bluuebunny/crossref_metadata_2025 huggingface dataset:
143 Rh-Disease Awareness and Prevention (RhAP): Knowledge Assessment of Obstetrical Patients
Authors: Woolf Maya , Nallathamby Shanthiya , Gnanalingam Aasha , Sgro Michael , Berger Howard , Baker Jillian
Published: October 2021

Primary Subject area

Maternal-Fetal Medicine

Background

Rhesus hemolytic disease of the newborn (RhD) was once the most common and severe form of hemolytic disease of the newborn with outcomes including anemia, jaundice, stillbirth and death. Approximately 15% of Canadian women are Rh-negative, yet RhD is relatively unknown due to prevention by Rh immunoglobulin (RhIG). There is a need to advocate for the ongoing prevention of RhD in high-income countries (HICs) due to low incidence, vaccine hesitancy and misinformation, and in low-income countries (LICs) where lack of access to RhIG contributes to over 350,000 annual cases worldwide.

Objectives

Our present aim is to assess the current state of knowledge of RhD among women in our centre.

Design/Methods

Questionnaires were administered to a consecutive sample of pregnant women of all blood types (5-42 weeks gestation) attending an urban Obstetrics Clinic between January - March 2020, and included demographics and self-reporting of current RhD awareness.

Results

Of the 586 participants surveyed, 43% did not know their blood type and 16% identified as Rh-negative (Table 1). Sixty-one percent of participants recalled receiving information about their blood type, and only 31% knew their partner’s blood type. Only 45% of the Rh-negative subset (Table 2) in their third trimester (or postpartum) knew that they had been given RhIG (routinely offered at 28 weeks gestation). While 84% of Rh-negative women had received information about RhD from various sources (physician, online, etc.), there was a lack of depth in their knowledge with two-thirds having no knowledge of the common sequelae of RhD. The majority of Rh-negative participants expressed interest in contributing to local efforts (58/92), including interest in our advocacy group.

Conclusion

As expected, many participants did not know their Rh status, despite routine testing in pregnancy. Many were unaware of the potential sequelae associated with RhD and rationale for its prevention, even in the Rh-negative subgroup. Not all Rh-negative women were aware of having received RhIG, presumably having received it without knowledge or understanding. We are concerned that lack of awareness, especially among Rh-negative women in HICs may lead to increased complacency, RhIG refusal, and missed opportunities for patient self-advocacy. Our questionnaire results provide further impetus to advocate for increased RhD education for the patients and their care providers. Next steps include the creation of a patient-led focus group that aims to improve local and global awareness of RhD to help decrease the burden of this potentially devastating and preventable disorder.
144 Characterizing the Pain Experience of Children with Acute Gastroenteritis Based on Identified Pathogens
Authors: Ma Keon , Ali Samina , Xie Jianling , Maki Claudia , Lee Bonita , Chui Linda , Pang Xiao-Li , Zhuo Ran , Parsons Brendon , Vanderkooi Otto G , Poonai Naveen , MacDonald Shannon E , Tarr Phillip , Freedman Stephen
Published: October 2021

Primary Subject area

Emergency Medicine - Paediatric

Background

Many children with acute gastroenteritis (AGE) experience moderate-to-severe pain. To date, the relationship between specific enteropathogens and pain intensity in children with AGE is poorly characterized.

Objectives

To describe pain severity experienced by children with AGE, by enteropathogen type (i.e., bacteria, virus, co-detection) during the 24 hours prior to emergency department (ED) presentation and while in the ED. We also sought to describe analgesic medication use in AGE.

Design/Methods

Children 0 to under 18 years with symptoms of AGE (vomiting and/or diarrhea, less than 7 days duration) were prospectively recruited in two pediatric EDs from December 2014 to August 2018. Rectal swabs and stool specimens were analyzed with a commercial enteric panel, an in-house viral panel, and standard enteric bacterial culture. Pain severity was reported by caregivers, with input from the child whenever possible, using a validated 11-point Verbal Numerical Rating Scale from 0 (no pain) to 10 (maximum pain).

Results

2686 children with AGE participated in the study. The overall maximal mean pain score was 5.50 (SD 3.00) during the 24 hours preceding the ED visit. Children with bacteria detected in their stool had a significantly higher mean pain score (difference: 1.10 [95% CI: 0.36, 1.84]) prior to ED visit and 1.32 (95% CI: 0.54, 2.10) while in the ED, compared to those with no pathogen identified. They also had significantly higher mean pain scores (difference: 1.10 [95%CI: 0.39, 1.81]) prior to ED visit and 1.44 (95%CI: 0.69, 2.20) while in the ED when compared to AGE caused by a single virus. Using a multivariable regression model, the association between pain severity and enteropathogen type was no longer demonstrated; however, longer illness duration (p=0.01), fever (p < 0.0001), increased number of diarrheal (p < 0.0001) and vomiting (p=0.03) episodes, and respiratory symptoms (p=0.03) were all associated with greater pain at home. Overall, analgesic use was low, with 41.6% (1117/2686) and 20.0% (538/2686) of participants receiving an analgesic at home and in the ED, respectively.

Conclusion

Enteropathogen type was not predictive of greater pain severity after adjustment for clinical symptoms (i.e., vomiting and diarrhea). The clinical constellation of symptoms accompanying any particular pathogen may differ between pathogens, and this clinical picture may play the greater role in pain experience. Analgesic use was low in children with this painful condition.
150 Osteoporosis Risk Factors in Children with Cerebral Palsy
Authors: Spenard Sarah , Rahman Arifur , Power Heather , O'Dea Jennifer , Ricci M Florencia
Published: October 2021

Primary Subject area

Complex Care

Background

Cerebral palsy (CP) is a common motor disability in children. Due to their medical complexity, children with CP are prone to osteoporosis, and consequently, fractures. The prevalence of osteoporosis and its risk factors are poorly understood within this population.

Objectives

To determine the prevalence and predictors of osteoporosis among a provincial cohort of Canadian children with CP.

Design/Methods

We performed a retrospective descriptive cohort study in a single Canadian tertiary care pediatric hospital. The medical charts of the 187 children with CP currently followed by the rehabilitation team were reviewed. Primary outcomes were indicators of osteoporosis, including vertebral compression fractures (VCF), long bone fractures and BMD Z-score. Osteoporosis risk factors, including medications, chronic or endocrine disorders linked to secondary osteoporosis, feeding method, and mobilization level (GMFCS), were collected. Two-tail p-values were calculated using the Chi-squared Person’s cumulative test.

Results

Of the 187 included children, the majority were male (59%) and were living in a rural area (62%). Seven (3.7%) individuals met diagnostic criteria for osteoporosis with a VCF without history of high-energy trauma or local disease. Of these, four were females and three were males. Osteoporosis risk factors are presented in Table 1. GMFCS, feeding method and medications linked to secondary osteoporosis had a significant statistical difference in the children diagnosed with a VCF compared to participants without osteoporosis diagnostic criteria.

Conclusion

3.7% of children followed by the provincial rehabilitation team have osteoporosis. This is one of the first studies that establishes the frequency of osteoporosis among a provincial cohort of Canadian children with CP. Mobilization level, feeding method and consumption of medications linked to secondary osteoporosis seem to be major risk factors for osteoporosis in children with CP. Larger prospective studies are needed to confirm this association, in order to improve prevention strategies.
153 Cost of Hospitalization in Infants with Hypoxic Ischemic Encephalopathy Treated with Therapeutic Hypothermia in a Quebec Tertiary Neonatal Intensive Care Unit and Validation of the Canadian Neonatal Network Costing Algorithm
Authors: Basfar Wijdan , Jabbour Elias
Published: October 2021

Primary Subject area

Neonatal-Perinatal Medicine

Background

Therapeutic hypothermia (TH) is the standard treatment for neonatal hypoxic ischemic encephalopathy (HIE) to improve mortality and long-term impairment. Accurate costing algorithms are essential to evaluate cost-effective interventions and identify cost drivers.

Objectives

We aimed to validate the Canadian Neonatal Network (CNN) costing algorithm for HIE infants treated with TH against costs obtained from hospital-based finance software (CPSS) and compare the costs of TH for infants with mild/moderate to those with severe HIE. We aimed to validate the Canadian Neonatal Network (CNN) costing algorithm for HIE infants treated with TH against costs obtained from hospital-based finance software (CPSS) and compare the costs of TH for infants with mild/moderate to those with severe HIE.

Design/Methods

Retrospective cohort study including 98 infants admitted with HIE and receiving TH in a tertiary NICU between 2016 and 2018. Clinical characteristics and CNN costing data were collected from the local CNN database and actual cost were obtained from CPSS. The primary outcome was the difference in total hospital stay cost between CNN algorithm and CPSS. The differences between both algorithms were also identified in 8 different cost centres such as nursing, respiratory, imaging, etc. Costs per patients using both algorithms were compared using Pearson correlation coefficient (r) and paired t-test. Characteristics and costs per infant were compared between infants with mild/moderate HIE and those with severe HIE.

Results

Among the 98 patients with HIE that received TH, 2 (2%) had mild HIE, 75 (77%) had moderate HIE and 21 (21%) had severe HIE on admission. Mortality rate was 10% (10/98) and median length of stay was 12 days [IQR 10-16]. Total mean cost per infant using the CNN algorithm was $32,727 (SD $23,751 and correlated highly to the CPSS mean $28.373(SD $28.989) (r=0.93, p<0.01). There was no significant difference in mean total costs estimated between the algorithms ($1051, 95% CI $-1073, $3174). There was a strong correlation between cost estimates using the CNN algorithm and CPSS in nursing, physician, transfusion and indirect costs (r range 0.94-0.99) (Figure 1). Mean daily costs per infant with mild/moderate HIE ($1579, SD 808) were lower compared to infants with severe HIE ($2069, SD 1518). In both groups, daily costs were higher in the first days of hospitalization and slightly decreased over time (Figure 2).

Conclusion

The CNN algorithm accurately predicts hospital stay costs for infants diagnosed with HIE and received TH in our centre. Severity of encephalopathy and severity of illness are associated with higher hospital costs.
FIELD MEASUREMENT OF THE UNATTACHED FRACTION AND ACTIVITY CONCENTRATION RATIO OF RADON PROGENY IN TYPICAL DWELLINGS
Authors: Sun Changhao , Wang Yunxiang , Zhang Lei , Wang Hao , Guo Qiuju , Xiao Detao , Liang Juncheng , Wang Shanqiang
Published: October 2021

The unattached fraction (fp) and activity concentration ratio of radon progeny (${\boldsymbol C}_{{}{}^{\bf 218}\bf{Po}}:{\boldsymbol C}_{{}{}^{\bf 214}\bf{Pb}}:{\boldsymbol C}_{{}{}^{\bf 214}\bf{Bi}}$) are important for radon exposure dose evaluation. For getting these characteristic parameters in dwellings, a series of field measurement was carried out. For comparison, a semi-continuous measurement was carried out in an office room and outdoors. Results show that the average fp is 4.5% ± 2.2% and 3.8% ± 1.7% in city dwellings and in rural dwellings, respectively. The average activity concentration ratios are 1:0.94:0.70 for radon progeny and 1:0.07:0.06 for unattached radon progeny in city dwellings, while those in rural dwellings are 1:0.88:0.66 and 1:0.09:0.07. The average values of fp are 5.1% ± 0.9% and 5.4% ± 3.1% in the office room and in outdoors without significant difference. The average activity concentration ratios are 1:0.88:0.77 for radon progeny and 1:0.11:0.11 for unattached radon progeny in outdoors.
Associations of sleep measures with neural activations accompanying fear conditioning and extinction learning and memory in trauma-exposed individuals
Authors: Seo Jeehye , Oliver Katelyn I , Daffre Carolina , Moore Kylie N , Gazecki Samuel , Lasko Natasha B , Milad Mohammed R , Pace-Schott Edward F
Published: October 2021

Study Objectives

Sleep disturbances increase risk of posttraumatic stress disorder (PTSD). Sleep effects on extinction may contribute to such risk. Neural activations to fear extinction were examined in trauma-exposed participants and associated with sleep variables.

Methods

Individuals trauma-exposed within the past 2 years (N = 126, 63 PTSD) completed 2 weeks actigraphy and sleep diaries, three nights ambulatory polysomnography and a 2-day fMRI protocol with Fear-Conditioning, Extinction-Learning and, 24 h later, Extinction-Recall phases. Activations within the anterior cerebrum and regions of interest (ROI) were examined within the total, PTSD-diagnosed and trauma-exposed control (TEC) groups. Sleep variables were used to predict activations within groups and among total participants. Family wise error was controlled at p < 0.05 using nonparametric analysis with 5,000 permutations.

Results

Initially, Fear Conditioning activated broad subcortical and cortical anterior-cerebral regions. Within-group analyses showed: (1) by end of Fear Conditioning activations decreased in TEC but not PTSD; (2) across Extinction Learning, TEC activated medial prefrontal areas associated with emotion regulation whereas PTSD did not; (3) beginning Extinction Recall, PTSD activated this emotion-regulatory region whereas TEC did not. However, the only between-group contrast reaching significance was greater activation of a hippocampal ROI in TEC at Extinction Recall. A greater number of sleep variables were associated with cortical activations in separate groups versus the entire sample and in PTSD versus TEC.

Conclusions

PTSD nonsignificantly delayed extinction learning relative to TEC possibly increasing vulnerability to pathological anxiety. The influence of sleep integrity on brain responses to threat and extinction may be greater in more symptomatic individuals.
Effect of rearing cross-fostered piglets in litters of differing size relative to sow functional teat number on preweaning growth and mortality
Authors: Vande Pol Katherine D , Bautista Raphael O , Olivo Alicia , Harper Heath , Shull Caleb M , Brown Catherine B , Ellis Michael
Published: October 2021

Litter sizes of commercial sows have increased considerably over recent decades, and often exceed the number of functional teats on the sow. The objective of this study was to evaluate the effect of litter size after cross-fostering relative to sow functional teat number on piglet preweaning growth and mortality. A total of 39 litters (561 piglets) were used in a randomized complete block design; blocking factors were farrowing day and sow parity, body condition score, and functional teat number. Three Litter Size treatments were compared (relative to sow functional teat number): Decreased (two piglets less); Control (same number of piglets); Increased (two piglets more). Piglets were randomly allotted to treatment at 24 h after birth to form litters of the appropriate size, with similar mean and CV of birth weight within block. Weaning weights (WW) were collected at 19.5 ± 0.50 d of age; preweaning mortality (PWM) was recorded. Litter sizes were between 11 and 17 piglets, depending on block and treatment. The Decreased treatment had lower (P ≤ 0.05) PWM than the Increased (7.7% and 17.9%, respectively); the Control was intermediate (11.5%) and not different (P > 0.05) from the other treatments. The rate of decline in litter size from birth to weaning was greater (P ≤ 0.05) for the Increased than the Decreased treatment (−0.16 vs. −0.05 piglets per day), with the Control (−0.09 piglets per day) being intermediate and different (P ≤ 0.05) to the other two treatments. Litter sizes at weaning were greater (P ≤ 0.05) for the Increased than the Decreased treatment (13.3 and 11.3, respectively); the Control treatment was intermediate (12.6) and not different (P > 0.05) to the other treatments. The log odds of PWM increased with the decreasing birth weight, at a similar rate (P > 0.05) for all Litter Size treatments. However, the intercept was greater (P ≤ 0.05) for the Increased compared with the Decreased treatment; the Control was intermediate and different (P > 0.05) to the other two treatments. Mean WW tended (P = 0.07) to be greater for the Decreased (6.17 kg) compared to the Control and Increased treatments (5.86 and 5.84 kg, respectively). In conclusion, increasing litter size after cross-fostering relative to the number of functional teats of the sow increased piglet PWM, and tended to decrease WW.
A mixed-methods study to test a tailored coaching program for health researchers to manage stress and achieve work-life balance
Authors: Steketee Abby , Chen Susan , Nelson Rachel A , Kraak Vivica I , Harden Samantha M
Published: October 2021

Dissemination and implementation (D&I) researchers serve critical scientific, practical, and personal roles in translating science to public health benefit. However, they face multifaceted barriers that may erode their capacity to plan, lead, and evaluate implementation. Individualized coaching focused on human flourishing is an unexplored approach to fully actualize D&I researchers’ capacity to bridge the research-practice gap. The purpose of this exploratory pilot study was to investigate a tailored coaching program to support human flourishing among D&I researchers. A pragmatic, mixed-methods approach guided by the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance) Framework was used to evaluate an individualized, nine session coaching program called FUEL (Focus, Unplug, Exercise, Love). Reach and Implementation were assessed through descriptive statistics and rapid qualitative analysis of surveys and coaching logs. Effectiveness and Maintenance were assessed through descriptive statistics and iterative content analysis of participant surveys, as well as iterative content analysis of proxy (e.g., colleague) semi-structured interviews. Reach results indicated that demand for coaching exceeded study enrollment capacity (n = 16 participants). Implementation results showed that the coach spent 12.96 ± 2.82 hr per participant over 3 months. Effectiveness and Maintenance results indicated that FUEL was well-received and provided participants with myriad psychological and professional benefits. Preliminary evidence suggests that the FUEL coaching program is a promising and feasible approach to enhance flourishing among D&I researchers. Future research is needed to evaluate Adoption and scalability. This pilot study may inform future D&I capacity-building initiatives that address researchers’ holistic situatedness within the implementation process.
Experimental study on the effect of canyon cross wind on temperature distribution of buoyancy-induced smoke layer in tunnel fires
Authors: Fan Chuangang , Yang Liliang , Luan Dia , Chen Tao , Jiao Ao , Ouyang Richeng , Wang Juan , Chen Changkun
Published: October 2021

Experiments were conducted in a 1:20 arced tunnel model to investigate the effect of canyon cross wind on buoyancy-induced smoke flow characteristics of pool fires, involving smoke movement behaviour and longitudinal temperature distribution of smoke layer. The canyon wind speed, longitudinal fire location and fire size were varied. Results show that there are two special smoke behaviours with the fire source positioned at different flow field zones. When the fire source is positioned at the negative pressure zone, with increasing canyon wind speed, the smoke always exists upstream mainly due to the vortex, and the smoke temperature near the fire source increases first and then decreases. However, when the fire source is located in the transition zone and the unidirectional flow zone, there is no smoke appearing upstream with a certain canyon wind speed. Meanwhile, the smoke temperature near the fire sources are decreases with increasing canyon wind speed. The dimensionless temperature rise of the smoke layer ΔTs* along the longitudinal direction of the tunnel follows a good exponential decay. As the canyon wind speed increases, the longitudinal decay rate of ΔTs* decreases. The longitudinal decay rate of ΔTs* downstream of the fire is related to the fire location and canyon wind speed, and independent of the fire size. The empirical correlations for predicting the longitudinal decay of ΔTs* downstream of the fire are established. For a relatively large-scale fire, the longitudinal decay rate of ΔTs* upstream of the fire increases as the distance between the fire source and the upstream portal increases, especially for larger canyon wind speeds.
Retired High-Flyers: Exploring the Impact of Accomplishment on Well-being in Retired Female CEOs
Authors: Kronsbein Kristiane , Belovski Meggy , Burke Jolanta
Published: October 2021

While literature about the relationship between well-being and accomplishment exists, previous studies were mainly quantitative and neglected the subjective experience of female retirees, which the current study aimed to address. Three female retired charity CEOs based in the United Kingdom were interviewed using in-depth, semi-structured interviews. The interpretative phenomenological analysis yielded 3 themes: (1) “accomplishment and well-being—a potentially negative interaction,” (2) “accomplishment and well-being—a positive link through interaction with other well-being domains,” and (3) “retirement—a moderator for negative direct impacts.” The results provided a complex picture of how high-achieving women postretirement perceived accomplishment as a contributor to their well-being. By highlighting an intricate link between accomplishment and other domains of well-being, particularly positive relationships, the findings critique that positive psychology overemphasizes the individual and highlight the need for further research into the interaction between different domains of well-being. The study also contributes to the debate about the relationship between age and well-being by illuminating the individuality of the experience depending on circumstances and environment. Finally, discussed are the implications of the current study in the context of retired high-fliers.
Two rTMS sessions per week: a practical approach for treating major depressive disorder
Authors: Armas-Castañeda Gabriela , Ricardo-Garcell Josefina , Reyes Julian V. , Heinze Gerhard , Salín Rafael J , González Jorge J.
Published: October 2021

Introduction

Depression is one of the leading causes of disability in the world, and a disease that contributes greatly to the global burden of disease. Repetitive transcranial magnetic stimulation (rTMS) has proven to be a well-tolerated, effective treatment for depression. The present study was designed to evaluate the efficacy of an rTMS treatment scheme with a fewer number of sessions per week.

Methods

In total 91 adult university students with major depressive disorder (MDD). This was a double-blind, randomized clinical trial in which 15 sessions of rTMS were given to each one of two treatment groups made up of adults with active MDD. One treatment group received two sessions per week, the other received five. The study protocol included their respective sham rTMS groups. The patients who received active rTMS also participated in a follow-up procedure that consisted of two sessions of active rTMS per month for three more months.

Results

Measurements by the Hamilton Rating Scale for Depression (HAMD) showed that the groups which received active rTMS had higher percentages of antidepressant response at 96 and 95.5% for five and two sessions/week, respectively, compared to the sham rTMS groups: 27.3 and 4.5% for five and two sessions/week, respectively. Observations at the end of the 3-month follow-up phase showed that the improvements in HAMD scores were maintained in both groups.

Conclusion

This study contributes to demonstrating that rTMS with a more practical schedule of two sessions/week is an effective antidepressant treatment that could be considered the first choice for managing symptoms of depression.
Bi-allelic variants in CHKA cause a neurodevelopmental disorder with epilepsy and microcephaly
Authors: Klöckner Chiara , Fernandez Murray J. Pedro , Tavasoli Mahtab , Sticht Heinrich , Stoltenburg-Didinger Gisela , Scholle Leila Motlagh , Bakhtiari Somayeh , Kruer Michael C. , Darvish Hossein , Firouzabadi Saghar Ghasemi , Pagnozzi Alex , Shukla Anju , Girisha Katta Mohan , Narayanan Dhanya Lakshmi , Kaur Parneet , Maroofian Reza , Zaki Maha S. , Noureldeen Mahmoud M. , Merkenschlager Andreas , Gburek-Augustat Janina , Cali Elisa , Banu Selina , Nahar Kamrun , Efthymiou Stephanie , Houlden Henry , Jamra Rami Abou , Williams Jason , McMaster Christopher R. , Platzer Konrad
Published: October 2021

The Kennedy pathways catalyze the de novo synthesis of phosphatidylcholine and phosphatidylethanolamine, the most abundant components of eukaryotic cell membranes. In recent years, these pathways have moved into clinical focus since four out of ten genes involved have been associated with a range of autosomal recessive rare diseases such as a neurodevelopmental disorder with muscular dystrophy (CHKB), bone abnormalities and cone-rod dystrophy (PCYT1A), and spastic paraplegia (PCYT2, SELENOI).

We identified six individuals from five families with bi-allelic variants in CHKA presenting with severe global developmental delay, epilepsy, movement disorders, and microcephaly. Using structural molecular modeling and functional testing of the variants in a in a cell-based S. cerevisiae model, we determined that these variants reduce the enzymatic activity of CHKA and confer a significant impairment of the first enzymatic step of the Kennedy pathway.

In summary, we present CHKA as a novel autosomal recessive gene for a neurodevelopmental disorder with epilepsy and microcephaly.
Improving the diagnosis of severe malaria in African children using platelet counts and plasma Pf HRP2 concentrations
Authors: Watson James A , Uyoga Sophie , Wanjiku Perpetual , Makale Johnstone , Nyutu Gideon M , Mturi Neema , George Elizabeth C , Woodrow Charles J , Day Nicholas PJ , Bejon Philip , Opoka Robert O. , Dondorp Arjen M , John Chandy C , Maitland Kathryn , Williams Thomas N , White Nicholas J
Published: October 2021

Background

Severe falciparum malaria is difficult to diagnose accurately in children in high transmission settings. Platelet counts and plasma concentrations of P. falciparum histidinerich protein-2 (Pf HRP2) are potential biomarkers to increase diagnostic accuracy.

Methods

We fitted Bayesian latent class models to platelet counts and Pf HRP2 concentrations in 2,649 patients enrolled in four studies of severe illness in three countries (Bangladesh, Kenya, and Uganda). We estimated receiver operating characteristic curves and compared parasite densities, haematocrits, total white blood cell counts, blood culture positivity rates, and haemoglobin S genotypes (HbAS and HbSS) across the subgroups defined by the probabilistic models.

Findings

The platelet count and the plasma Pf HRP2 concentration have substantial diagnostic value in severe malaria. In severely ill patients with clinical features consistent with severe malaria, a combined platelet count ≤ 150,000 per µL and a plasma Pf HRP2 concentration ≥ 1,000 ng/mL had an estimated sensitivity of 74% and specificity of 93% in identifying ‘true’ severe falciparum malaria. We estimate one third of African children enrolled in the two clinical studies of severe malaria had another cause of severe illness. Under the model, patients with severe malaria had higher parasite densities, lower haematocrits, lower rates of invasive bacterial disease, and a lower prevalence of both HbAS and HbSS than children misdiagnosed. Mortality in ‘true’ severe malaria was consistent across the African sites at ∼ 10%.

Interpretation

Studies of severe falciparum malaria in African children would be improved by including only patients with platelet counts ≤ 150,000 per µL and plasma Pf HRP2 concentrations ≥ 1,000 ng/mL.

Funding

Wellcome
Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer
Authors: Ivancevic Atma , Simpson David M. , Joyner Olivia M. , Bagby Stacey M. , Nguyen Lily L. , Bitler Ben G. , Pitts Todd M. , Chuong Edward B.
Published: October 2021

Cancer cells exhibit rewired transcriptional regulatory networks that promote tumor growth and survival. However, the mechanisms underlying the formation of these pathological networks remain poorly understood. Through a pan-cancer epigenomic analysis, we found that primate-specific endogenous retroviruses (ERVs) are a rich source of enhancers displaying cancer-specific activity. In colorectal cancer and other epithelial tumors, oncogenic AP1/MAPK signaling drives the activation of enhancers derived from the primate-specific ERV family LTR10. Functional studies in colorectal cancer cells revealed that LTR10 elements regulate tumor-specific expression of multiple genes associated with tumorigenesis, such asATG12andXRCC4. Within the human population, individual LTR10 elements exhibit germline and somatic structural variation resulting from a highly mutable internal tandem repeat region, which affects AP1 binding activity. Our findings reveal that ERV-derived enhancers contribute to transcriptional dysregulation in response to oncogenic signaling and shape the evolution of cancer-specific regulatory networks.
Modulatory potentials of zerumbone isolated from ginger (Zingiber zerumbet) on eicosanoids: evidence from LPS induced peripheral blood leukocytes
Authors: Uppin Vinayak , Kamala Hamsavi Gopal , Kempaiah Bettadaiah Bheemanakere , Talahalli Ramaprasad Ravichandra
Published: October 2021

Several bioactive molecules from plant origin have been studied for their anti-inflammatory properties. In this study, we deciphered the anti-eicosanoid properties of zerumbone (sesquiterpene) isolated from ginger (Zingiber zerumbet) in LPS induced peripheral blood leukocytes from rats. Molecular interaction between zerumbone (Z) and eicosanoid metabolizing enzymes (COX-2, 5-LOX, FLAP, and LTA4-hydrolase) and receptors (EP-4, BLT-1, and ICAM-1) along with NOS-2 were assessed using Auto-Dock 4.2 docking software. Further, the rat peripheral blood leukocytes were isolated and treated with zerumbone (5μM) and activated using bacterial lipopolysaccharide (10nM). Oxidative stress (OS) markers, reactive oxygen species, antioxidant enzymes, COX-2, 5-LOX, BLT-1, EP-4 were assessed along with the activity of COX-2. Zerumbone showed a higher binding affinity with mPGES-1, NOS-2, FLAP, COX-2, LTA-4-hydrolase, and BLT-1 mediators of the eicosanoid pathway. Further, zerumbone significantly (p<0.05) inhibited COX-2, 5-LOX, NOS-2, EP-4, BLT-1, and ICAM-1 expression in LPS induced peripheral blood leukocytes from rats. Zerumbone positively modulates critical enzymes and receptors of eicosanoids in leukocytes activated with lipopolysaccharides. Thus, zerumbone offers a promising therapeutic strategy in the management of inflammation.
Near-infrared carbon nanotube tracking reveals the nanoscale extracellular space around synapses
Authors: Paviolo Chiara , Ferreira Joana S. , Lee Antony , Hunter Daniel , Groc Laurent , Cognet Laurent
Published: October 2021

We provide evidence of a local synaptic nano-environment in the brain extracellular space (ECS) lying within 500 nm of postsynaptic densities. To reveal this brain compartment, we developed a correlative imaging approach dedicated to thick brain tissue based on single-particle tracking of individual fluorescent single wall carbon nanotubes (SWCNTs) in living samples and on speckle-based HiLo microscopy of synaptic labels. We show that the extracellular space around synapses bears specific properties in terms of morphology at the nanoscale and inner diffusivity. We finally show that the ECS juxta-synaptic region changes its diffusion parameters in response to neuronal activity, indicating that this nano-environment might play a role in the regulation of brain activity.
Double-edged role of resource competition in gene expression noise and control
Authors: Goetz Hanah , Stone Austin , Zhang Rong , Lai Ying-Cheng , Tian Xiao-Jun
Published: October 2021

Despite extensive investigation demonstrating that resource competition can significantly alter the circuits’ deterministic behaviors, a fundamental issue is how resource competition contributes to the gene expression noise and how the noise can be controlled. Utilizing a two-gene circuit as a prototypical system, we uncover a surprising double-edged role of resource competition in gene expression noise: the competition decreases noise through a resource constraint but generates its own type of noise which we name as “resource competitive noise.” Utilization of orthogonal resources enables retaining the noise reduction conferred by resource constraint while removing the added resource competitive noise. The noise reduction effects are studied using three negative feedback controller types: negatively competitive regulation (NCR), local, and global controllers, each having four placement architectures in the protein biosynthesis pathway (mRNA or protein inhibition on transcription or translation). Our results show that both local and NCR controllers with mRNA-mediated inhibition are efficacious at reducing noise, with NCR controllers demonstrating a superior noise-reduction capability. We also find that combining negative feedback controllers with orthogonal resources can improve the local controllers. This work provides deep insights into the origin of stochasticity in gene circuits with resource competition and guidance for developing effective noise control strategies.
Effect of G4C2 Repeat Expansions on the Motion of Lysosomes Inside Neurites
Authors: Mytiliniou Maria , Wondergem Joeri A. J. , Feliksik Marleen , Schmidt Thomas , Heinrich Doris
Published: October 2021

The G4C2 hexanucleotide repeat expansion in the c9orf72 locus is one among a plethora of mutations associated with amyotrophic lateral sclerosis. It accounts for the majority of disease cases. The exact processes underlying the pathology of this mutation remain elusive, yet recent evidence suggests a mechanism that disrupts axonal trafficking. Here, we used a neuronal cell line with and without the G4C2 repeats, and implemented time-resolved local mean squared displacement analysis to characterize the motion of lysosomes inside neurites. Neurites were either aligned along chemically patterned lines, or oriented randomly on the substrate. We confirmed that in the presence of the G4C2 repeats, lysosome motion was affected. Lysosomes had a smaller reach exhibited lower velocity, especially inside aligned neurites. At the same time they became more active with increasing length of the G4C2 repeats when the neurites were randomly oriented. The duration of diffusive and super-diffusive lysosome transport remained unaffected for both neurite geometries and for all lengths of the repeats, but the displacement and velocity was decreased on varying the repeat number and neurite geometry. Lastly, the ratio of anterograde/retrograde/neutral trajectories was affected disparately for the two neurite geometries. Our observations support the hypothesis that impaired axonal trafficking emerges in the presence of the G4C2 hexanucleotide repeat expansion.
Maintenance of copy number variation at the human salivary agglutinin gene (DMBT1) by balancing selection driven by host-microbe interactions
Authors: Alharbi Adel F. , Sheng Nongfei , Nicol Katie , Strömberg Nicklas , Hollox Edward J.
Published: October 2021

Most genetic variation in humans occurs in a pattern consistent with neutral evolution, but a small subset is maintained by balancing selection. Identifying loci under balancing selection is important not only for understanding the processes explaining variation in the genome, but also to identify loci with alleles that affect response to the environment and disease. Several genome scans using genetic variation data have identified the 5’ end of theDMBT1gene as a region undergoing balancing selection.DMBT1encodes the pattern-recognition glycoprotein DMBT1, also known as SALSA, gp340 or salivary agglutinin. It binds to a wide variety of pathogens through a tandemly-arranged scavenger receptor cysteine-rich (SRCR) domain, with the number of SRCR domains varying in humans. Here we use expression analysis, linkage in pedigrees, and long range single transcript sequencing, to show that the signal of balancing selection is driven by one haplotype usually carrying shorter SRCR repeats, and another usually carrying a longer SRCR repeat, within the coding region ofDMBT1. The DMBT1 protein size isoform encoded by a shorter SRCR domain repeat allele showed complete loss of binding of a cariogenic and invasiveStreptococcus mutansstrain in contrast to the long SRCR allele. Taken together, our results suggest that balancing selection atDMBT1is due to host-microbe interactions of encoded SRCR tandem repeat alleles.
Liberibacter solanacearum interacts with host psyllid vitellogenin with its membrane proteins
Authors: Sarkar Poulami , Ghanim Murad
Published: October 2021

Candidatus Liberibacter solanacearum (CLso) haplotype D, transmitted by the carrot psyllid Bactericera trigonica is a major constraint in carrot production in Israel. Understanding the molecular interactions between the psyllid vector and CLso can facilitate non-chemical approaches for controlling CLso caused-diseases. In this study, we used CLso outer membrane protein (OmpA) and flagellin as baits to screen for psyllid interacting proteins in a yeast-two hybrid assay. We identified psyllid vitellogenin (Vg) protein to interact with both OmpA and flagellin of CLso. As Vg is often involved in innate immunity with its expression tightly linked to autophagy, a major component of the immune response in the cell, we also analyzed the expression of autophagy-related genes to further elucidate this interaction. We used the juvenile hormone (JH-III) to induce the expression of Vg, thapsigargin for suppressing autophagy, and rapamycin for inducing autophagy. The results revealed that Vg negatively regulates autophagy and vice versa. JH-III induced Vg expression significantly suppressed autophagy and, the levels of CLso significantly increased resulting in a significant mortality of the insect. Although the specific role of Vg remains obscure, the findings presented here identify Vg as an important component in the insect immune responses against CLso and may help in understanding the initial molecular response in the vector against Liberibacter.
Sulfotyrosine, an interaction specificity determinant for extracellular protein-protein interactions
Authors: Stewart Valley , Ronald Pamela C.
Published: October 2021

Tyrosine sulfation, a post-translational modification, can enhance and often determine protein-protein interaction specificity. Sulfotyrosyl residues (sTyr) are formed by tyrosyl-protein sulfotransferase during maturation in the golgi apparatus, and most often occur singly or as a cluster of two or three sTyr within a six-residue span. With both negative charge and aromatic character, sTyr enables numerous atomic contacts as visualized in binding interface structural models, and so there is no discernible binding site consensus. Found exclusively in secreted proteins, sTyr residues occur in four broad sequence contexts. First, a single sTyr residue is critical for diverse high-affinity interactions between peptide hormones and their receptor in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of processes including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with many chemokine receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters occurs in the context of conserved acidic sequences termed hirudin-like motifs that enable several proteins to interact with thrombin, central to normal blood-clotting. Consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyr residues for their activity. Fourth, a few proteins that interact with collagen or other proteins contain one or more sTyr residues within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in MS and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
A comprehensive evaluation of CRISPR lineage recorders using TraceQC
Authors: Hu Jingyuan , Jeong Hyun-Hwan , Al-Ouran Rami , Bado Igor , Zhang Weijie , Zhang Xiang , Liu Zhandong
Published: October 2021

The CRISPR-Cas9 genome editing-based lineage tracing system is emerging as a powerful tool to track cell lineages at unprecedented scale and resolution. However, the complexity of CRISPR-Cas9 induced mutations has raised challenges in lineage reconstruction, which requires a unique computational analysis framework. Meanwhile, multiple distinctive CRISPR-based high-throughput lineage recorders have been developed over the years in which the data analysis is incompatible across platforms. To address these challenges, first, we present the TraceQC, a cross-platform open-source package for data processing and quality evaluation of CRISPR lineage tracing data. Second, by using the TraceQC package, we performed a comprehensive analysis across multiple CRISPR lineage recorders to uncover the speed and distribution of CRISPR-induced mutations. Together, this work provides a computational framework for the CRISPR lineage tracing system that should broadly benefit the design and application of this promising technology.
Intracellular pH links energy metabolism to lymphocyte death and proliferation
Authors: Zeng Wei-ping , Yang Shuangshuang , Zhou Baohua
Published: October 2021

The role of intracellular pH (pHi) of lymphocytes in the control of the magnitude of immune response is unknown. We found that low pHi induces apoptosis of proliferating lymphocytes, whereas high pHi promotes their survival. In the ovalbumin sensitization and challenge model, energy metabolism is a major mechanism for regulating pHi. TCA cycle using carbohydrates lowers whereas glutaminolysis or aerobic glycolysis increases pHi. Proliferation powered by high mitochondrial membrane potentials (MMPs) in lymphocytes of low but not high pHi causes apoptosis. After antigenic challenge, lymphocytes of high pHi gradually increase and assume a positive relation between pHi and MMPs while lymphocytes of low pHi and an inverse relation between pHi and MMPs diminish. This change is at least partly dependent on glutaminolysis and aerobic glycolysis.

One Sentence Summary

TCA cycle fueled with carbohydrates but not glutaminolysis or aerobic glycolysis lowers intracellular pH to induce apoptosis.
Natural transformation protein ComFA exhibits single-stranded DNA translocase activity
Authors: Foster Hannah R. , Lin Xiaoxuan , Srikant Sriram , Cueny Rachel R. , Falbel Tanya G. , Keck James L. , Gaudet Rachelle , Burton Briana M.
Published: October 2021

Natural transformation is one of the major mechanisms of horizontal gene transfer in bacterial populations and has been demonstrated in numerous species of bacteria. Despite the prevalence of natural transformation, much of the molecular mechanism remains unexplored. One major outstanding question is how the cell powers DNA import, which is rapid and highly processive. ComFA is one of a handful of proteins required for natural transformation in gram-positive bacteria. Its structural resemblance to the DEADbox helicase family has led to a long-held hypothesis that ComFA acts as a motor to help drive DNA import into the cytosol. Here, we explored the helicase and translocase activity of ComFA to address this hypothesis. We followed the DNA-dependent ATPase activity of ComFA and, combined with mathematical modeling, demonstrated that ComFA likely translocates on single-stranded DNA from 5’ to 3’. However, this translocase activity does not lead to DNA unwinding in the conditions we tested. Further, we analyzed the ATPase cycle of ComFA and found that ATP hydrolysis stimulates the release of DNA, providing a potential mechanism for translocation. These findings help define the molecular contribution of ComFA to natural transformation and support the conclusion that ComFA plays a key role in powering DNA uptake.

Importance

Competence, or the ability of bacteria to take up and incorporate foreign DNA in a process called natural transformation is common in the bacterial kingdom, but understanding of the mechanism is still limited. Increasing evidence in several bacteria confirms that long, contiguous stretches of DNA are imported into cells, and yet how bacteria power processive transformation remains unclear. Our finding that ComFA, a DExD-box helicase required for competence in gram-positive bacteria, translocates on single-stranded DNA from 5’ to 3’, supports the long held hypothesis that ComFA may be the motor powering DNA transport during natural transformation. Moreover, ComFA may be a previously unidentified type of DExD-box helicase—one with the capability of extended translocation on single-stranded DNA.
Illumina But With Nanopore: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
Authors: Zee Alexander , Deng Dori Z. Q. , Adams Matthew , Schimke Kayla D. , Corbett-Detig Russell , Russell Shelbi L. , Zhang Xuan , Schmitz Robert J. , Vollmers Christopher
Published: October 2021

High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays exist today to take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities, and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the ONT MinION by using the R2C2 method to circularize and amplify the short library molecules. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, as well as regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.