bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth and Metabolic Changes After Antiretroviral Initiation in South African Children
Authors: Masi-Leone Michela , Arpadi Stephen , Teasdale Chloe , Yuengling Katharine A. , Mutiti Anthony , Mogashoa Mary , Rivadeneira Emilia D. , Abrams Elaine J. , Jao Jennifer
Published: July 2021

Background:

Poor growth and metabolic disturbances remain concerns for children living with HIV (CLHIV). We describe the impact of viral load (VL) on growth and lipid outcomes in South African CLHIV <12 years initiating World Health Organization recommended first-line antiretroviral therapy (ART) from 2012 to 2015.

Methods:

Z scores for length-for-age (LAZ), weight-for-age (WAZ) and body mass index-for-age were calculated. Lipids (total cholesterol, low-density lipoprotein and high-density lipoprotein) were measured. Hemoglobin A1C ≥5.8 was defined as at risk for type 2 diabetes. Mixed effects models were used to assess the association of VL at ART initiation with Z scores and lipids over time.

Results:

Of 241 CLHIV, 151 (63%) were <3 years initiating LPV/r-based ART and 90 (37%) were ≥3 years initiating EFV-based ART. Among CLHIV <3 years, higher VL at ART initiation was associated with lower mean LAZ (ß: −0.30, P=0.03), WAZ (ß: −0.32, P=0.01) and low-density lipoprotein (ß: −6.45, P=0.03) over time. Among CLHIV ≥3, a log 10 increase in pretreatment VL was associated with lower mean LAZ (ß: −0.29, P=0.07) trending towards significance and lower WAZ (ß: −0.32, P=0.05) as well as with more rapid increases in LAZ (ß: 0.14 per year, P=0.01) and WAZ (ß: 0.19 per year, P=0.04). Thirty percent of CLHIV were at risk for type 2 diabetes at ART initiation.

Conclusions:

CLHIV initiating ART <3 years exhibited positive gains in growth and lipids, though high viremia at ART initiation was associated with persistently low growth and lipids, underscoring the need for early diagnosis and rapid treatment initiation. Future studies assessing the long-term cardiometabolic impact of these findings are warranted.
“COVID Toes” in Three Siblings
Authors: Feder Henry M.
Published: July 2021

Dermatologists reported an outbreak of pernio (red to purple swollen painful toes) during the COVID-19 pandemic. Most subjects lacked positive CoV-19 polymerase chain reaction (PCR) or antibodies or a preceding illness. The dermatologists termed the illness “COVID toes.” Pernio usually affects adults versus “COVID toes” usually children. Pernio is preceded by a clear history of exposure to wet and cold. Patients with “COVID toes” lack this history. Also, it is not unusual for multiple family members to have “COVID toes.” Our case report describes “COVID toes” in an 18-year-old with no preceding illness, a negative SARS-CoV-19 PCR, and an initially negative SARS-CoV-19 antibody, and also his 2 siblings also developed “COVID toes.” In our index case, repeat SARS-CoV-19 antibodies were positive. Seroconversion has rarely been reported in patients with “COVID toes.” Why most “COVID toes” patients lack a clinical history of COVID-19 and are SARS-CoV-19 PCR and antibody negative is a mystery.
Blood Perfusion of Human Upper Eyelid Skin Flaps Is Better in Myocutaneous than in Cutaneous Flaps
Authors: Berggren Johanna V. , Tenland Kajsa , Bunke Josefine , Albinsson John , Hult Jenny , Merdasa Aboma , Sheikh Rafi , Lindstedt Sandra , Malmsjö Malin
Published: July 2021

Background:

The aim of this study was to monitor blood perfusion in human upper eyelid skin flaps and examine how the perfusion is affected by the thickness of the flap.

Methods:

Twenty upper eyelids were dissected as part of a blepharoplasty procedure in patients. The medial end of the blepharoplasty flap remained attached to mimic a flap design often used in reconstruction in the periocular area, a myocutaneous flap in which the blood supply follows the fibers of the orbicularis muscle and is thus parallel to the long axis of the flap. The muscle was thereafter dissected from the flap to create a cutaneous flap. Blood perfusion in the 2 types of flaps was compared using laser speckle contrast imaging.

Results:

Blood perfusion decreased gradually from the base to the tip of all the flaps. Perfusion was significantly higher in the myocutaneous flaps than in the cutaneous flaps (p < 0.0004): 69% in the myocutaneous flaps and 43% in the cutaneous flaps, measured 5 mm from the base. Blood perfusion was preserved to a greater extent distally in the myocutaneous flaps (minimum value seen at 25 mm) than in the cutaneous flaps (minimum seen at 11 mm).

Conclusions:

Blood perfusion was better preserved in myocutaneous flaps, including both skin and the orbicularis oculi muscle, than in cutaneous flaps. This may be of clinical interest in patients with poor microcirculation in which a long flap is required for reconstructive surgery.
Inadvertent Intraocular Soft Tissue Filler Injection During a Facial Enhancement Procedure
Authors: Liu Fei , Ma Yue , Tang Meiting , Zeng Xueying , Kikkawa Don O. , Lu Wei
Published: July 2021

Iatrogenic needle penetrating ocular injuries are rare but can result in serious consequences. The authors report a case of inadvertent intraocular hyaluronic acid injection during esthetic periorbital facial enhancement. Visual field, visual evoked potential, and electroretinogram were used for monitoring potential side effects.
Modifications of intravitreal injections in response to the COVID-19 pandemic
Authors: Weng Chang-Chi , Lin Ting-Yi , Yang Yi-Ping , Hsiao Yu-Jer , Lin Tzu-Wei , Lai Wei-Yi , Lin Yi-Ying , Chou Yu-Bai , Lin Tai-Chi , Chiou Shih-Hwa , Hwang De-Kuang , Chen Shih-Jen
Published: July 2021

The Coronavirus disease 2019 (COVID-19) pandemic has caused unprecedented disruption to the normal operation of the healthcare system. On a worldwide scale, hospitals suspended nonurgent surgeries and outpatient visits to downsize clinical loadings to redistribute manpower to counteract the pandemic’s impact. So far, there is no evidence-based guideline defining a clear line between urgent and nonurgent indications of intravitreal injections (IVI). Herein, we aimed to summarize IVI algorithm modifications and discuss the patient prioritization according to medical needs in the hostile environment in the COVID crisis. Assessing current literature, we found that neovascular age-related macular degeneration is considered the utmost priority among conditions that require IVI. Other conditions assigned with a high priority include monocular or quasi-monocular patients (only one eye > 20/40), neovascular glaucoma, and new patients with significant vision loss. Although patients with central retinal vein occlusion and proliferative diabetic retinopathy are not advised to delay treatments, we found no consistent evidence that correlated with a worse outcome. Diabetic macular edema and branch retinal vein occlusion patients undertaking treatment delay should be regularly followed up every 2 to 3 months. Serving as the principle of management behind the algorithm modifications, the reduction of both patient visit and IVI therapy counts should be reckoned together with the risk of permanent visual loss and COVID infection.
“Every One of Us Is a Strand in That Basket”: Weaving Together Stories of Indigenous Wellness and Resilience From the Perspective of Those With Lived and Living Experience With HIV/Hepatitis C Virus
Authors: Heidebrecht Luke , Iyer Subhashini , Laframboise Sandy Leo , Madampage Claudia , King Alexandra
Published: July 2021

This article primarily focuses on the stories shared by Indigenous women with living and/or lived experiences of HIV/hepatitis C virus from the Vancouver Downtown East Side who attended the “Awakening our Wisdom” retreat. Weaving together the story of an Indigenous approach to research that informed the design of the retreat and the findings that emerged, a basket is formed that highlights the ways settler-colonialism within Canada has produced a system of health care that has neglected the Indigenous experience. The emerging themes of Connection, Disconnection, and Reconnection offers teachings for Indigenous journeys of resilience and wellness for those living with HIV/hepatitis C virus. These findings may help health care practitioners identify health care places and spaces that are in need of decolonization and offer, from an Indigenous perspective, the next steps forward for a health care system that promotes Indigenous engagement and retention in care.
Medullary thyroid carcinoma
Authors: Jaber Tania , Dadu Ramona , Hu Mimi I.
Published: July 2021

Purpose of review

To summarize recent developments in the diagnosis and management of patients with medullary thyroid cancer (MTC), with a focus on pathogenesis, systemic therapy, and future directions.

Recent findings

The addition of mutational analysis to cytological assessment of thyroid nodules has improved the diagnostic accuracy of MTC. The discovery of new genomic alterations and overexpression of certain factors allows for improved prognostication in MTC and provides potentially new therapeutic agents. New data suggest that tumor environment may be more immunogenic than previously thought in a subset of MTCs with identification of a new MTC-specific antigen leading to a revival of investigating immune-based therapy for this disease. The newly approved selective rearranged during transfection (RET0-inhibitors, selpercatinib and pralsetinib, offer promising results, and tolerability for patients with RET-mutated MTC; however, the development of resistance mechanisms may be problematic.

MTC has witnessed remarkable advancements in recent years. Our new understanding of some of the driver mutations in MTC allows for therapeutics with more tolerable adverse event profiles. However, there is still a need for more effective treatment strategies for subsets of patients without actionable mutations and for those who develop resistance to currently available therapies.
Outcomes of Primary Ileocolic Resection for Pediatric Crohn Disease in the Biologic Era
Authors: Spencer Elizabeth A. , Jarchin Lauren , Rolfes Priya , Khaitov Sergey , Greenstein Alexander , Dubinsky Marla C.
Published: July 2021

Objectives:

Current clinical algorithms position surgery as the last option in pediatric Crohn disease (CD). Studies suggest improved outcomes with earlier surgery, but pediatric postoperative outcomes data in the biologic era are limited. We aimed to describe the preoperative management and postoperative outcomes in a pediatric CD cohort who underwent ileocolic resection (ICR) at a tertiary care inflammatory bowel disease center over the last decade.

Methods:

Single‐center, retrospective study of pediatric (<18 years) CD patients who underwent ICR between 2008 and 2019 with primary outcome of rate of endoscopic recurrence (Rutgeerts’ >i2) at 2 years post‐ICR. Key secondary outcomes included endoscopic remission (Rutgeerts’ i0), frequency of 30‐day postoperative complications, anthropometric changes, and histologic recurrence. Uni‐ and multivariable analyses examined associations of clinical/laboratory characteristics with endoscopic recurrence. Factors predictive of 30‐day complications were also analyzed.

Results:

Seventy‐eight children underwent ICR a median of 17.8 months (interquartile range [IQR] 2.6–53.9) from diagnosis. Median age at diagnosis and surgery was 13.8 (11.1–16.7) and 16.8 years (15.1–17.8), respectively. In the 41 patients with >1 post‐operative endoscopy, the rate of endoscopic recurrence was 46% at 2 years (median time to recurrence: 10 [7–20] months). Histologic recurrence was present in 44% in endoscopic remission (κ = 0.11, P = 0.53). Endoscopic recurrence was associated with younger age at diagnosis and longer disease duration. 30‐day complications occurred at a rate of 18%; only 1% experienced severe complications. All anthropometric measures significantly improved after surgery.

Conclusions:

Given the inherent risk of postoperative recurrence associated with age and disease duration, children would benefit from postoperative surveillance and effective prophylaxis.
Bay Leaf
Authors: Singletary Keith
Published: July 2021

Bay leaf or bay laurel is a culinary herb obtained from the small evergreen tree Laurus nobilis L. (family Lauraceae). This plant is native to the Mediterranean region and enjoys widespread cultivation in the warm climates of the southern United States, Central America, Europe, the Middle East, and Asia. As a culinary herb, it is known to flavor numerous cuisines of Turkey, India, Italy, and France. It is a common component in the French mixture of herbs “bouquet garni” and is added to various dishes during cooking such as sauces, soups, stocks, casseroles, sausages, and stews and then removed before consumption. Many uses of bay leaf and its oil in traditional and folk medicines have been documented. These include as treatment of respiratory disorders and infections, gastrointestinal discomfort and irregularity, diarrhea, and amenorrhea and as an emetic, stimulant, and diuretic, to name a few. To date, few human studies have examined the health benefits of bay leaves. This narrative review summarizes relevant clinical trials and preclinical animal investigations, and highlights future research needs.
Exsanguination From Superficial Lower Extremity Trauma
Authors: Prahlow Samuel P. , Abadi Arad , Prahlow Joseph A.
Published: July 2021

Deaths related to exsanguination are not rare; however, most are related to large-caliber blood vessel or organ disruption. This article reports 2 deaths from external hemorrhage arising from superficial lower extremity trauma in persons with peripheral vascular disease and anticoagulant therapy. The first involved a 78-year-old woman who was found unconscious in her home by a relative, with a plastic bag tied around her left foot and evidence of profuse hemorrhage arising from a left great toenail partial avulsion injury. The second involved a 48-year-old male resident of an adult group home who was involved in a physical altercation with a group home employee, who reportedly kicked the decedent in the right shin, resulting in extensive hemorrhage and death. The cases highlight the fact that lethal exsanguination can occur from superficial trauma. Persons with peripheral vascular disease and those taking anticoagulants may be at particular risk for such deaths.
The Analysis of Hospital Readmission Rates After the Implementation of Hospital Readmissions Reduction Program
Authors: Muchiri Steve , Azadeh-Fard Nasibeh , Pakdil Fatma
Published: July 2021

Objectives

This study aims to analyze the impact of Hospital Readmissions Reduction Program (HRRP) on the nationwide optimization efforts of length of stay (LOS) and readmissions in the United States.

Methods

We use the Nationwide Readmission Database between 2010 and 2016 provided in the Healthcare Cost and Utilization Project by the Agency for Healthcare Research and Quality. The study focuses on acute myocardial infarction, chronic obstructive pulmonary disease, congestive heart failure (CHF), pneumonia monitored by the HRRP and 2 conditions, septicemia, and mood disorders that were not monitored by the HRRP but had among the highest readmissions. Patient demographics and readmissions were analyzed based on insurance type, LOS, and Charlson Comorbidity Index.

Results

The readmissions vary by conditions, LOS, and insurance types. Congestive heart failure has the highest readmissions among the 6 analyzed conditions at approximately 25%. The readmission rate of CHF rises to 30% for the Medicaid patients and varies between 30% and 35% by LOS. Patients with CHF with higher Charlson Comorbidity Index demonstrates the highest readmissions among 6 conditions. The patients with longer LOSs had higher readmissions, and Medicare patients have a higher reduction in readmissions in acute myocardial infarction and mood disorders compared with the other forms of payments.

Conclusions

Our figures show that targeted programs, such as HRRP, may have a positive impact on readmission rates. We, however, observe some graphical evidence that nontargeted conditions could exhibit similar trends. Because of heterogeneity in hospital and patient characteristics, it is pivotal for researcher to consider them in formal analyses.
Use of Dental Impression Silicone to Fabricate Simple Surgical Guides in Mandibular Reconstruction∗
Authors: Matsui Chihiro , Mizuno Hiroshi , Roche Nathalie
Published: July 2021

Background:

Several recent reports have described the development and use of three-dimensional (3D) printed surgical osteotomy guides. However, these methods: are usually costly. Here, we introduce a novel method of manufacturing surgical guides built from inexpensive, easy-to-use, and sterilizable dental impression silicone.

Methods:

Mandibular and fibular models were prepared using a 3D printer for 10 patients undergoing free fibula flap transfer after mandibular resection. During preoperative simulation surgery, Protesil labor, a dental silicone, was molded to the same size as the fibular models to act as surgical guides.

Results:

The authors compared pre- and post-operative bone angles and bone lengths for all cases using simulation surgery models and postoperative 3D computed tomography. Mean bone angle difference was 2.6° and mean bone length difference was 1.7 mm. Cost of the dental silicone was approximately US$5/patient.

Conclusions:

In our series this method allowed the surgeon to perform an accurate osteotomy, inexpensively and time-efficiently.
Cerebellum Tumor Presenting Itself With Positional Vertigo and Benign Paroxysmal Positional Vertigo
Authors: Kinar Abdullah , Günebakan Ceren , Kinar Ayşe Kübra Şap
Published: July 2021

The purpose of this case is to describe the positional vertigo observed in a patient diagnosed with cerebellar arteriovenous malformation, pay attention to the importance of medical history taking and physical examination in vertigo patients.

A 51-year-old patient went to the Ear, Nose, and Throat clinic with a complaint of vertigo. His vertigo was like peripheral vertigo at the beginning. Dizziness was triggered by head movements. He experienced tinnitus in the left ear during vertigo attacks. The patient also had neck pain. In physical examination, natural bilateral tympanic membrane and facial examination were observed. Other physical examinations were normal. In the positional vertigo tests, the right Dix-Hall Pike test was positive and a downbeating geotropic nystagmus was found. The patient was treated with canalith repositioning maneuver (Epley maneuver). Oral medical treatment started and after 4 days, the patient reported that his gait balance was disturbed and his neck pain continued. After that magnetic resonance imaging was requested. Magnetic resonance imaging was consistent with cerebellar arteriovenous malformation. The patient was consulted to the neurology service.

Cerebellar arteriovenous malformation had features like to peripheral vertigo, and the correct diagnosis is made due to suspected headache and other neurological symptoms.
Risk Factors for Occipital Step-Off Deformities in Posterior Vault Distraction Osteogenesis
Authors: Zapatero Zachary D. , Carlson Anna R. , Card Elizabeth B. , Kosyk Mychajlo S. , Kalmar Christopher L. , Swanson Jordan W. , Bartlett Scott P. , Taylor Jesse A.
Published: July 2021

Purpose:

The goal of this study was to investigate patient specific factors and surgical techniques that affect occipital step-off deformity in children undergoing posterior vault distraction osteogenesis (PVDO).

Methods:

Patients who underwent PVDO were retrospectively reviewed and included if a high resolution three-dimensional computed tomography scan was available 1-year post-distractor removal. Two craniofacial surgeons were blinded to individual subjects and presented with 3 still images of three-dimensional bone reconstructions and asked to rate the degree of step off: none, mild, moderate, or severe. The data were analyzed with multinomial logistic regressions and other appropriate statistics.

Results:

Forty-one patients met inclusion criteria. All patients had multisuture or bicoronal craniosynostosis. Multinomial logistic regression identified age at PVDO (Cox and Snell = 0.487, P < 0.001) as a predisposing factor and one potentially protective factor, height of osteotomy (Cox and Snell = 0.394, P = 0.004) in univariate models. Post-hoc pairwise Mann–Whitney U test revealed there was decreased step-off rating when comparing osteotomy below torcula (median 0, [IQR 0, 3]) and above torcula (median 3 [IQR 1, 4]; P = 0.036) as well as a decreased step-off when below inion (median 0 [IQR 0, 1]; P = 0.001) was compared to above the torcula.

Conclusions:

Older age at PVDO predict increased risk of developing an occipital step-off deformity after PVDO, while design of the occipital osteotomy below the inion is protective. Barrel staves with greenstick outfracture did not lower the risk of occipital step-off in this sample, the reasons for which are unclear.
Orbital Septum Fat Flap Transfer for Upper Eyelid Depression
Authors: Zhang Shan , Ding Kun , Bai Xinran , Cao Zhe , Liang Xiaoqin
Published: July 2021

Background:

Sunken upper eyelid makes people's eyes look gaunt and aging. At present, more and more people are paying attention to eye rejuvenation, and more and more people are asking for correction of sunken upper eyelid. Orbital septum fat plays an important role in the display of eye contour. Therefore, the position of orbital septum fat can be adjusted surgically to improve the upper eyelid depression.

Objective:

This article discusses the clinical effect of orbital septum fat flap transfer in the upper eyelid depression of mild to moderate.

Methods:

Thirty patients with single eyelid depression in our hospital from April to September 2020 were selected. After blepharoplasty, the orbital septum fat was fully released and the lateral orbital fat transfer was fixed to the mid-medial upper eyelid depression.

Results:

After the operation, 29 patients were satisfied with the results, with good incision healing, bilateral basic symmetry no obvious scar, and negative effect of non-convex and concave eyelid inequality. One patient did not achieve the expected results and was treated with a second autologous fat filling.

Conclusions:

For patients with mild to moderate sunken upper eyelid, orbital septal fat flap metastasis during blepharoplasty has not only good effect, natural appearance, and smooth upper eyelid skin, but also only 1 incision for upper eyelid formation, which has high acceptance and satisfaction of patients and can be widely used in clinical practice.
Revisiting the Cervicodeltopectoral Flap for Reconstruction of Cutaneous Head and Neck Defects: Technique Description and Clinical Presentation Correlates
Authors: Parrish Andrew J. , Anderson Spencer R. , Mulenga Musunga A. , Wimalawansa Sunishka M. , Kadakia Sameep P.
Published: July 2021

Study Design:

Technique Description with clinical presentation Correlates.

Purpose:

Revisit and discuss the advantages of the cervicodeltopectoral flap (CDP) as an alternative to microvascular reconstruction for head and neck cutaneous defects.

Methods:

Retrospective chart review was performed on 2 patients with prior large cutaneous facial defects after tumor resection followed by cervicodeltopectoral flap reconstruction. These cases were performed at a single institution. The tumor resections, flap reconstructions, and postoperative management were led by the listed senior author (SPK).

Results:

A 78-year-old (Clinical presentation 1) and 62-year-old (Clinical presentation 2) were evaluated for large nonmelanoma skin cancers of the face. Due to significant comorbidities, neither patient was an ideal candidate for microsurgical reconstruction. In both cases, lesion resection and CDP flap reconstruction was performed. The reconstruction allowed for successful coverage without significant donor site morbidity for each patient.

Conclusions:

The authors propose the addition of the CDP flap to the armamentarium of the head and neck reconstructive surgeon as a safe and reliable alternative to microvascular reconstruction.
Impact of Immune Response in Short-term and Long-term Outcomes After Minimally Invasive Surgery for Colorectal Liver Metastases: Results From a Randomized Study
Authors: Lopez-Lopez Victor , Gómez Ruiz Alvaro , Pelegrin Pablo , Abellán Beatriz , Lopez-Conesa Asunción , Brusadin Roberto , Cayuela Valentin , García Ana , Robles Campos Ricardo
Published: July 2021

Background:

The potential benefit related to laparoscopic liver surgery (LLS) for colorectal liver metastases outcomes is not well known.

Materials and Methods:

Serum cytokines associated with Th1 (tumor necrosis factor-α) and Th2 [interleukin (IL)-10 and IL-6] phenotypes were measured in 36 patients operated on for colorectal liver metastases by open liver surgery (OLS) and LLS. Measurements were performed at 3 time points: 1 day before surgery, day 3 postoperative, and 1 month postoperative. We compared the postoperative inflammatory response influence between LLS and OLS on long-term outcomes.

Results:

In both groups, only IL-6 levels on day 3 postoperative were higher than those measured preoperatively and at 1 month. Comparing the tumor necrosis factor-α levels between the LLS and OLS groups, preoperative (7.28 vs. 2.36), day 3 (7.99 vs. 4.08) and 1 month (7.39 vs. 1.99) postoperative levels were higher in the OLS group (P<0.01, <0.01, and <0.01, respectively). In contrast, IL-10 levels were higher in the LLS group preoperatively (7.51 vs. 4.57) and on day 3 postoperative (13.40 vs. 4.57) (P=0.03 and 0.01, respectively). A cut-off IL-6 level of ≥4.41 in the first month was associated with a higher risk of recurrence (logrank=4.8, P=0.02).

Conclusions:

Both LLS and OLS induce an initial increase in IL-6 that normalizes one month after surgery, showing a similar pattern. In addition, a cut-off IL-6 value of 4.41 pg/mL was established, with a higher concentration at 1 month postoperative possibly related to a higher risk or recurrence.
Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing
Authors: Luo Lijuan , Payne Michael , Kaur Sandeep , Hu Dalong , Cheney Liam , Octavia Sophie , Wang Qinning , Tanaka Mark M. , Sintchenko Vitali , Lan Ruiting
Published: July 2021

Salmonella enterica

serovar Enteritidis is a major cause of foodborne

Salmonella

infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.
Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients
Authors: Veschetti Laura , Sandri Angela , Patuzzo Cristina , Melotti Paola , Malerba Giovanni , Lleo Maria M.
Published: July 2021

Achromobacter

species are increasingly being detected in cystic fibrosis (CF) patients, where they can establish chronic infections by adapting to the lower airway environment. To better understand the mechanisms contributing to a successful colonization by

Achromobacter

species, we sequenced the whole genome of 54 isolates from 26 patients with occasional and early/late chronic lung infection. We performed a phylogenetic analysis and compared virulence and resistance genes, genetic variants and mutations, and hypermutability mechanisms between chronic and occasional isolates. We identified five

Achromobacter

species as well as two non-affiliated genogroups (NGs). Among them were the frequently isolated

Achromobacter xylosoxidans

and four other species whose clinical importance is not yet clear: Achromobacter insuavis, Achromobacter dolens, Achromobacter insolitus and

Achromobacter aegrifaciens

. While

A. insuavis

and

A. dolens

were isolated only from chronically infected patients and

A. aegrifaciens

only from occasionally infected patients, the other species were found in both groups. Most of the occasional isolates lacked functional genes involved in invasiveness, chemotaxis, type 3 secretion system and anaerobic growth, whereas the great majority (>60%) of chronic isolates had these genomic features. Interestingly, almost all (n=22/23) late chronic isolates lacked functional genes involved in lipopolysaccharide production. Regarding antibiotic resistance, we observed a species-specific distribution of blaOXA
genes, confirming what has been reported in the literature and additionally identifying blaOXA-2
in some

A. insolitus

isolates and observing no blaOXA
genes in

A. aegrifaciens

or NGs. No significant difference in resistance genes was found between chronic and occasional isolates. The results of the mutator genes analysis showed that no occasional isolate had hypermutator characteristics, while 60% of early chronic (<1 year from first colonization) and 78% of late chronic (>1 year from first colonization) isolates were classified as hypermutators. Although all A. dolens, A. insuavis and NG isolates presented two different mutS genes, these seem to have a complementary rather than compensatory function. In conclusion, our results show that

Achromobacter

species can exhibit different adaptive mechanisms and some of these mechanisms might be more useful than others in establishing a chronic infection in CF patients, highlighting their importance for the clinical setting and the need for further studies on the less clinically characterized

Achromobacter

species.
Elevated levels of the cytokine LIGHT in Crohn’s disease
Authors: Cardinale Christopher J. , Abrams Debra J. , Mentch Frank D. , Cardinale John A. , Kao Charlly , Sleiman Patrick M.A. , Hakonarson Hakon
Published: July 2021

LIGHT, encoded by the TNFSF14 gene, is a cytokine belonging to the tumor necrosis factor superfamily. Upon binding to its receptors, HVEM and LTBR, it activates inflammatory responses. We used a single-molecule immunoassay to determine the circulating levels of free LIGHT in plasma from pediatric patients with Crohn’s disease (N = 183) and a panel of healthy pediatric reference samples (N = 9). LIGHT levels were greatly elevated in Crohn’s disease (average of 305 pg/ml versus 57 pg/ml in controls, P < 0.0001). We performed correlational analyses between LIGHT levels and the clinical characteristics of the Crohn’s cohort, including age, Montreal classification, family history, medical/surgical therapy, and routine blood test parameters. We found statistically significant correlation between white blood cell count and free LIGHT (P < 0.046). Our results support the hypothesis that elevated levels of the cytokine contribute to the pathology of Crohn’s disease and that therapies to neutralize free LIGHT with antibodies may be beneficial.
Leveraging of SARS-CoV-2 PCR cycle thresholds values (Ct) to forecast COVID-19 trends
Authors: Yin Nicolas , Dellicour Simon , Daubie Valery , Franco Nicolas , Wautier Magali , Faes Christel , Van Cauteren Dieter , Nymark Liv , Hens Niel , Gilbert Marius , Hallin Marie , Vandenberg Olivier
Published: July 2021

Introduction

We assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB (a consolidated microbiology laboratory located in Brussels, Belgium) for monitoring the epidemic’s dynamics at local and national levels and for improving forecasting models.

Methods

SARS-CoV-2 RT-PCR Ct values produced from April 1, 2020, to May 15, 2021, were compared with national COVID-19 confirmed cases notifications according to their geographical and time distribution. These Ct values were evaluated against both a phase diagram predicting the number of COVID-19 patients requiring intensive care and an age-structured model estimating COVID-19 prevalence in Belgium.

Results

Over 155,811 RT-PCR performed, 12,799 were positive and 7,910 Ct values were available for analysis. The 14-day median Ct values were negatively correlated with the 14-day mean daily positive tests with a lag of 17 days. In addition, the 14-day mean daily positive tests in LHUB-ULB were strongly correlated with the 14-day mean confirmed cases in the Brussels-Capital and in Belgium with coinciding start, peak and end of the different waves of the epidemic. Ct values decreased concurrently with the forecasted phase-shifts of the diagram. Similarly, the evolution of 14-day median Ct values was negatively correlated with daily estimated prevalence for all age-classes.

Conclusion

We provide preliminary evidence that trends of Ct values can help to both follow and predict the epidemic’s trajectory at local and national levels, underlining that consolidated microbiology laboratories can act as epidemic sensors as they gather data that are representative of the geographical area they serve.
Deep Optical Blood Analysis: COVID-19 Detection as a Case Study in Next Generation Blood Screening
Authors: Cooke Colin L. , Kim Kanghyun , Xu Shiqi , Chaware Amey , Yao Xing , Yang Xi , Neff Jadee , Pittman Patricia , McCall Chad , Glass Carolyn , Jiang Xiaoyin Sara , Horstmeyer Roarke
Published: July 2021

A wide variety of diseases are commonly diagnosed via the visual examination of cell morphology within a peripheral blood smear. For certain diseases, such as COVID-19, morphological impact across the multitude of blood cell types is still poorly understood. In this paper, we present a multiple instance learning-based approach to aggregate high-resolution morphological information across many blood cells and cell types to automatically diagnose disease at a per-patient level. We integrated image and diagnostic information from across 236 patients to demonstrate not only that there is a significant link between blood and a patient’s COVID-19 infection status, but also that novel machine learning approaches offer a powerful and scalable means to analyze peripheral blood smears. Our results both backup and enhance hematological findings relating blood cell morphology to COVID-19, and offer a high diagnostic efficacy; with a 79% accuracy and a ROC-AUC of 0.90.
Heart-centered positioning and tailored beam-shaping filtration for reduced radiation dose in coronary artery calcium imaging: a MESA study
Authors: Colvert Brendan , Rigoli Marzia , Craine Amanda , Criqui Michael , Contijoch Francisco
Published: July 2021

Purpose

Cardiac CT has a clear clinical role in the evaluation of coronary artery disease and assessment of coronary artery calcium (CAC) but the use of ionizing radiation limits clinical use. Beam shaping “bow-tie” filters determine the radiation dose and the effective scan field-of-view diameter (SFOV) by delivering higher X-ray fluence to a region centered at the isocenter. A method for positioning the heart near the isocenter could enable reduced SFOV imaging and reduce dose in cardiac scans. However, a predictive approach to center the heart, the extent to which heart centering can reduce the SFOV, and the associated dose reductions have not been assessed. The purpose of this study is to build a heart-centered patient positioning model, to test whether it reduces the SFOV required for accurate CAC scoring, and to quantify the associated reduction in radiation dose.

Methods

The location of 38,184 calcium lesions (3,151 studies) in the Multi-Ethnic Study of Atherosclerosis (MESA) were utilized to build a predictive heart-centered positioning model and compare the impact of SFOV on CAC scoring accuracy in heart-centered and conventional body-centered scanning. Then, the positioning model was applied retrospectively to an independent, contemporary cohort of 118 individuals (81 with CAC>0) at our institution to validate the model’s ability to maintain CAC accuracy while reducing the SFOV. In these patients, the reduction in dose associated with a reduced SFOV beam-shaping filter was quantified.

Results

Heart centering reduced the SFOV diameter 25.7% relative to body centering while maintaining high CAC scoring accuracy (0.82% risk reclassification rate). In our validation cohort, imaging at this reduced SFOV with heart-centered positioning and tailored beam-shaping filtration led to a 26.9% median dose reduction (25-75th percentile: 21.6 to 29.8%) without any calcium risk reclassification.

Conclusions

Heart-centered patient positioning enables a significant radiation dose reduction while maintaining CAC accuracy.
State-dependent patterns and coupling between the vaccination schedule, population mobility and the COVID epidemic outline, in the US states
Authors: Rǎdulescu Anca , Alonso Tatiana , Reid Norman , Sanchez Johanna
Published: July 2021

We study the evolution of the COVID-19 epidemic in the US, since January 2020 until May 2021. Our primary goal is to understand some of the complex coupled dynamics between factors that ultimately regulate the epidemic case load. As potentially crucial factors, we focus on population mobility and vaccination patters (both related to risk of contracting the SARS-Cov2 virus). These factors may in turn depend on demographic parameters (which are unrelated to the epidemic evolution), but also on the population response to the epidemic outbreak itself. In our work, we use correlation analyses, in conjunction with open source data from US states, to investigate the type and strength (1) of the relationships between demographic measures and epidemic, mobility and vaccination timelines during our established time window; (2) of the bidirectional coupling between these timelines.

We showed that the wide between-state differences in epidemic outcome correspond to between-state differences in demographic measures (such as density, income, political affiliation). As a potential underlying mechanism, we found that demographic measures are also predictive of the degree of coupling between epidemic timelines (on one hand) and vaccination and mobility timelines (on the other hand), coupling which can be broadly interpreted as the population’s behavioral response to the epidemic. In support of this idea, our analysis shows this response to be tightly correlated with epidemic outcome.

This suggests that a state’s demographic profile may be invaluable to generating predictions on the epidemic evolution in the respective state, and that this information may be used to understand the weaknesses of a state and how to compensate for them to improve epidemic outcome (e.g., via state centralized incentives, and customized mitigation strategies).
SARS-CoV-2-specific Humoral Immune Responses after A Single dose of Inactivated Whole-virus SARS-CoV-2 Vaccine in Kidney Transplant Recipients: An Initial Report
Authors: Bruminhent Jackrapong , Boongird Sarinya , Assanatham Montira , Kiertiburanakul Sasisopin , Malathum Kumthorn , Nongnuch Arkom , Phuphuakrat Angsana , Chaumdee Pongsathon , Jirasiritham Sopon , Janphram Chitimaporn , Tossiri Sansanee , Upama Supparat , Sethaudom Chavachol
Published: July 2021

We presented an initial pilot study report focused on immunogenicity and safety following an inactivated whole-virus severe acute respiratory syndrome coronavirus 2 vaccination among kidney transplant (KT) recipients. At four weeks after the first dose of vaccine, the level of anti–receptor-binding domain IgG antibody was not significantly different compared to before vaccination in 30 KT recipients (p = 0.45). Moreover, a significant lower mean (95% CI) anti–receptor-binding domain IgG antibody was observed compared to 30 immunocompetent controls (2.4 [95% CI 1.3-3.5] vs. 173.1 [95% CI 88.3-2,457.9] AU/mL, p < 0.001). Mild adverse events included fever (17%) and localized pain at the injection site (14%) were observed after vaccination.
Public Opinion and Sentiment Before and at the Beginning of COVID-19 Vaccinations in Japan: Twitter Analysis
Authors: Niu Qian , Liu Junyu , Kato Masaya , Shinohara Yuki , Matsumura Natsuki , Aoyama Tomoki , Nagai-Tanima Momoko
Published: July 2021

Background

The pandemic of COVID-19 is causing a crisis in public health, food systems, and employment. Vaccination is considered as one of the most effective ways for containing the pandemic, but widespread vaccine hesitation on social media may curtail uptake progress. Fully comprehending public sentiment towards the COVID-19 vaccine is critical to building confidence on the vaccines and achieving herd immunity, especially in Japan with inadequate vaccine confidence.

Objective

This study aims to explore the opinion and sentiment towards the COVID-19 vaccine in Japanese tweets, before and at the beginning of large-scale vaccinations.

Methods

We collected 144,101 Japanese tweets containing COVID-19 vaccine-related keywords between August 1, 2020, and June 30, 2021. We visualized the trend of number of tweets and identified the critical events that triggered a surge and provided high-frequency unigram and bigram tokens. Also, we performed sentiment analysis and calculated the correlation of number of tweets and positive/negative sentiments with infection, death, and vaccinated cases. we also used the latent Dirichlet allocation (LDA) model to identify topics of tweets. In addition, we conducted analysis on three vaccine brands (Pfizer/Moderna/AstraZeneca).

Results

Daily number of tweets continued growing and the growth accelerated since the large-scale vaccinations in Japan. The sentiment of around 85% tweets were neutral, and the negative sentiment overwhelmed the positive sentiment in the other tweets. Number of tweets strongly correlated (r≥0.5) with infection/death/vaccinated cases, and the number of negative tweets correlated strongly with the number of infection/death cases but weakened after the first vaccination in Japan. LDA identified three public-concerned topics: vaccine appointment and distribution strategy; Different vaccines development progress and approval status of countries; Side effects and effectiveness against mutated viruses. Among vaccines of the three manufactures, Pfizer won the most attention and Moderna the least.

Conclusions

Our findings indicated that negative sentiment towards vaccines dominated than positive sentiment in Japan. Changes in number of tweets and sentiments might be driven by critical events related to the COVID-19 vaccine, and negative sentiment continued increasing when numerous adverse accidents occurred at the beginning of large-scale vaccinations. Under the negative sentiment, the concerns of three vaccine brands remains effectiveness and safety with slight differences. The policymakers should provide more evidence about the effectiveness and safety of vaccines and optimize the process of vaccinations.
All-cause mortality during SARS-CoV-2 Pandemic in India: Nationally-representative estimates independent of official death registry
Authors: Ramachandran Sabareesh , Malani Anup
Published: July 2021

We estimate excess deaths in India during the COVID pandemic using monthly deaths in the sample of a privately-conducted, nationally-representative, large, panel data set. The data set includes roughly 174,000 households (1.2 million members) and spans January 2015 - June 2021. We estimate COVID is associated with 3.36 million (95% CI: 2.08-4.63 million) excess deaths, a 17.3% increase in the all-cause death rate, until April 2021. Excess deaths spike during the peaks of the 2 infection waves in India. The second wave is associated with significantly more excess deaths than the first. The age-pattern of deaths is skewed towards the elderly relative to baseline.
mRNA Vaccine Effectiveness against COVID-19 among Symptomatic Outpatients Aged ≥16 Years in the United States, February – May 2021
Authors: Kim Sara S , Chung Jessie R , Belongia Edward A , McLean Huong Q , King Jennifer P , Nowalk Mary Patricia , Zimmerman Richard K , Balasubramani Goundappa K , Martin Emily T , Monto Arnold S , Lamerato Lois E , Gaglani Manjusha , Smith Michael E , Dunnigan Kayan M , Jackson Michael L , Jackson Lisa A , Tenforde Mark W , Verani Jennifer R , Kobayashi Miwako , Schrag Stephanie , Patel Manish M , Flannery Brendan
Published: July 2021

Evaluations of vaccine effectiveness (VE) are important to monitor as COVID-19 vaccines are introduced in the general population. Research staff enrolled symptomatic participants seeking outpatient medical care for COVID-19-like illness or SARS-CoV-2 testing from a multisite network. VE was evaluated using the test-negative design. Among 236 SARS-CoV-2 nucleic acid amplification test-positive and 576 test-negative participants aged ≥16 years, VE of mRNA vaccines against COVID-19 was 91% (95% CI: 83-95) for full vaccination and 75% (95% CI: 55-87) for partial vaccination. Vaccination was associated with prevention of most COVID-19 cases among people seeking outpatient medical care.
Low uptake of COVID-19 lateral flow testing among university students: a mixed methods evaluation
Authors: French C.E. , Denford S. , Brooks-Pollock E. , Wehling H. , Hickman M.
Published: July 2021

Objective

To evaluate COVID-19 lateral flow testing (LFT) among asymptomatic university students.

Study design

Mixed methods evaluation of LFT among University of Bristol students.

Methods

i) An analysis of testing uptake and exploration of demographic variations in uptake using logistic regression; ii) an online student survey about views on university testing; and iii) qualitative interviews to explore participants’ experiences of testing and subsequent behaviour, analysed using a thematic approach.

Results

12,391 LFTs were conducted on 8025/36,054 (22.3%) students. Only one in 10 students had the recommended two tests. There were striking demographic disparities in uptake with those from ethnic minority groups having lower uptake (e.g. 3% of Chinese students were tested vs. 30.7% of White students), and variations by level and year of study (ranging from 5.3% to 33.7%), place of residence (29.0% to 35.6%) and faculty (15.2% to 32.8%). Differences persisted in multivariable analyses.

A total of 436 students completed the online survey, and twenty in-depth interviews were conducted. Barriers to engagement with testing included a lack of awareness, knowledge and understanding, and concerns about the accuracy and safety. Students understood limitations of LFTs but requested further information about test accuracy. Tests were used to inform behavioural decisions, often in combination with other information, such as the potential for exposure to the virus and perceptions of vulnerability.

Conclusions

The low uptake of testing brings into question the role of mass LFT in university settings. Innovative strategies may be needed to increase LFT uptake among students.