We performed a systematic review (SR) and meta-analysis (MA) to determine the diagnostic accuracy of chest ultrasound (US) compared with a pericardial window (PW) for the diagnosis of occult penetrating cardiac injuries in hemodynamically stable patients with penetrating thoracic trauma.

METHODS

A literature search in five databases identified relevant articles for inclusion in this SR and MA. Studies were eligible if they evaluated the diagnostic accuracy of chest US, compared with a PW, for the diagnosis of occult penetrating cardiac injuries in hemodynamically stable patients presenting with penetrating thoracic trauma. Two investigators independently assessed articles for inclusion and exclusion criteria and selected studies for final analysis. Methodological quality was evaluated using Quality Assessment of Diagnostic Accuracy Studies-2. We performed a MA of binary diagnostic test accuracy within the bivariate mixed-effects logistic regression modeling framework.

RESULTS

We included five studies in our SR and MA. These studies included a total of 556 trauma patients. The MA found that, compared with PW, the US was 79% sensitive and 92% specific for detecting occult penetrating cardiac injuries in hemodynamically stable patients. The presence of a concomitant left hemothorax was frequent in patients with false-negative results.

CONCLUSION

This SR and MA found that, compared with PW, US was 79% sensitive and 92% specific for detecting occult penetrating cardiac injuries in hemodynamically stable patients with penetrating thoracic trauma. Caution interpretation of pericardial US results is suggested in the presence of left hemothorax. In these cases, a second diagnostic test should be performed.

LEVEL OF EVIDENCE

Systematic Review and Meta-analysis, level II.
Increasing BMI is associated with higher mortality, worsening outcomes and highly specific injury patterns following trauma: A multi-institutional analysis of 191,274 patients
Authors: Fakhry Samir M. , Morse Jennifer L. , Garland Jeneva M. , Wilson Nina Y. , Shen Yan , Wyse Ransom J. , Watts Dorraine D.
Published: January 2021

BACKGROUND

As the prevalence of obesity has increased, trauma centers are faced with managing this expanding demographics’ unique care requirements. Research on the effects of body mass index (BMI) in trauma patients remains conflicting. This study aims to evaluate the impact of BMI on patterns of injury and patient outcomes following trauma.

METHODS

Patients from 87 hospitals’ trauma registries were selected. Those missing height, weight, disposition, or who died in the emergency department were excluded. The BMI categories were calculated from admission height and weight and verified against the electronic medical records. Patients were grouped by the National Institutes of Health–defined obesity class and compared by rate of mortality and in-hospital complications. Logistic regression was used to estimate associations, adjusting for age, gender, race, Injury Severity Score, and number of comorbidities.

RESULTS

There were 191,274 patients, 53% male; mean age was 60.4 years, mean Glasgow Coma Scale score 14.4, mean Injury Severity Score of 8.8, and 40.4% normal weight. Increased BMI was associated with an injury pattern of increased rates of extremity fractures (humerus, femur, tibia/fibula) and decreased rates of hip fractures and head injuries. Compared with the normal weight group, patients were more likely to die if they were Underweight (adjusted odds ratio [AOR], 1.18; 95% confidence interval [CI], 1.01–1.38), obese class II (AOR, 1.24; 95% CI, 1.07–1.45), or obese class III (AOR, 1.55; 95% CI, 1.29–1.87). Obese class III was associated with higher odds of a National Trauma Data Standard complication (AOR, 1.20; 95% CI, 1.11–1.30).

CONCLUSION

In this large multicenter study, increasing BMI and lower than normal BMI were strongly associated with higher mortality. Increasing BMI was also associated with longer length of stay, increased complications, and unique injury patterns. These untoward outcomes, coupled with a distinct injury pattern, warrant care guidelines specific to trauma patients with higher BMI, as well as those with BMI lower than normal.

LEVEL OF EVIDENCE

Epidemiological, Level III.
A clinical practice guideline using percentage of predicted forced vital capacity improves resource allocation for rib fracture patients
Authors: Billings Joshua D. , Khan Abid D. , Clement L. Paige , Douville Alyssa A. , Brown Eric W. , Schroeppel Thomas J.
Published: January 2021

BACKGROUND

Predicting rib fracture patients that will require higher-level care is a challenge during patient triage. Percentage of predicted forced vital capacity (FVC%) incorporates patient-specific factors to customize the measurements to each patient. A single institution transitioned from a clinical practice guideline (CPG) using absolute forced vital capacity (FVC) to one using FVC% to improve triage of rib fracture patients. This study compares the outcomes of patients before and after the CPG change.

METHODS

A review of rib fracture patients was performed over a 3-year retrospective period (RETRO) and 1-year prospective period (PRO). RETRO patients were triaged by absolute FVC. Percentage of predicted FVC was used to triage PRO patients. Demographics, mechanism, Injury Severity Score, chest Abbreviated Injury Scale score, number of rib fractures, tube thoracostomy, intubation, admission to intensive care unit (ICU), transfer to ICU, hospital length of stay (LOS), ICU LOS, and mortality data were compared. A multivariable model was constructed to perform adjusted analysis for LOS.

RESULTS

There were 588 patients eligible for the study, with 269 RETRO and 319 PRO patients. No significant differences in age, gender, or injury details were identified. Fewer tube thoracostomy were performed in PRO patients. Rates of intubation, admission to ICU, and mortality were similar. The PRO cohort had fewer ICU transfers and shorter LOS and ICU LOS. Multivariable logistic regression identified a 78% reduction in odds of ICU transfer among PRO patients. Adjusted analysis with multiple linear regression showed LOS was decreased 1.28 days by being a PRO patient in the study (B = −1.44; p < 0.001) with R2 = 0.198.

CONCLUSION

Percentage of predicted FVC better stratified rib fracture patients leading to a decrease in transfers to the ICU, ICU LOS, and hospital LOS. By incorporating patient-specific factors into the triage decision, the new CPG optimized triage and decreased resource utilization over the study period.

LEVEL OF EVIDENCE

Therapeutic/Care Management. Trauma, Rib, Triage, level IV.
Prevalence of and Factors Associated With Sarcopenia Among Older Adults With Knee Osteoarthritis
Authors: Thaweechotiphat Chanthanee , Kuptniratsaikul Vilai , Boonjareonbuathong Suroj , Akkathep Piyapong , Suesuwan Oiythip
Published: January 2021

Objective:

To determine the prevalence of sarcopenia in knee osteoarthritis (SKOA) and associated factors among age, gender, body mass index (BMI), nutritional status, knee pain score, knee pain duration, physical activity, and exercise frequency.

Methods:

Knee osteoarthritis (OA) and sarcopenia were diagnosed using American College of Rheumatology and Asian Working Group for Sarcopenia criteria, respectively.

Results:

Prevalence of SKOA using grip strength and quadriceps strength was 2.2% and 9.4%, respectively. There was no significant association between sarcopenia and knee OA. Low BMI and poor nutritional status were significantly associated with SKOA.

Conclusions:

No association between sarcopenia and knee OA was found in this study.
Muscle-Specific Tyrosine Kinase Antibody Positive Myasthenia Gravis With Peripheral Nerve Hyperexcitability: Case Report and Literature Review
Authors: Yang Li
Published: January 2021

Objectives

Administration of acetylcholinesterase inhibitors can bring about peripheral nerve hyperexcitability symptom in muscle-specific tyrosine kinase antibody positive myasthenia gravis, but the changes in electromyography before and after drug withdrawal have not been described in detail.

Methods

Electromyography was performed on a case of muscle-specific tyrosine kinase antibody positive myasthenia gravis with peripheral nerve hyperexcitability correlated with the administration of pyridostigmine bromide before and after drug withdrawal, respectively.

Results

Afterdischarges close after M waves appeared on the tibial nerve, common peroneal nerve, median nerve, and ulnar nerve, and these presented unique characteristics in repetitive nerve stimulation. Ten days after pyridostigmine bromide withdrawal, the second electromyography examination was carried out and showed that the afterdischarges on all nerves disappeared dramatically and the amplitude of tibial nerve F waves was elevated than before.

Conclusions

Afterdischarges can be an important indicator of muscle-specific tyrosine kinase antibody positive myasthenia gravis with peripheral nerve hyperexcitability correlated with acetylcholinesterase inhibitors.
Bitemporal Hemianopia Secondary to Acute Zonal Occult Outer Retinopathy
Authors: Zaslavsky Kirill , Eshtiaghi Arshia , Jeeva-Patel Trishal , Christakis Panos G. , Margolin Edward
Published: January 2021

A 58-year-old man noticed shadows in the temporal visual field of each eye and photopsias within these scotomas for the past year. Formal visual fields demonstrated bitemporal hemianopia. MRI of the sella was normal, but fundus autofluorescence (FAF) demonstrated an area of hyperautofluorescence in the nasal retina of each eye corresponding to the loss of retinal pigment epithelium and photoreceptors. A diagnosis of acute zonal occult outer retinopathy was made based on the presence of trizonal involvement on FAF. This case is a reminder that bitemporal hemianopia can be caused by a retinopathy involving nasal retina in each eye, and FAF is a very useful test when assessing patients with suspected outer retinal disorders.
Importance of the “Rule of the Pupil” in the Modern Neuroimaging Era
Authors: Garg Anubhav , Micieli Jonathan A.
Published: January 2021

The “Rule of the Pupil” states that when aneurysms compress the oculomotor nerve, a dilated or sluggishly reactive pupil will result. In previous decades, when cerebral angiography was required to detect an intracranial aneurysm, the “Rule of the Pupil” was used to determine the relative risk of angiography and the likelihood of aneurysmal compression in patients with third nerve palsies (3NPs). Noninvasive imaging including computed tomography angiography (CTA) and magnetic resonance angiography has become readily accessible and can detect all aneurysms large enough to cause 3NPs. It is therefore recommended that all patients with 3NP undergo neuroimaging regardless of pupil status because the consequences of missing an aneurysm are high. The question therefore remains as to whether the “Rule of the Pupil” still has relevance in today's era of modern neuroimaging. We describe a 73-year-old man who developed a left complete, pupil-sparing 3NP and was found to have a paraclinoid meningioma in the left cavernous sinus. As compressive lesions are expected to impair the iris sphincter muscle, no intervention was recommended and his 3NP spontaneously improved within 3 months. We also describe a 54-year-old woman with diabetes and a complete 3NP with a dilated, nonreactive pupil. Initial CTA was reported as normal, but re-review of imaging revealed a posterior communicating artery aneurysm and immediate intervention to coil the aneurysm occurred. The “Rule of the Pupil” is still important in the modern neuroimaging era as demonstrated in cases of incidentally found lesions along the course of the oculomotor nerve and missed radiological findings.
The gut microbiota metabolite propionate ameliorates intestinal epithelial barrier dysfunction-mediated Parkinson’s disease via the AKT signaling pathway
Authors: Huang Tingting , Shi Hongjuan , Xu Yuanfeng , Ji Lili
Published: January 2021

Objective

Parkinson’s disease is a common neurodegenerative disease. Here, we investigated the protective effect and potential mechanisms of propionate on the intestinal epithelial barrier in mice with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinson’s disease.

Methods

Gas chromatography was used to determine short-chain fatty acids (SCFA) concentrations in the fecal samples of Parkinson’s disease patients and healthy controls. The stepping test was used to analyze forelimb akinesia, whisker test was used to analyze sensorimotor injury, cylinder test was used to analyze sensorimotor function, and Western blotting was used to analyze protein expression.

Results

The concentrations of SCFAs, including acetate, butyrate and propionate, were significantly downregulated in the fecal samples of Parkinson’s disease patients, and among the SCFAs, propionate decreased the most. Propionate administration improved the stepping test score, whisker test score and cylinder test score of MPTP-induced Parkinson’s disease mice. Additionally, propionate administration increased the protein expression of zonula occludens-1 and occludin. Moreover, the effects of propionate on motor behavior and the intestinal epithelial barrier were dependent on the proteirrserinc-threonine kinases (AKT) signaling pathway. More importantly, treatment with SC79, a specific AKT agonist, abolished the effects of propionate on the intestinal epithelial barrier and motor behavior.

Conclusion

Our results demonstrated that propionate, which was decreased in the fecal samples of Parkinson’s disease patients, exerted beneficial effects on intestinal epithelial barrier function and improved motor behavior in MPTP-induced Parkinson’s disease mice through the AKT signaling pathway.
Morphological and phylogeographic evidence for budding speciation: an example in hominins
Authors: Parins-Fukuchi Caroline
Published: January 2021

Parametric phylogenetic approaches that attempt to delineate between distinct ‘modes’ of speciation (splitting cladogenesis, budding cladogenesis and anagenesis) between fossil taxa have become increasingly popular among comparative biologists. But it is not yet well understood how clearly morphological data from fossil taxa speak to detailed questions of speciation mode when compared with the lineage diversification models that serve as their basis. In addition, the congruence of inferences made using these approaches with geographical patterns has not been explored. Here, I extend a previously introduced maximum-likelihood approach for the examination of ancestor–descendant relationships to accommodate budding speciation and apply it to a dataset of fossil hominins. I place these results in a phylogeographic context to better understand spatial dynamics underlying the hypothesized speciation patterns. The spatial patterns implied by the phylogeny hint at the complex demographic processes underlying the spread and diversification of hominins throughout the Pleistocene. I also find that inferences of budding are driven primarily by stratigraphic, versus morphological, data and discuss the ramifications for interpretations of speciation process in hominins specifically and from phylogenetic data in general.
Fish from urban rivers and with high pollutant levels have shorter telomeres
Authors: Molbert Noëlie , Angelier Frédéric , Alliot Fabrice , Ribout Cécile , Goutte Aurélie
Published: January 2021

Environmental pressures, such as urbanization and exposure to pollutants may jeopardize survival of free-living animals. Yet, much remains to be known about physiological and ecological responses to currently-released pollutants, especially in wild vertebrate ectotherms. We tested the effect of urbanization and pollution (phthalates, organochlorine and pyrethroid pesticides, polychlorobiphenyls, polybromodiphenylethers, polycyclic aromatic hydrocarbons, and some of their metabolites) on telomere length, a suggested biomarker of life expectancy, in the European chub,
Squalius cephalus
, from urban and agricultural rivers of the Marne hydrographic network, France. We showed that telomere length was reduced in chub from urban rivers. Moreover, among the wide range of anthropogenic contaminants investigated, high levels of phthalate metabolites in liver were associated with shorter telomeres. This study suggests that urbanization and chemical pollution may compromise survival of wild fish, by accelerating telomere attrition.
Joint assessment of density correlations and fluctuations for analysing spatial tree patterns
Authors: Villegas P. , Cavagna A. , Cencini M. , Fort H. , Grigera T. S.
Published: January 2021

Inferring the processes underlying the emergence of observed patterns is a key challenge in theoretical ecology. Much effort has been made in the past decades to collect extensive and detailed information about the spatial distribution of tropical rainforests, as demonstrated, e.g. in the 50 ha tropical forest plot on Barro Colorado Island, Panama. These kinds of plots have been crucial to shed light on diverse qualitative features, emerging both at the single-species or the community level, like the spatial aggregation or clustering at short scales. Here, we build on the progress made in the study of the density correlation functions applied to biological systems, focusing on the importance of accurately defining the borders of the set of trees, and removing the induced biases. We also pinpoint the importance of combining the study of correlations with the scale dependence of fluctuations in density, which are linked to the well-known empirical Taylor’s power law. Density correlations and fluctuations, in conjunction, provide a unique opportunity to interpret the behaviours and, possibly, to allow comparisons between data and models. We also study such quantities in models of spatial patterns and, in particular, we find that a spatially explicit neutral model generates patterns with many qualitative features in common with the empirical ones.
Granular size segregation in silos with and without inserts
Authors: Cliff A. , Fullard L. A. , Breard E. C. P. , Dufek J. , Davies C. E.
Published: January 2021

The storage of granular materials is a critical process in industry, which has driven research into flow in silos. Varying material properties, such as particle size, can cause segregation of mixtures. This work seeks to elucidate the effects of size differences and determine how using a flow-correcting insert mitigates segregation during silo discharge. A rotating table was used to collect mustard seeds discharged from a three-dimensional (3D)-printed silo. This was loaded with bidisperse mixtures of varying proportions. A 3D-printed biconical insert was suspended near the hopper exit to assess its effect on the flow. Samples were analysed to determine the mass fractions of small particle species. The experiments without the insert resulted in patterns consistent with segregation. Introducing the insert into the silo eliminated the observed segregation during discharge. Discrete element method simulations of silo discharge were performed with and without the insert. These results mirrored the physical experiment and, when complimented with coarse graining analysis, explained the effect of the insert. Most of the segregation occurs at the grain–air free surface and is driven by large velocity gradients. In the silo with an insert, the velocity gradient at the free surface is greatly reduced, hence, so is the degree of segregation.
Tunable mechanical diode of nonlinear elastic metamaterials induced by imperfect interface
Authors: Li Zhen-Ni , Wang Yi-Ze , Wang Yue-Sheng
Published: January 2021

In this investigation, the non-reciprocal transmission in a nonlinear elastic metamaterial with imperfect interfaces is studied. Based on the Bloch theorem and stiffness matrix method, the band gaps and transmission coefficients with imperfect interfaces are obtained for the fundamental and double frequency cases. The interfacial influences on the transmission behaviour are discussed for both the nonlinear phononic crystal and elastic metamaterial. Numerical results for the imperfect interface structure are compared with those for the perfect one. Furthermore, experiments are performed to support the theoretical analysis. The present research is expected to be helpful to design tunable devices with the non-reciprocal transmission and diode behaviour of the elastic metamaterial.
Nocardioides cynanchi sp. nov., isolated from soil of rhizosphere of Cynanchum wilfordii
Authors: Suh Min Kuk , Lee Keun Chul , Kim Ji-Sun , Han Kook-Il , Kim Han Sol , Eom Mi Kyung , Shin Yong Kook , Lee Jung-Sook
Published: January 2021

A novel actinobacterial strain, SB3-45T, was isolated from soil of Cynanchum wilfordii rhizosphere, Jaecheon-si, Chungcheongbuk-do, Republic of Korea. Strain SB3-45T, was Gram-stain-positive, aerobic and coccoid to short rod-shaped bacterium. Growth occurred at 4–37 °C (optimum 28 °C), pH 5–8 (optimum pH 7) and 0–2.5 % NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain SB3-45T belonged to the genus

Nocardioides

and was closely related to

Nocardioides opuntiae

OS-21T (96.2%) and

Nocardioides panacihumi

Gsoil 616T (95.9%). ll-DAP as the diamino acid in the peptidoglycan and the menaquinone MK-8(H4) as the predominant isoprenoid quinone were detected. The polar lipids of strain SB3-45T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unidentified phospholipid. The major cellular fatty acids (>5%) of strain SB3-45T were iso-C16 : 0, C18 : 1 ω9c and C17 : 0. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-45T represents a novel species of the genus Nocardioides, for which the name Nocardioides cynanchi sp.nov. is proposed. The type strain is SB3-45T (=KCTC 49133T=NBRC 114107T).
Complement activity in myasthenia gravis is independent of autoantibody titer and disease severity
Authors: Fichtner Miriam L. , Hoarty Michelle D. , Vadysirisack Douangsone D. , Nowak Richard J. , O’Connor Kevin C.
Published: January 2021

Acetylcholine receptor (AChR) autoantibodies, found in patients with autoimmune myasthenia gravis (MG), can directly contribute to disease pathology through activation of the classical complement pathway. Accordingly, complement inhibitors are used as a therapeutic strategy, but the response can be heterogeneous even though AChR autoantibodies are present. The mechanisms underlying the variable response are not defined. Yet there is a need for further understanding so that responses can be better predicted. There is a broad spectrum of circulating complement activity levels activity among MG patients. It is not clear whether this activity associates with disease burden or the circulating levels of autoantibodies. We measured complement activity and investigated these associations in MG patients as a means to explore candidate biomarkers. Most study subjects had complement activity within the range defined by healthy controls and no association between this activity and disease burden or AChR autoantibody titer was observed. Assays measuring the complement activating properties of AChR autoantibodies are needed to identifying patients expected to respond to complement inhibitor-based treatments.
Estimating Effect-sizes to Infer if COVID-19 transmission rates were low because of Masks, Heat or High because of Air-conditioners, Tests
Authors: Sruthi C. K. , Biswal Malay Ranjan , Saraswat Brijesh , Joshi Himanshu , Prakash Meher K.
Published: January 2021

How does one interpret the observed increase or decrease in COVID-19 case rates? Did the compliance to the non-pharmaceutical interventions, seasonal changes in the temperature influence the transmission rates or are they purely an artefact of the number of tests? To answer these questions, we estimate the effect-sizes from these different factors on the reproduction ratios (Rt) from the different states of the USA during March 9 to August 9. Ideally Rt should be less than 1 to keep the pandemic under control and our model predicts many of these factors contributed significantly to the Rt’s: Post-lockdown opening of the restaurants and nightclubs contributed 0.04 (CI 0.04-0.04) and 0.11 (CI. 0.11-0.11) to Rt. The mask mandates helped reduce Rt by 0.28 (CI 0.28-0.29)), whereas the testing rates which may have influenced the number of infections observed, did not influence Rt beyond 10,000 daily tests 0.07 (CI -0.57-0.42). In our attempt to understand the role of temperature, the contribution to the Rt was found to increase on both sides of 55 F, which we infer as a reflection of the climatization needs. A further analysis using the cooling and heating needs showed contributions of 0.24 (CI 0.18-0.31) and 0.31 (CI 0.28-0.33) respectively. The work thus illustrates a data-driven approach for estimating the effect-sizes on the graded policies, and the possibility of prioritizing the interventions, if necessary by weighing the economic costs and ease of acceptance with them.
Development and validation of a multiple-choice question-based delirium care knowledge quiz for critical care nurses
Authors: Ho Mu-Hsing
Published: January 2021

Aims

To develop and psychometrically test a multiple choice questions (MCQs)-based quiz of delirium care knowledge for critical care nurses.

Design

Instrument development and psychometric evaluation study.

Methods

The development and validation process including two phases. Phase I focused on the quiz development, conducted by the following steps: (1) generated initial 20-item pool; (2) examined content validity and (3) face validity; (4) conducted pilot testing, data were collected from 217 critical care nurses via online survey during 01 October to 07 November, 2020; (5) performed item analysis and eliminated items based on the item difficulty and discrimination indices. The MCQs quiz was finalised through the development process. Then, phases II emphasised the quiz validation, to estimate the internal consistency, split-half and test-retest reliability, and construct validity using parallel analysis with the exploratory factor analysis (EFA).

Results

A final 16-item MCQs quiz was emerged from the item analysis. The Kuder– Richardson Formula 20 coefficient for the overall quiz showed good internal consistency (0.85), and the intraclass correlation coefficient with a 30-day interval also indicated that the questionnaire had satisfactory stability (0.96). The EFA confirmed appropriate construct validity for the quiz, four factors could explain the total variance of 60.87%.

Conclusion

This study developed the first MCQs quiz for delirium care knowledge and it is a reliable and valid tool that can be implemented to assess the level of delirium care knowledge.

Impact

This study offers an evidence-based quiz designed for future research and education purposes in delirium care that has significant implications for knowledge test by using MCQs in clinical practice.
Individual-Specific Areal-Level Parcellations Improve Functional Connectivity Prediction of Behavior
Authors: Kong Ru , Yang Qing , Gordon Evan , Xue Aihuiping , Yan Xiaoxuan , Orban Csaba , Zuo Xi-Nian , Spreng Nathan , Ge Tian , Holmes Avram , Eickhoff Simon , Yeo B.T. Thomas
Published: January 2021

Resting-state functional MRI (rs-fMRI) allows estimation of individual-specific cortical parcellations. We have previously developed a multi-session hierarchical Bayesian model (MS-HBM) for estimating high-quality individual-specific network-level parcellations. Here, we extend the model to estimate individual-specific areal-level parcellations. While network-level parcellations comprise spatially distributed networks spanning the cortex, the consensus is that areal-level parcels should be spatially localized, i.e., should not span multiple lobes. There is disagreement about whether areal-level parcels should be strictly contiguous or comprise multiple non-contiguous components, therefore we considered three areal-level MS-HBM variants spanning these range of possibilities. Individual-specific MS-HBM parcellations estimated using 10min of data generalized better than other approaches using 150min of data to out-of-sample rs-fMRI and task-fMRI from the same individuals. Resting-state functional connectivity (RSFC) derived from MS-HBM parcellations also achieved the best behavioral prediction performance. Among the three MS-HBM variants, the strictly contiguous MS-HBM (cMS-HBM) exhibited the best resting-state homogeneity and most uniform within-parcel task activation. In terms of behavioral prediction, the gradient-infused MS-HBM (gMS-HBM) was numerically the best, but differences among MS-HBM variants were not statistically significant. Overall, these results suggest that areal-level MS-HBMs can capture behaviorally meaningful individual-specific parcellation features beyond group-level parcellations. Multi-resolution trained models and parcellations are publicly available (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Kong2022_ArealMSHBM).
Combined Enhanced Biological Phosphorus Removal (EBPR) and Nitrite Accumulation for Treating High-strength Wastewater
Authors: Yuan Zhihang , Kang Da , Li Guangyu , Lee Jangho , Han IL , Wang Dongqi , Zheng Ping , Reid Matthew C. , Gu April Z.
Published: January 2021

The enhanced biological phosphorus removal (EBPR) has been widely applied in treating domestic wastewater, while the performance on high-strength P wastewater is less investigated and the feasibility of coupling with short-cut nitrogen removal process remains unknown. This study first achieved the simultaneous high-efficient P removal and stable nitrite accumulation in one sequencing batch reactor for treating the synthetic digested manure wastewater. The average effluent P could be down to 0.8 ± 1.0 mg P/L and the P removal efficiency was 99.5 ± 0.8%.CandidatusAccumulibacter was the dominant polyphosphate accumulating organism (PAO) with the relative abundance of 14.2-33.1% in the reactor. Examination of the micro-diversity ofCandidatusAccumulibacter using 16s rRNA gene-based oligotyping analysis revealed one unique Accumulibacter oligotype that different from the conventional system, which accounted for 64.2-87.9% of the total Accumulibacter abundance. The presence of high-abundant glycogen accumulating organisms (GAO) (15.6-40.3%,DefluviicoccusandCandidatusCompetibacter) did not deteriorate the EBPR performance. Moreover, nitrite accumulation happened in the system with the effluent nitrite up to 20.4 ± 6.4 mg N/L and the nitrite accumulation ratio was nearly 100% maintained for 140 days (420 cycles).Nitrosomonaswas the dominant ammonia-oxidizing bacteria with relative abundance of 0.3-2.4% while nitrite-oxidizing bacteria were almost undetected (<0.1%). The introduction of extended anaerobic phase and high volatile fatty acid concentrations were proposed to be the potential selector forces to promote partial nitrification. This is the first study that combined EBPR with nitrite-accumulation for digested manure wastewater treatment, and it provided new sights in strategies to combine the EBPR and short-cut nitrogen removal via nitrite to achieve simultaneous nitrogen and phosphorus removal.
Cognitive function and vitamin B12 and D in elders from Ecuador
Authors: Veloz Andrés Fernando Vinueza , Arias Tannia Valeria Carpio , Mejía Jenifer Sthefania Vargas , Veloz Estephany Carolina Tapia , Andrade Jefferson Santigo Piedra , Cifuentes Tomás Marcelo Nicolalde , Aguirre Susana Isabel Heredia , Veloz María Fernanda Vinueza
Published: January 2021

Introduction

Current evidence still does not support the role of vitamin B12 or vitamin D in age-associated cognitive impairment.

Objective

Evaluate the association between vitamin B12 and D and cognitive function in elders.

Methodology

Sample included 1733 individuals 60 years old and older, who participated in the SABE study that was carried out in Ecuador. Cognitive function was measured using abbreviated version of minimental state examination (MMSE). Vitamin B12 and D were measured in blood. Data were analyzed through linear regression models with restricted cubic splines (RCSs). Models were adjusted by sex, years of education, region (urban highland, urban coast, rural highlands, rural coast), socioeconomic status, and ethnicity.

Results

Independently from sex, age, years of education, ethnicity, socioeconomic status and geographical zone of residence, we found that vitamin B12 but not vitamin D levels were associated with cognitive function in a representative group of Ecuadorian elders. Elders with lower levels of vitamin B12 showed lower MMSE scores in comparison to elders with higher levels of vitamin B12. Moreover, a statically significant non linear interaction was found between vitamin B12 and age with respect to cognitive function. In this way, we observed that in elders 75 years old and older whose levels of vitamin B12 were 271 pg/ml or less, the drop of cognitive function was particularly steep in comparison to elders whose levels of vitamin B12 were 647 pg/ml or more.

Conclusions

Low levels of vitamin B12 but not of vitamin D are associated with low cognitive functioning.
Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism
Authors: Srivastava Avi , Zakeri Mohsen , Sarkar Hirak , Soneson Charlotte , Kingsford Carl , Patro Rob
Published: January 2021

Transcript and gene quantification is the first step in many RNA-seq analyses. While many factors and properties of experimental RNA-seq data likely contribute to differences in accuracy between various approaches to quantification, it has been demonstrated (1) that quantification accuracy generally benefits from considering, during alignment, potential genomic origins for sequenced fragments that reside outside of the annotated transcriptome.

Recently, Varabyou et al. (2) demonstrated that the presence of transcriptional noise leads to systematic errors in the ability of tools — particularly annotation-based ones — to accurately estimate transcript expression. Here, we confirm the findings of Varabyou et al. (2) using the simulation framework they have provided. Using the same data, we also examine the methodology of Srivastava et al.(1) as implemented in recent versions of salmon (3), and show that it substantially enhances the accuracy of annotation-based transcript quantification in these data.