bluuebunny/crossref_metadata_2025 huggingface dataset:
Slit-lamp Pars Plana Needle Hyaloidotomy-Zonulotomy-Iridotomy for the Treatment of Spontaneous Malignant Glaucoma
Authors: Thomas Merina , Boese Erin A. , Lieu Philip , Shah Manjool
Published: February 2020

An 88-year-old woman with a history of recent complicated pacemaker insertion presented with acute-onset malignant glaucoma recalcitrant to conservative medical therapy. Surgical intervention was discussed; however, given her complex cardiac history and recent postoperative state, the risk of anesthesia-related systemic adverse events was deemed unacceptably high. As such, a slit-lamp procedure was recommended to break the attack of malignant glaucoma. Here within, we report a novel technique of breaking an attack of malignant glaucoma by needling the anterior hyaloid face at the slit lamp. With this technique, a 25-G needle was entered through the pars plana and was advanced through the anterior hyaloid face, zonules, and peripheral iridotomy to create a unicameral eye and successfully break the malignant closure attack.
The Impact of Routinely Measuring IOP in Younger Adults to Screen for Glaucoma in a Large Eye Hospital
Authors: Garzon Catalina , Odayappan Annamalai , Kavitha Srinivasan , Venkatesh Rengaraj , Friedman David S.
Published: February 2020

Precis:

Intraocular pressure (IOP) screening in adults 18 to 40 years of age identified 1 in 535 young adults with or at risk for developing glaucoma in India with a cost of about Indian rupee 596 (USD 8) per patient diagnosed.

Purpose:

The purpose of this study was to evaluate the outcomes of routine noncontact tonometry as a screening modality for glaucoma in young adults receiving an eye examination at Aravind Eye Hospital, Pondicherry, India.

Methods:

Retrospective chart review of adults 18 to 40 years of age screened for IOP from November 2017 to June 2018. The diagnoses were determined by a glaucoma specialist using gonioscopy, dilated fundus examination, and occasionally, Humphrey Field Analyzer, and/or optical coherence tomography. Analyses include detection of glaucoma, ocular hypertension (OHT), angle closure, and calculation of the yield of this screening paradigm.

Results:

A total of 28,369 younger adults were screened and 296 (1.05%) were referred to the glaucoma unit, 84 for an IOP >21 mm Hg and 208 for other reasons. The hypertensive group had a mean screening IOP of 29.3±8.4 mm Hg and the following diagnoses: OHT (19%), secondary raised IOP (14%), glaucoma (26%), angle closure (4%), healthy (11%) and need for further examination (26%). Fifty-five percent of those with glaucoma were previously undiagnosed. In comparison, the normotensive group had a mean IOP of 16±2.5 mm Hg and the following diagnoses: OHT (1%), glaucoma (5%), occludable angles (8%), healthy (47%) and need of further examination (33%). Nearly 40% of these patients with glaucoma were previously undiagnosed.

Conclusions:

One of every 535 young adults screened had both IOP >21 mm Hg and angle closure, OHT, secondary raised IOP or glaucoma. Given their young age and the potential to treat and delay progression, the benefits seem to outweigh the low cost of this screening.
Effect of Nonthermal Processing on Human Milk Bactericidal Activity Against Escherichia coli
Authors: Barbarska Olga , Strom Kamila , Oledzka Gabriela , Calvo Javier , Gayà Antoni , López‐Mendoza María Carmen , Rutkowska Malgorzata , Rosiak Elzbieta , Wesolowska Aleksandra Maria
Published: February 2020

Nonthermal methods are more efficient at preserving various biological properties of human milk, as compared with holder pasteurization (HoP), which is the most common preservation method. This study was performed to assess the effects of nonthermal processing on bactericidal activity against Escherichia coli in human milk. Milk samples obtained from the Regional Human Milk Bank in Warsaw at Holy Family Hospital were processed by HoP, irradiated with ultraviolet‐C (UV‐C) for 5, 10, and 15 minutes (6720 J/L each minute), subjected to 2 variations of high‐pressure processing (HPP): 450 MPa for 15 minutes and 200 MPa for 10 minutes + 400 MPa for 10 min, with a 10‐minutes break. The samples were then evaluated by a bactericidal assay (raw untreated human milk was used as a control). The bactericidal capacity after HoP was preserved in 12.1% of samples, showing a significant reduction in bactericidal properties compared with in raw milk (P < 0.05). The differences between samples preserved by nonthermal methods and raw milk were not significant (P > 0.05). Nonthermal methods of human milk treatment better preserve the bactericidal capacity compared with holder pasteurisation. Those alternative technologies to HoP can be proposed after further investigation for milk processing for Human Milk Banks facilities.
Preventing Hypothermia during Cesarean Birth
Authors: Dendis Michelle , Hooven Katie
Published: February 2020

Purpose:

The purpose of this integrative review was to assess common warming measures used for prevention of hypothermia during the perioperative period for women having cesarean birth and to determine their efficacy.

Methods:

A literature search was conducted via electronic databases EBSCO, PUBMED, Academic Search Premier, Google Scholar, and CINAHL using keyword search terms hypothermia, cesarean, and warming. Inclusion criteria were articles written in English and published between 2006 and 2018.

Results:

Seventeen articles were included in the review, covering three common warming measures; intravenous (IV) fluid warming, forced-air warming, and combined IV fluid and forced-air warming. Several other warming modalities were noted including warming mattresses and various combinations of interventions.

Clinical Implications:

Maternal hypothermia risk is increased during the perioperative period for women having cesarean birth without use of warming measures. Warming modalities that are beneficial in preventing maternal hypothermia in women having cesarean birth are IV fluid warming, upper body force-air warming, ambient OR temperature, and warming mattresses. National standards and guidelines from the American Society of PeriAnesthesia Nurses, the Association of Perioperative Registered Nurses, and the Association of Women's Health, Obstetric, and Neonatal Nurses are consistent with current evidence and should be in place and followed in every maternity unit caring for women having cesarean birth.
Geometric Measurements of Nipple Position in Breasts Reconstructed with Transverse Rectus Abdominis Musculocutaneous Flap: A 5-Year Prospective Study
Authors: Cha Han Gyu , Kim Hyung Bae , Yun Ji Young , Lee Taik Jong , Ahn Misung , Maldonado Andrés A. , Kim Eun Key
Published: February 2020

Background:

After breast reconstruction, nipple position and other long-term changes in the reconstructed breast relative to the contralateral breast remain poorly understood. In this prospective cohort study, the authors performed serial nipple position measurements over 5 years in patients who had undergone breast reconstruction with a transverse rectus abdominis musculocutaneous (TRAM) flap. The effects of adjuvant radiotherapy on nipple position over time were also investigated.

Methods:

The authors studied 150 patients who had undergone nipple-sparing mastectomy, using radial incision followed by immediate unilateral pedicled TRAM flap breast reconstruction. Measurements of sternal notch–to-nipple, midline-to-nipple, and inframammary fold–to-nipple distances were performed 1 day before reconstruction and 6, 12, 36, and 60 months after surgery, on patients’ reconstructed and nonoperated breasts.

Results:

The average sternal notch–to-nipple distance increased in both reconstructed and nonoperated breasts at every follow-up visit, with an average difference of 0.393 cm at the 60-month visit (p < 0.0001). Comparing the pattern of distance change, reconstructed breasts tend to change more slowly than nonoperated breasts until 36 months postoperatively. In irradiated breasts, the sternal notch–to-nipple distance was significantly smaller than in nonirradiated breasts, and nipple position changed minimally between 1 and 3 years after surgery.

Conclusions:

Nipple position in TRAM flap–reconstructed breasts changed over time compared with that in nonoperated breasts, especially along the vertical axis. The pattern of nipple position change in reconstructed breasts became similar to nonoperated breasts 3 years after surgery. In patients who had undergone adjuvant radiation therapy, nipple position remained consistent for 1 to 3 years.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Opioid Prescribing and Use Patterns in Postsurgical Facial Trauma Patients
Authors: Lapidus Jodi B. , Santosa Katherine B. , Skolnick Gary B. , Som Avira , Cho Gerald J. , Waljee Jennifer F. , AuBuchon Jacob D. , Patel Kamlesh B.
Published: February 2020

Background:

Facial fractures are painful injuries routinely managed by opioids after surgical repair. Studies have identified patient risk factors and prescribing patterns associated with opioid use in medicine and general surgery; however, little is known about these entities in the facial trauma population.

Methods:

A retrospective cohort study of opioid-naive patients undergoing surgical repair of facial fractures was conducted using the Truven Health MarketScan Commercial Claims and Encounters (2006 to 2015) and Medicaid Multi-State Databases (2011 to 2015). Eligible procedures included nasal, nasoorbitoethmoid, orbital, mandible, and Le Fort fracture repair. Opioid type, daily dosage, and prescription duration were analyzed. Multivariable logistic regression was performed to determine independent predictors of prescription refill.

Results:

A total of 20,191 patients undergoing surgical repair of facial fractures were identified. Of these, 15,861 patients (78.6 percent) filled a perioperative opioid prescription. Refill (58.7 percent) and potentially inappropriate prescribing (39.4 percent) were common among this population. Patient factors including prior substance use (adjusted OR, 1.84; 95 percent CI, 1.63 to 2.07) and history of mental health disorder (adjusted OR, 1.43; 95 percent CI, 1.06 to 1.91) were independent predictors of refill. Increased odds of refill were seen in patients prescribed tramadol (OR, 1.98; 95 percent CI, 1.48 to 2.66) and those who underwent multiple surgical repairs (OR, 3.38; 95 percent CI, 2.54 to 4.50).

Conclusions:

Refill and potentially inappropriate prescribing occurred at high rates in facial trauma patients undergoing surgical repair. Additional studies are needed to develop guidelines for proper opioid prescribing in this population.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, III.
A Novel Hump Reinsertion Technique to Reconstruct the Nasal Dorsum
Authors: Öztürk Güncel
Published: February 2020

Nasal hump removal and modification is a commonly performed procedure in rhinoplasty. The spreader flap is most commonly used in the reconstruction technique and involves suturing the medial end of the upper lateral cartilage (ULC) onto the septum. In this study, author presents a new hump removal technique that includes a novel procedure for hump reinsertion and suturing that is easy and comfortable to apply in hump removal operations. The records of the patients were assessed retrospectively from private practice. Patients who had undergone hump removal operations using a hump reinsertion graft were included. In total, 54 patients met the inclusion and exclusion criteria, and their records were assessed. The hump was divided into 3 parts longitudinally. The septum, which is a part of the nasal hump, was prepared as a strut graft, and the ULCs were prepared as spreader grafts. A novel suturing technique was used while the spreader grafts were fixed. This technique was used if the ULC was larger than 3 mm. The patients were evaluated using the “Rhinoplasty Outcome Evaluation” (ROE) 12 months after surgery. The initial median ROE score was 40.5; after surgery, it increased to 88.5. The ROE score changed significantly (P < .001). The postoperative results were satisfactory. After assessments, no asymmetry or functional problems were found in all participants. This technique allows for closed rhinoplasty without the need for an additional graft from the septum, enhancing the prevention of displacement and improving functionality.
Resuscitation From Hemorrhagic Shock With Fresh and Stored Blood and Polymerized Hemoglobin
Authors: Williams Alexander T. , Lucas Alfredo , Muller Cynthia R. , Munoz Carlos , Bolden-Rush Crystal , Palmer Andre F. , Cabrales Pedro
Published: February 2020

Background:

Hemoglobin (Hb)-based oxygen carriers (HBOCs) have been proposed as alternatives to blood for decades. Previous studies demonstrated that large molecular diameter HBOCs based on polymerized bovine Hb (PolybHb) attenuate Hb side-effects and toxicity. The objective of this study was to test the safety and efficacy of tense state PolybHb after long-term storage.

Methods and Results:

PolybHb was subjected to diafiltration to remove low molecular weight (< 500 kDa) species and stored for 2 years. PolybHb was studied in parallel with blood, collected from rats and stored leukodepleted under blood bank conditions for 3 weeks. Rats were hemorrhaged and resuscitated to 90% of the blood pressure before the hemorrhage with fresh blood, stored blood, fresh PolybHb, or 2-year-stored PolybHb. Hemorrhagic shock impaired oxygen delivery and cardiac function. Resuscitation restored blood pressure and cardiac function, but stored blood required a significantly larger transfusion volume to recover from shock compared with fresh blood and PolybHb (fresh and stored). Stored blood transfusion elevated markers of organ damage compared with all other groups.

Conclusions:

These studies indicate that large molecular diameter PolybHb is as efficacious as fresh blood in restoring cardiac function and confirm the lack of degradation of PolybHb's safety or efficacy during long-term storage.
Deciding Our Future: Consensus Conference Summary Report
Authors: Siddiqui Nazema Y. , Dunivan Gena C. , Chermansky Christopher J. , Bradley Catherine S.
Published: February 2020

Objectives

There are few quality measures that allow for optimization of care for pelvic organ prolapse (POP). In coordination with the American Urogynecologic Society (AUGS), a prior group agreed upon health care provider–reported data elements that are important for large-scale quality measurement. The primary objective was to review existing patient-reported outcome (PRO) measurement tools for POP and consider where improvements are needed for inclusion in a quality measurement tool. A secondary objective was to discuss enhanced strategies to improve the quality of care for women with mesh complications.

Methods

The AUGS Scientific Committee convened a 1-day meeting titled “Deciding our Future: Consensus Conference on Prolapse Outcomes and Best Practices for Mesh Complications.” Speakers discussed the current state of POP outcome measurement and meaningful ways of measuring and improving quality. Furthermore, past and future work for standardization of care regarding mesh complications was discussed.

Results

Conference participants included invited speakers, representatives from AUGS and partner societies, 5 patient representatives from the AUGS Patient Advisory Committee, and 38 registered participants from academic institutions, community practices, and industry. Participants developed a roadmap for incorporating PROs into a national POP quality improvement registry. Participants also discussed important gaps in our knowledge of treatment of mesh complications and previewed proposed terminology and treatment algorithms.

Conclusions

Using appropriate methodology, existing PRO measurement tools can be collapsed into one concise tool for POP quality measurement. Over the next year, work will continue toward this goal. Proposed updates to mesh terminology and treatment algorithms will be published separately.
Incidence and Outcomes of Significant Weight Changes After Pancreas Transplant Alone
Authors: Swanson Kurtis J. , Joachim Emily , Arunachalam Annamalai , Aziz Fahad , Garg Neetika , Mohamed Maha , Djamali Arjang , Redfield Robert R. , Kaufman Dixon B. , Odorico Jon , Mandelbrot Didier , Parajuli Sandesh
Published: February 2020

Background.

Weight change, primarily weight gain, is a common problem among solid organ transplant recipients. The incidence of weight gain or loss after successful pancreas transplant alone (PTA) and the effect on graft survival is unknown.

Methods.

This was a single-center observational study among PTA recipients, transplanted at our center between January 1, 2005, and July 31, 2017, who had a functional pancreas graft for at least 1 year and documented weight change at the 1-year clinic visit.

Results.

In this cohort study of 105 PTA recipients, 28 had significant weight gain, 27 had significant weight loss, and the remaining 50 did not have significant weight change at 1-year posttransplant. When comparing the weight gain and no weight change groups, the weight gain cohort started to gain weight at 3 months posttransplant to 5 years or last follow up. Similarly, the weight loss group lost weight at 3 months posttransplant up to last follow up. Clinically significant weight gain or weight loss were not associated with uncensored or death censored graft failure in univariate regression and Kaplan-Meier survival analysis. Also, there were no significant differences between the groups in the glycated hemoglobin at last follow up.

Conclusions.

Approximately 50% of PTA recipients had a significant weight change at 1-year posttransplant, of which 25% gained significant weight and 25% loss. There was no significant difference in graft survival due to the significant weight changes. Further research is needed in this field.
Thoracic scales of moths as a stealth coating against bat biosonar
Authors: Neil Thomas R. , Shen Zhiyuan , Robert Daniel , Drinkwater Bruce W. , Holderied Marc W.
Published: February 2020

Many moths are endowed with ultrasound-sensitive ears that serve the detection and evasion of echolocating bats. Moths lacking such ears could still gain protection from bat biosonar by using stealth acoustic camouflage, absorbing sound waves rather than reflecting them back as echoes. The thorax of a moth is bulky and hence acoustically highly reflective. This renders it an obvious target for any bat. Much of the thorax of moths is covered in hair-like scales, the layout of which is remarkably similar in structure and arrangement to natural fibrous materials commonly used in sound insulation. Despite this structural similarity, the effect of thorax scales on moth echoes has never been characterized. Here, we test whether and how moth thorax scales function as an acoustic absorber. From tomographic echo images, we find that the thin layer of thoracic scales of diurnal butterflies affects the strength of ultrasound echoes from the thorax very little, while the thorax scales of earless moths absorbs an average of 67 ± 9% of impinging ultrasonic sound energy. We show that the thorax scales of moths provide acoustic camouflage by acting as broadband (20–160 kHz) stealth coating. Modelling results suggest the scales are acting as a porous sound absorber; however, the thorax scales of moths achieve a considerably higher absorption than technical fibrous porous absorbers with the same structural parameters. Such scales, despite being thin and lightweight, constitute a broadband, multidirectional and efficient ultrasound absorber that reduces the moths' detectability to hunting bats and gives them a survival advantage.
Speckle tracking echocardiography could detect the difference of pressure overload-induced myocardial remodelling between young and adult rats
Authors: Niu Pei , Li Li , Yin Zhongjie , Du Jie , Tan Wenchang , Huo Yunlong
Published: February 2020

The assessment by speckle tracking echocardiography (STE) provides useful information on regional and global left ventricular (LV) functions. The aim of the study is to investigate if STE-based strain analysis could detect the difference of pressure overload-induced myocardial remodelling between young and adult rats. Physiological, haemodynamic, histological measurements were performed post-operatively in young and adult rats with transverse aortic constriction (TAC) as well as the age-matched shams. Two-way ANOVA was used to detect the statistical difference of various measured parameters. Pressure overload decreased the ejection fraction, fractional shortening, d
p
/d
t
max
and

|

d
p

/

d

t

min

|

, but increased the LV end-diastolic (ED) pressure in adult rat hearts for nine weeks after TAC operation than those in young rat hearts. Pressure overload also resulted in different changes of peak strain and strain rate in the free wall, but similar changes in the interventricular septum of young and adult rat hearts. The changes in myocardial remodelling were confirmed by the histological analysis including the increased apoptosis rate of myocytes and collagen area ratio in the free wall of adult rat hearts of LV hypertrophy when compared with the young. Pressure overload alters myocardial components in different degrees between young and adult animals. STE-based strain analysis could detect the subtle difference of pressure overload-induced myocardial remodelling between young and adult rats.
Bacteraemia with Moryella indoligenes and Fastidiosipila sanguinis: a case report
Authors: Kjær Hansen Sanne , Løfberg Sandra Valborg , Nielsen Dorte Kassentoft , Kobberø Hanne , Justesen Ulrik Stenz
Published: February 2020

Moryella indoligenes

and

Fastidiosipila sanguinis

are obligate anaerobic Gram-positive bacteria that are rarely involved in human infections. We present the first case of bacteraemia with

M. indoligenes

, which was part of a co-infection with

F. sanguinis

. Both micro-organisms were identified by 16S rRNA gene sequencing and

M. indoligenes

was also identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Prostate cancer involving the bladder suggests that the urinary tract was the most likely primary site of infection.
Filimonas effusa sp. nov., isolated from a freshwater river
Authors: Chen Wen-Ming , Chen Tzu-Ying , Li Zhi-Hao , Kwon Soon-Wo , Sheu Shih-Yi
Published: February 2020

Strain TTM-71T, isolated from a freshwater river in Taiwan, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-71Tis affiliated with species in the genusFilimonas. The 16S rRNA gene sequence similarity indicated that strain TTM-71Tis closely related to species within the genusFilimonas(94.7–95.5 % sequence similarity) and had a high sequence similarity withFilimonas endophyticaSR 2-06T(95.5 %). Strain TTM-71Tshowed 70.3 % average nucleotide identity and 24.9 % digital DNA–DNA hybridization identity withFilimonas lacunaeYT21T. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed beige-colored colonies. Optimal growth occurred at 20 °C, pH 8, and in the presence of 0.5 % NaCl. The major fatty acids of strain TTM-71Twere iso-C15 : 0, iso-C15 : 1G and summed feature 3 (comprising C16 : 1 ω7cand/or C16 : 1 ω6c). The predominant hydroxy fatty acid was iso-C17 : 03-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, four uncharacterized aminophospholipids, one uncharacterized aminolipid, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamine was homospermidine. The only isoprenoid quinone was MK-7. Genomic DNA G+C content was 45.6 mol%. On the basis of the polyphasic evidence presented, strain TTM-71Tis considered to represent a novel species of the genusFilimonas, for which the nameFilimonas effusasp. nov. is proposed. The type strain is TTM-71T(=BCRC 81160T=LMG 31017T=KCTC 62871T).
Agromyces badenianii sp. nov., isolated from plateau pika (Ochotona curzoniae)
Authors: Li Junqin , Lu Shan , Jin Dong , Yang Jing , Lai Xin-He , Mi Fei , Zhang Dezhu , Zhang Gui , Tian Zhi , Dong Kui , Zhang Sihui , Lei Wenjing , Pu Ji , Wu Xiaomin , Huang Ying , Ren Zhihong , Wang Suping , Xu Jianguo
Published: February 2020

Two aerobic, Gram-stain-positive, catalase-positive, non-motile and rod-shaped bacterial strains, designated MF30-AT and MF845, were isolated from the intestinal contents of plateau pika collected from the Qinghai–Tibet Plateau. Optimal growth of these two strains was observed under aerobic conditions at pH 7.0 and 28 °C. The 16S rRNA gene sequences of the isolates had highest similarities of 98.5 and 98.4 % to

Agromyces fucosus

, respectively. In the 16S rRNA gene and polygenetic trees, strains MF30-AT and MF845 were clearly distinct from other species. The two strains could not produce acid from arbutin, d-fructose, D-sucrose, glycogen, salicin or starch. Production of β-glucosidase by these strains was negative. The major fatty acids of these strains were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain MF30-AT contained galactose, rhamnose and ribose as cell wall sugars and MK-12 and MK-11 as predominant menaquinones. The major polar lipids in strain MF30-AT were diphosphatidylglycerol, phosphatidylglycerol and a glycolipid, while the peptidoglycan contained alanine, glutamic acid, glycine and 2,4-diaminobutyric acid. The G+C contents of the DNA of strains MF30-AT and MF845 were 69.8 mol% and 69.7 mol%, respectively. The average nucleotide identity and digital DNA–DNA relatedness values of the two strains with all available genomes of the genus

Agromyces

were far below the respective thresholds of 95 and 70 %, respectively. All genotypic and phenotypic data indicated that strains MF30-AT and MF845 should be classified as novel members of the genus

Agromyces

, for which the name Agromyces badenianii sp. nov. is proposed. The type strain is MF30-AT (=CGMCC 1.16469T=DSM 106183T).
Leaky scanning translation generates a second A49 protein that contributes to vaccinia virus virulence
Authors: Neidel Sarah , Torres Alice A. , Ren Hongwei , Smith Geoffrey L.
Published: February 2020

Vaccinia virus (VACV) strain Western Reserve gene A49L encodes a small intracellular protein with a Bcl-2 fold that is expressed early during infection and has multiple functions. A49 co-precipitates with the E3 ubiquitin ligase β-TrCP and thereby prevents ubiquitylation and proteasomal degradation of IκBα, and consequently blocks activation of NF-κB. In a similar way, A49 stabilizes β-catenin, leading to activation of the wnt signalling pathway. However, a VACV strain expressing a mutant A49 that neither co-precipitates with β-TrCP nor inhibits NF-κB activation, is more virulent than a virus lacking A49, indicating that A49 has another function that also contributes to virulence. Here we demonstrate that gene A49L encodes a second, smaller polypeptide that is expressed via leaky scanning translation from methionine 20 and is unable to block NF-κB activation. Viruses engineered to express either only the large protein or only the small A49 protein both have lower virulence than wild-type virus and greater virulence than an A49L deletion mutant. This demonstrates that the small protein contributes to virulence by an unknown mechanism that is independent of NF-κB inhibition. Despite having a large genome with about 200 genes, this study illustrates how VACV makes efficient use of its coding potential and from gene A49L expresses a protein with multiple functions and multiple proteins with different functions.
N-terminal region of Helicobacter pylori CagA induces IL-8 production in gastric epithelial cells via the β1 integrin receptor
Authors: Zeng Bangwei , Chen Chu , Yi Qingfeng , Zhang Xiaoyan , Wu Xiangyan , Zheng Shurong , Li Neng , She Feifei
Published: February 2020

Introduction.

Helicobacter pylori

is associated with gastrointestinal disease, most notably gastric cancer. Cytotoxin-associated antigen A (CagA), an important virulence factor for

H. pylori

pathogenicity, induces host cells to release inflammatory factors, especially interleukin-8 (IL-8). The mechanism by which C-terminal CagA induces IL-8 production has been studied extensively, but little is known about the role of the N-terminus.

Aim. To investigate the effect of CagA303–456aa (a peptide in the N-terminal CagA) on IL-8 production by gastric epithelial cells.

Methodology. CagA303-456aa was produced by a prokaryotic expression system and purified by Strep-tag affinity chromatography. An integrin β1 (ITGB1)-deficient AGS cell line was constructed using the CRISPR/Cas9 technique, and NCTC 11637 cagA and/or cagL knockout mutants were constructed via homologous recombination. The levels of IL-8 production were determined by enzyme-linked immunosorbent assay (ELISA), and p38 and ERK1/2 phosphorylation were examined by Western blot.

Results. CagA303-456aa induced IL-8 expression by AGS cells. IL-8 induction by CagA303-456aawas specifically inhibited by ITGB1 deficiency. Notably, CagA303-456aa activated the phosphorylation of both p38 and ERK1/2, and blocking p38 and ERK1/2 activity significantly reduced IL-8 induction by CagA303-456aa. ITGB1 deficiency also inhibited the activation of p38 phosphorylation by CagA303-456aa. Finally, experiments in CagA and/or CagL knockout bacterial lines demonstrated that extracellular CagA might induce IL-8 production by AGS cells.

Conclusion. Residues 303–456 of the N-terminal region of CagA induce IL-8 production via a CagA303-456–ITGB1–p38–IL-8 pathway, and ERK1/2 is also involved in the release of IL-8. Extracellular CagA might induce IL-8 production before translocation into AGS cells.
Highly multidrug-resistant Morganella morganii clinical isolates from Nepal co-producing NDM-type metallo-β-lactamases and the 16S rRNA methylase ArmA
Authors: Shrestha Shovita , Tada Tatsuya , Sherchan Jatan B. , Uchida Hiroki , Hishinuma Tomomi , Oshiro Satoshi , Morioka Shinichiro , Kattel Hari , Kirikae Teruo , Sherchand Jeevan B.
Published: February 2020

Morganella morganiican harbour extended-spectrum β-lactamases and carbapenemases, resulting in increased resistance to multiple antibiotics and a high mortality rate. This study describes the emergence of highly multidrug-resistant clinical isolates ofM. morganiifrom Nepal co-producing NDM-type metallo-β-lactamases, including NDM-1 and NDM-5, and the 16S rRNA methylase ArmA. This is the first report ofM. morganiiclinical isolates from Nepal co-producing NDM-1/-5 and ArmA. It is important to establish infection control systems and effective treatments against multidrug-resistantM. morganii.
Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction
Authors: Basher Abdur Rahman M. A. , Hallam Steven J.
Published: February 2020

Metabolic pathway reconstruction from genomic sequence information is a key step in predicting regulatory and functional potential of cells at the individual, population and community levels of organization. Although the most common methods for metabolic pathway reconstruction are gene-centric e.g. mapping annotated proteins onto known pathways using a reference database, pathway-centric methods based on heuristics or machine learning to infer pathway presence provide a powerful engine for hypothesis generation in biological systems. Such methods rely on rule sets or rich feature information that may not be known or readily accessible. Here, we present pathway2vec, a software package consisting of six representational learning based modules used to automatically generate features for pathway inference. Specifically, we build a three layered network composed of compounds, enzymes, and pathways, where nodes within a layer manifest inter-interactions and nodes between layers manifest betweenness interactions. This layered architecture captures relevant relationships used to learn a neural embedding-based low-dimensional space of metabolic features. We benchmark pathway2vec performance based on node-clustering, embedding visualization and pathway prediction using MetaCyc as a trusted source. In the pathway prediction task, results indicate that it is possible to leverage embeddings to improve pathway prediction outcomes.

Availability and implementation

The software package, and installation instructions are published ongithub.com/pathway2vec

Contact

shallam@mail.ubc.ca
LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium
Authors: Zwiggelaar Rosalie T. , Lindholm Håvard T. , Fosslie Madeleine , Pedersen Marianne T. , Ohta Yuki , Díez-Sánchez Alberto , Martín-Alonso Mara , Ostrop Jenny , Matano Mami , Parmar Naveen , Kvaløy Emilie , Spanjers Roos R. , Nazmi Kamran , Rye Morten , Drabløs Finn , Arrowsmith Cheryl , Dahl John Arne , Jensen Kim B. , Sato Toshiro , Oudhoff Menno J.
Published: February 2020

Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify new regulators of neonatal intestinal epithelial development by testing a small library of epigenetic modifier inhibitors in Paneth cell-skewed organoid cultures. We found that Lysine-specific demethylase 1A (Kdm1a/Lsd1) is absolutely required for Paneth cell differentiation.Lsd1-deficient crypts, devoid of Paneth cells, are still able to form organoids without a requirement of exogenous or endogenous Wnt. Mechanistically, we find that LSD1 represses genes that are normally expressed in fetal and neonatal epithelium. This gene profile is similar to what is seen in repairing epithelium, and indeed, we find thatLsd1-deficient epithelium has superior regenerative capacities after irradiation injury. In summary, we found an important regulator of neonatal intestinal development and identified a druggable target to reprogram intestinal epithelium towards a reparative state.
Supervising the PhD: identifying common mismatches in expectations between candidate and supervisor to improve research training outcomes
Authors: Cardilini Adam P.A. , Risely Alice , Richardson Mark F.
Published: February 2020

The relationship between a PhD candidate and their supervisor is influential in not only successful candidate completion, but maintaining candidate satisfaction and mental health. We quantified potential mismatches between the PhD candidates and supervisors expectations as a potential mechanism that facilitates poor candidate experiences and research training outcomes. 114 PhD candidates and 52 supervisors ranked the importance of student attributes and outcomes at the beginning and end of candidature. In relation to specific attributes, supervisors indicated the level of guidance they expected to give the candidate and candidates indicated the level of guidance they expected to receive. Candidates also report on whether different aspects of candidature influenced their mental well-being. We identified differences between candidates and supervisors perceived supervisor teaching responsibility and influences on mental well-being. Our results indicate that the majority of candidates were satisfied overall with their supervision, and find alignment of many expectations between both parties. Yet, we find that candidates have much higher expectations of achieving quantitative outcomes than supervisors. Supervisors believed they give more guidance to candidates than candidates perceive they received, and supervisors often only provided guidance when the candidate explicitly asked. Personal expectations and research progress significantly and negatively influenced over 50% of candidate’s mental well-being. Our results highlight the importance of candidates and supervisors explicitly communicating the responsibilities and expectations of the roles they play in helping candidates develop research skills. We provide four suggestions to supervisors that may be particularly effective at increasing communication, avoiding potential conflict and promoting candidate success and wellbeing.
Evolution of the standard genetic code
Authors: Yarus Michael
Published: February 2020

A near-universal Standard Genetic Code (SGC) implies a single origin for Earthly life. To study this unique event, I compute paths to the SGC, comparing different plausible histories. Notably, SGC-like coding emerges from traditional evolutionary mechanisms, and a superior path can be identified.

To objectively measure evolution, progress values from 0 (random coding) to 1 (SGC-like) are defined: these measure fractions of random-code-to-SGC distance. Progress types arespacing/distance/deltaPolarRequirement, detecting space between identical assignments /mutational distance to the SGC/chemical order, respectively. A coding system was based on known RNAs performing aminoacyl-RNA synthetase reactions. Acceptor RNAs exhibit SGC-like wobble; alternatively, non-wobbling triplets uniquely encode 20 amino acids/start/stop. Triplets acquire 22 functions by stereochemistry, selection, coevolution, or randomly. Assignments also propagate to an assigned triplet’s neighborhood via single mutations, but can also decay.

Futile evolutionary paths are plentiful due to the vast code universe. Thus SGC evolution is critically sensitive to disorder from random assignments. Evolution also inevitably slows near coding completion. Coding likely avoided these difficulties, and two suitable paths are compared. Inlate wobble, a majority of non-wobble assignments are made before wobble is adopted. Incontinuous wobble, a uniquely advantageous early intermediate supplies the gateway to an ordered SGC. Revised coding evolution (limited randomness, late wobble, concentration on amino acid encoding, chemically conservative coevolution with a chemically-ordered elite) produces varied full codes with excellent joint progress values. A population of only 600 independent coding tables includes SGC-like members; a Bayesian path toward more accurate SGC evolution is available.
Tree diversity effects on forest productivity increase through time because of spatial partitioning
Authors: Tatsumi Shinichi
Published: February 2020

Background

Experimental manipulations of tree diversity have often found overyielding in mixed-species plantations. While most experiments are still in the early stages of stand development, the impacts of tree diversity are expected to accumulate over time. Here, I present findings from a 31-year-old tree diversity experiment (as of 2018) in Japan.

Results

I find that the net diversity effect on stand biomass increased linearly through time. The species mixture achieved 64% greater biomass than the average monoculture biomass 31 years after planting. The complementarity effect was positive and increased exponentially with time. The selection effect was negative and decreased exponentially with time. In the early stages (≤3 years), the positive complementarity effect was explained by enhanced growths of early- and mid-successional species in the mixture. Later on (≥15 years), it was explained by their increased survival rates owing to vertical spatial partitioning — i.e., alleviation of self-thinning via canopy stratification. The negative selection effect resulted from suppressed growths of late-successional species in the bottom layer.

Conclusions

The experiment provides pioneering evidence that the positive impacts of diversity-driven spatial partitioning on forest biomass can accumulate over multiple decades. The results indicate that forest biomass production and carbon sequestration can be enhanced by multispecies afforestation strategies.
Methods for Running a Successful Women-in-STEM Organization on an Academic Campus
Authors: Rupert Deborah D. , Nowlan Alexandra C. , Tam Oliver H. , Hammell Molly Gale
Published: February 2020

The current academic culture facing women in science, technology, engineering, and math (STEM) fields in the United States has sparked the formation of grassroots advocacy groups to empower female scientists-in-training. However, the impact of these initiatives often goes unmeasured and underappreciated. Our Women in Science and Engineering (WiSE) organization serves post-doctoral researchers, graduate students, and research technicians (trainees) at a private research institute for biological sciences. Here we propose the following guidelines for cultivating a successful women-in-STEM-focused group based upon survey results from our own scientific community as well as the experience of our WiSE group leaders. We hope these recommendations can provide guidance to advocacy groups at other research and academic organizations that wish to strengthen their efforts. While our own group specifically focuses on the underrepresented state of women in science, we hope these guidelines may be adapted and applied to groups that advocate for any minority group within the greater scientific community (i.e. those of gender, race/ethnicity, socioeconomic background, sexual orientation, etc.).
Molecular epidemiology of third-generation cephalosporin-resistant Enterobacteriaceae from Southeast Queensland, Australia
Authors: Stewart AG , Price EP , Schabacker K , Birikmen M , Harris PNA , Choong K , Subedi S , Sarovich DS
Published: February 2020

Synopsis

Third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae represent a major threat to human health. Here, we captured 288 3GC-R Enterobacteriaceae clinical isolates from 264 patients presenting at a regional Australian hospital over a 14-month period. Alongside routine mass spectrometry speciation and antibiotic sensitivity testing, isolates were examined using rapid (∼40 min) real-time PCR assays targeting the most common extended spectrum β-lactamases (ESBLs; CTX-M-1 and CTX-M-9 groups, plus TEM, SHV, and an internal 16S ribosomal DNA control). AmpC CMY β-lactamase prevalence was also examined.Escherichia coli(80.2%) andKlebsiella pneumoniae(17.0%) were dominant, withKlebsiella oxytoca, Klebsiella aerogenesandEnterobacter cloacaeinfrequently identified. Ceftriaxone and cefoxitin resistance were identified in 97.0% and 24.5% ofE. coli andK. pneumoniae isolates, respectively. Consistent with global findings in Enterobacteriaceae, most (98.3%) isolates harbored at least one β-lactamase gene, with 144 (50%) encodingblaCTX-M-1group, 92 (31.9%)blaCTX-M-9group, 48 (16.7%)blaSHV, 133 (46.2%)blaTEM, and 34 (11.8%)blaCMY. A subset of isolates (n=98) were subjected to whole-genome sequencing (WGS) to identify the presence of cryptic resistance determinants, and to verify genotyping accuracy. WGS of β-lactamase negative or carbapenem-resistant isolates identified uncommon ESBLs and carbapenemases, includingblaNDMandblaIMP, and confirmed all PCR-positive genotypes. We demonstrate that our PCR assays enable the rapid and cost-effective identification of ESBLs in the hospital setting, which has important infection control and therapeutic implications.
QMaker: Fast and accurate method to estimate empirical models of protein evolution
Authors: Minh Bui Quang , Dang Cuong Cao , Vinh Le Sy , Lanfear Robert
Published: February 2020

Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models, however, they are typically complicated and slow. In this paper, we propose QMaker, a new ML method to estimate a general time-reversibleQmatrix from a large protein dataset consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly function in the IQ-TREE software package (http://www.iqtree.org) supporting the use of multiple CPU cores so that biologists can easily estimate amino acid substitution models from their own protein alignments. We used QMaker to estimate new empirical general amino acid substitution models from the current Pfam database as well as five clade-specific models for mammals, birds, insects, yeasts, and plants. Our results show that the new models considerably improve the fit between model and data and in some cases influence the inference of phylogenetic tree topologies.
Consumption of a high energy density diet triggers microbiota dysbiosis, hepatic lipidosis, and microglia activation in the nucleus of the solitary tract in rats
Authors: Minaya Dulce M. , Turlej Anna , Joshi Abhinav , Nagy Tamas , Di Lorenzo Patricia , Hajnal Andras , Czaja Krzysztof
Published: February 2020

Obesity is a multifactorial chronic inflammatory disease. Consumption of high energy density (ED) diets is associated with hyperphagia, increased body weight and body fat accumulation, and obesity. Our lab has previously shown that short-term (4 weeks) consumption of a high ED diet triggers gut microbiota dysbiosis, gut inflammation, and reorganization of the gut-brain vagal communication. The aim of the current study was to investigate the effect of long-term (6 months) consumption of high ED diet on body composition, gut microbiome, hepatocellular lipidosis, microglia activation in the Nucleus of the Solitary Tract, and the development of systemic inflammation. Male Sprague-Dawley rats were fed a low ED diet (5% fat) for two weeks and then switched to a high ED (45% fat) diet for 26 weeks. Twenty-four hour food intake, body weight, and body composition were measured twice a week. Blood serum and fecal samples were collected at baseline, and 1, 4, 8, and 26 weeks after introduction of the high ED diet. Serum samples were used to measure insulin, leptin, and inflammatory cytokines using Enzyme-linked Immunosorbent Assay. Fecal samples were used for 16S rRNA genome sequencing. High ED diet induced microbiota dysbiosis within a week of introducing the diet. In addition, there was significant microglia activation in the intermediate NTS and marked hepatic lipidosis after four weeks of high ED diet. We further observed changes in the serum cytokine profile after 26 weeks of high ED feeding. These data suggest that microbiota dysbiosis is the first response of the organism to high ED diets and this, in turn, detrimentally affects liver fat accumulation, microglia activation in the brain, and circulating levels of inflammatory markers.
Plant SYP12 syntaxins mediate an evolutionarily conserved general immunity to filamentous pathogens
Authors: Rubiato Hector M. , Liu Mengqi , O’Connell Richard J. , Nielsen Mads E.
Published: February 2020

Filamentous fungal and oomycete plant pathogens that invade by direct penetration through the leaf epidermal cell wall, cause devastating plant diseases. Towards non-adapted filamentous pathogens, plant pre-invasive immunity is highly effective and durable. Pre- and post-invasive immunity correlates with the formation of evolutionarily conserved and cell-autonomous cell wall structures, named papillae and encasements. Yet, it is still unresolved how papillae/encasements are formed and whether these defense structures prevent pathogen ingress. Here we show that inArabidopsis, the two closely related members of the SYP12 clade of syntaxins (PEN1 and SYP122) are indispensable for the formation of papillae and encasements. Moreover, loss-of-function mutants were hampered in pre-invasive immunity towards a range of taxonomically distinct non-adapted filamentous pathogens, underlining the versatility and efficacy of this defense. Complementation studies using SYP12s from the early diverging land plant,Marchantia polymorpha, showed that the SYP12 clade immunity function has survived 470 My of independent evolution. These results suggest that ancestral land plants evolved the SYP12 clade to provide a broad and durable pre-invasive immunity to facilitate their life on land, and pave the way to a better understanding of how adapted pathogens overcome this ubiquitous plant defense strategy.