bluuebunny/crossref_metadata_2025 huggingface dataset:
Leptohadronic single-zone models for the electromagnetic and neutrino emission of TXS 0506+056
Authors: Cerruti M , Zech A , Boisson C , Emery G , Inoue S , Lenain J-P
Published: November 2018

While active galactic nuclei with relativistic jets have long been prime candidates for the origin of extragalactic cosmic rays and neutrinos, the BL Lac object TXS 0506+056  is the first astrophysical source observed to be associated with some confidence (∼3σ) with a high-energy neutrino, IceCube-170922A, detected by the IceCube Observatory. The source was found to be active in high-energy γ-rays with Fermi-LAT and in very-high-energy γ-rays with the MAGIC telescopes. To consistently explain the observed neutrino and multiwavelength electromagnetic emission of TXS 0506+056, we investigate in detail single-zone models of leptohadronic emission, assuming cospatial acceleration of electrons and protons in the jet, and synchrotron photons from the electrons as targets for photohadronic neutrino production. The parameter space concerning the physical conditions of the emission region and particle populations is extensively explored for scenarios where the γ-rays are dominated by either (1) proton synchrotron emission or (2) synchrotron-self-Compton emission, with a subdominant but non-negligible contribution from photohadronic cascades in both cases. We find that the latter can be compatible with the neutrino observations, while the former is strongly disfavoured due to the insufficient neutrino production rate.
Early spatial attention deployment toward and away from aggressive voices
Authors: Burra Nicolas , Kerzel Dirk , Munoz Tord David , Grandjean Didier , Ceravolo Leonardo
Published: November 2018

Salient vocalizations, especially aggressive voices, are believed to attract attention due to an automatic threat detection system. However, studies assessing the temporal dynamics of auditory spatial attention to aggressive voices are missing. Using event-related potential markers of auditory spatial attention (N2ac and LPCpc), we show that attentional processing of threatening vocal signals is enhanced at two different stages of auditory processing. As early as 200 ms post-stimulus onset, attentional orienting/engagement is enhanced for threatening as compared to happy vocal signals. Subsequently, as early as 400 ms post-stimulus onset, the reorienting of auditory attention to the center of the screen (or disengagement from the target) is enhanced. This latter effect is consistent with the need to optimize perception by balancing the intake of stimulation from left and right auditory space. Our results extend the scope of theories from the visual to the auditory modality by showing that threatening stimuli also bias early spatial attention in the auditory modality. Attentional enhancement was only present in female and not in male participants.
Trichoderma Species: Versatile Plant Symbionts
Authors: Guzmán-Guzmán Paulina , Porras-Troncoso María Daniela , Olmedo-Monfil Vianey , Herrera-Estrella Alfredo
Published: November 2018

Because of the need to provide food for the growing population, agricultural activity is faced with the huge challenge of counteracting the negative effects generated by adverse environmental factors and diseases caused by pathogens on crops, while avoiding environmental pollution due to the excessive use of agrochemicals. The exploitation of biological systems that naturally increase plant vigor, preparing them against biotic and abiotic stressors that also promote their growth and productivity represents a useful and viable strategy to help face these challenges. Fungi from the genus Trichoderma have been widely used in agriculture as biocontrol agents because of their mycoparasitic capacity and ability to improve plant health and protection against phytopathogens, which makes it an excellent plant symbiont. The mechanisms employed by Trichoderma include secretion of effector molecules and secondary metabolites that mediate the beneficial interaction of Trichoderma with plants, providing tolerance to biotic and abiotic stresses. Here we discuss the most recent advances in understanding the mechanisms employed by this opportunistic plant symbiont as biocontrol agent and plant growth promoter. In addition, through genome mining we approached a less explored factor that Trichoderma could be using to become successful plant symbionts, the production of phytohormones—auxins, cytokinins, abscisic acid, gibberellins, among others. This approach allowed us to detect sets of genes encoding proteins potentially involved in phytohormone biosynthesis and signaling. We discuss the implications of these findings in the physiology of the fungus and in the establishment of its interaction with plants.
Correlates of Treatment Retention and Opioid Misuse Among Postpartum Women in Methadone Treatment
Authors: Ellis Jennifer D. , Cairncross Molly , Struble Cara A. , Carr Meagan M. , Ledgerwood David M. , Lundahl Leslie H.
Published: November 2018

Objectives:

The postpartum period is a particularly challenging time for women in methadone treatment. Unfortunately, this is also the time when women are vulnerable to treatment discontinuation and opioid misuse. The purpose of the present exploratory study was to examine demographic, treatment, and delivery factors that may be associated with postbirth retention in treatment and opioid misuse.

Methods:

A chart review was conducted among postpartum women (n = 81) receiving opioid agonist treatment during pregnancy.

Results:

Results revealed that treatment discharge and postbirth opioid misuse were common after delivery. Longer treatment duration before delivery was associated with a lower likelihood of opioid misuse in the month after delivery. Women who delivered via cesarean section and received a discharge opioid medication were also more likely to engage in opioid misuse (ie, providing an opioid-positive urine toxicology screen outside the window of detection for the discharge opioid prescription) in the month after delivery.

Conclusions:

Increasing support to minimize the likelihood of treatment discontinuation or opioid misuse may be particularly important in this period, especially for this vulnerable group.
Antegrade Posterior Interosseous Flap for Nonhealing Wounds of the Elbow: Anatomical and Clinical Study
Authors: Zaidenberg Ezequiel Ernesto , Zancolli Pablo , Farias Cisneros Efrain , Miller Aden Gunnar , Moreno Rodrigo
Published: November 2018

Background:

The posterior interosseous artery (PIA) flap has been widely reported to cover defects at the dorsal aspect of the hand. However, the use of this flap to cover elbow defects has been rarely reported. The purpose of this study was to analyze the anatomical feasibility of the PIA flap to cover elbow soft-tissue defects and, additionally, to review the clinical outcomes of patients treated with this flap.

Methods:

An anatomical study was performed on 14 cadaveric specimens to assess the number of PIA perforators at the distal third of the forearm, along with the distance of the perforators from the ulnar styloid. Additionally, the pedicle distance from the pivot point to the lateral epicondyle was recorded. A clinical study in 4 patients with elbow soft-tissue defects treated with the antegrade PIA was also performed to assess viability and clinical outcomes.

Results:

A mean of 3 perforators (range, 2–4) of the PIA were found in the distal third of the forearm. The pedicle distance from the pivot point to the lateral epicondyle was 10 cm (range, 8–11.5 cm). In the clinical study, all cases treated with the antegrade PIA flap showed satisfactory outcomes without loss of the flap or significant partial necrosis.

Conclusion:

In this limited series, the antegrade PIA flap has shown to be a reliable and effective alternative for treatment of soft-tissue defects at the elbow. The PIA perforators in the distal forearm and the pedicle length allow the flap to easily reach the elbow.
Blood Loss and Transfusion Rates in Microsurgical Head and Neck Reconstruction
Authors: Nguyen Anson , Shin Hope , Saint-Cyr Michel , Verheyden Charles
Published: November 2018

Background:

Free flap reconstruction cases of the head and neck are often complex, long and have a multitude of risks. One of the greatest risks is intraoperative blood loss and need for transfusion. The purpose of this study was to examine basic patient and procedure characteristics in head and neck free flap reconstruction pre- and postoperatively that may help to predict severity of blood loss.

Methods:

A retrospective chart analysis of 67 free flap reconstructions for head and neck defects was performed. Patient characteristics, surgical variables, length of stay, and postoperative complications were reviewed and compared between the transfused and nontransfused patients. Characteristics between transfused and nontransfused patients were analyzed using two-tailed t tests and Fisher’s exact tests.

Results:

Of the 67 procedures, 19 reconstructions (28.4%) required a transfusion. Transfused patients were found to have a lower preoperative hemoglobin and elevated coagulation labs. The average length of stay was also statistically longer for transfused patients. There was no statistical difference in patient characteristics, length of surgery, type of free flap, or complication rate in the transfused versus nontransfused patients.

Conclusions:

Our study demonstrates that head and neck microsurgical resection and reconstruction presents patients with a transfusion risk of over 28%. We found that patients with a lower preoperative hemoglobin and abnormal coagulation levels are at a higher risk for receiving a transfusion. We also have demonstrated that patients who received a transfusion had a statistically significant longer length of stay.
Atypical Palmaris Profundus with Median Nerve Perforation Presenting Ultrasonically as an Intraneural Mass
Authors: Deglmann Claus J. , Nagi Michael
Published: November 2018

An accessory palmaris profundus tendon might cause carpal tunnel like symptoms and in addition is a known potential reason for persistent symptoms following carpal tunnel release. In our case, a 34-year-old female patient presented with paresthesia of the third digit. Electromyography was without pathological findings. Diagnostic high-resolution ultrasound showed an intraneural mass within the median nerve in the region of the distal forearm. A tumorous lesion was suspected and a microsurgical resection was planned. Intraoperatively, a palmaris profundus tendon was found, perforating the median nerve and keeping an intraneural course, before leaving the median nerve within the carpal tunnel to migrate into the distal retinaculum fibers. The resection of the intraneural tendon of the palmaris profundus led to a recovery of the digital paresthesia’s. We discuss the intraoperative findings and review the literature.
Importance of Colposcopy Impression in the Early Diagnosis of Posthysterectomy Vaginal Cancer
Authors: Cong Qing , Fu Zhongpeng , Zhang Di , Sui Long
Published: November 2018

Objective

The aim of the study was to investigate the value of cytology, high-risk human papillomavirus (hrHPV) status and colposcopy in the early diagnosis of vaginal cancer after hysterectomy.

Materials and Methods

A retrospective study was performed in the Obstetrics and Gynecology Hospital of Fudan University. Posthysterectomy patients who were diagnosed with vaginal high-grade intraepithelial lesion (HSIL) by colposcopy-directed biopsy with colposcopy impression of extensive HSIL or suspicion of cancer and underwent upper or total vaginectomy from January 2009 to December 2017 were included.

Results

Eighty-six posthysterectomy vaginal HSIL patients were included. Available abnormal cytology and positive hrHPV were observed in 90.7% (49/54) and 96.2% (51/53) of the patients, respectively. A total of 18.6% (16/86) of the patients were diagnosed with squamous cell cancer by vaginectomy, and the average interval between hysterectomy and vaginectomy was 3.5 years. Among them, 62.5% (10/16) cancers occurred after hysterectomy for cervical cancer, 31.2% (5/16) after hysterectomy for cervical precancer, and 6.3% (1/16) after hysterectomy for myoma. An indication for hysterectomy (cervical cancer vs HSIL, odds ratio = 7.2, 95% CI = 1.9–28.0, p = .004) and colposcopy impression of vaginal cancer (vaginal cancer vs HSIL, odds ratio = 5.9, 95% CI = 1.3–26.8, p = .021) were high-risk factors of cancer confirmed by vaginectomy in colposcopy-directed biopsy vaginal intraepithelial neoplasia 2/3 posthysterectomy in multiple logistic regression analysis.

Conclusions

Colposcopy is pivotal in the evaluation of abnormal cytology/hrHPV tests in follow-up of cervical cancer patients after hysterectomy and decision-making for vaginectomy in detecting early cancer.
Staff Nurses’ Perceptions of Their Nurse Managers’ Transformational Leadership Behaviors and Their Own Structural Empowerment
Authors: Khan Bernadette P. , Quinn Griffin Mary T. , Fitzpatrick Joyce J.
Published: November 2018

OBJECTIVE

The aim of this study was to investigate staff nurses’ perception of their nurse managers’ transformational leadership behaviors and their own structural empowerment.

BACKGROUND

Transformational leadership behaviors in nurse managers have been linked to increased staff nurse satisfaction and decreased turnover and burnout. Perception of nurse managers’ leadership behaviors by staff nurses and the relationship to the staff nurses’ structural empowerment is important to advance our understanding of the leadership role of nurse managers.

METHODS

A descriptive correlational design was used to examine the relationship between staff nurses’ perception of their nurse managers’ transformational leadership behaviors and their own structural empowerment. Staff nurses at a conference were offered an opportunity to participate in the study.

RESULTS

The transformational leadership behaviors of nurse managers were moderately correlated to staff nurses’ structural empowerment. Transactional leadership behaviors were associated with staff nurses’ structural empowerment to a lesser degree.

CONCLUSION

Nurses who perceived their nurse managers as demonstrating transformational leadership behaviors experienced higher structural empowerment.
Temporomandibular Disorders Clinical and Anatomical Outcomes After Fat-Derived Stem Cells Injection
Authors: Carboni Andrea , Amodeo Giulia , Perugini Maurizio , Arangio Paolo , Orsini Raniero , Scopelliti Domenico
Published: November 2018

Temporomandibular disorders (TMD) are common disorders that usually involve temporomandibular joint (TMJ), masticatory muscles, and other relevant structures. The symptoms may vary limiting the patients’ quality of life. Many treatment options were proposed during the last years with the aim to treat the pathology. In this article, we analyze the effect of the injection of the fat-derived stem cell in the joint as a new treatment option.
Technique of the Buccal Fat Pad Flap as an Alternative for the Surgical Defect of Pleomorphic Adenoma
Authors: Oliveira Neto Jair Queiroz de , Cetira Filho Edson Luiz , Andrade Gabriel Silva , Silveira Daniel Ximenes da , Carvalho Abrahão Cavalcante Gomes de Souza
Published: November 2018

Pleomorphic adenoma (PA) is the most common benign salivary gland neoplasm, and its malignant transformation rarely occurs. Diagnosis is based on clinical features of local or regional malignancy or distant metastasis, and histological identification of invasion and cellular atypia. Buccal fat pad, also called Bichat fat pad, is an excellent option to create tissue coverage over surgically treated areas, providing great blood supply. Thus, this study aims to report a surgical treatment of a patient who reported to the Oral and Maxillofacial Surgery and Traumatology service of a hospital in the city of Fortaleza, presenting a large lesion in the right side of the palate. Clinical examination revealed a nodular volume increase with smooth surface, sessile insertion, firm to palpation and coloration similar to the mucosa, no pain complaints, and 2 years of evolution. Orthopantomographic examination did not reveal alterations in the adjacent anatomical structures. After clinical and radiographic evaluation, an incisional biopsy was performed and histopathological diagnosis was PA. Patient was submitted to surgery for tumor excision with narrow surgical margins, including oral lining mucosa to reduce recurrence chances. In the same surgical act, after the excision of the lesion, the right buccal fat pad pedicle flap was sutured onto the residual mucosa in order to act as a framework for re-epithelialization of the palatal mucosa, phenomenon of metaplasia, and reduction of patient's morbidity. Surgical piece obtained was sent to anatomopathological study, confirming initial diagnosis. After 12-month follow-up, patient is esthetically and functionally rehabilitated, and satisfied with clinical and surgical plans executed.
A Protocol-Driven Assessment Promotes a More Accurate Diagnosis of Irritable Bowel Syndrome
Authors: Moore Judith S. , Gibson Peter R. , Perry Richard E. , Burgell Rebecca E.
Published: November 2018

A diverse range of conditions share symptoms commonly identified with irritable bowel syndrome. The objective of this study was to examine the diagnostic process in identifying additional diagnoses in women who are attending a clinic for evaluation of symptoms suggestive of irritable bowel syndrome. A retrospective audit was conducted of anonymous data gathered on consecutive female patients presenting to a specialist nurse-led service in Christchurch, New Zealand, with a provisional diagnosis of irritable bowel syndrome. A protocol containing routine pathology investigations and physical examination was used. Alarm features were identified and pertinent investigations were implemented. Rectocele was detected on rectal examination. Final diagnosis was noted and compared with baseline symptom data. Of 231 patients, 187 initially met Rome III criteria for irritable bowel syndrome. Red flags and abnormal investigations led to an alternate diagnosis in a further 27 patients. Of the 160 patients with irritable bowel syndrome, 31% were found to have a rectocele. They were seven times more likely to report a symptom associated with pelvic floor dysfunction (p < .0001) and four times more likely to report constipation (p = .0003). The use of a protocol including routine investigations and physical examination improves diagnostic yield. Pelvic floor dysfunction should be considered in those with unique symptom patterns and rectocele in the setting of irritable bowel syndrome.
Interprofessional Healthcare Student Training in the Care of Sexual Assault Patients Utilizing Standardized Patient Methodology
Authors: Lee Wendy J. , Clark Lou , Wortmann Kathleen , Taylor Laura A. , Pock Arnyce R.
Published: November 2018

Background

The medical assessment of sexual assault (SA) is challenging because SA patients are often hesitant to disclose their medical needs, which puts them at further physical and psychological risk, and because of provider unease in conducting SA examinations. This challenge is compounded by a lack of provider training.

Objectives

The study goals were to develop an interprofessional simulation event that would foster SA interview skills, foster effective communication with SA patients, and increase learner confidence in assessing SA patients.

Methods

Participants were senior-year school of medicine (n = 165) and advanced practice registered nursing (n = 30) students (N = 195) who were enrolled in a mandatory Military Sexual Assault Assessment and Treatment course, along with data provided by trained standardized patients (SPs, n = 16) who participated in the simulation event and in assessments of learners. Measures included the Sexual Assault Interview Skills Checklist, the Essential Elements of Communication, and the Confidence in SA Assessment scale. Data were analyzed using analysis of variance and t tests at the P < 0.05 threshold.

Results

Postsimulation Sexual Assault Interview Skills Checklist and Essential Elements of Communication scores demonstrated an acceptable level of competence according to both students and SPs. Confidence in SA assessment rose significantly from presimulation to postsimulation. Before simulation, medical students were significantly lower than nursing students, but the simulation event closed the confidence in SA assessment gap.

Conclusions

This interprofessional simulation event resulted in SA interview competence, communication skills competence, and improved confidence scores. Combined, these findings support the efficacy of simulation to train emerging healthcare providers to properly assess SA.
The Use of Statistical Process Control Charts to Evaluate Interprofessional Education Sessions Embedded Into a Pediatric Emergency In situ Resuscitation Program
Authors: Pirie Jonathan , Cardenas Sandra , Seleem Wail , Kljujic Dragan , Schneeweiss Suzan , Glanfield Carrie , Principi Tania
Published: November 2018

Summary Statement

The rigorous evaluation of simulation in healthcare to improve resuscitations and team functioning can be challenging. Statistical process control (SPC) charts present a unique methodology to enable statistical rigor when evaluating simulation. This article presents a brief overview of SPC charts and its advantages over traditional before and after methodologies, followed by an exemplar using SPC to evaluate an in situ team training program with embedded interprofessional education sessions.
Patient reported distress can aid clinical decision making in idiopathic pulmonary fibrosis: analysis of the PROFILE cohort
Authors: Stewart Iain , McKeever Tricia , Braybrooke Rebecca , Oballa Eunice , Simpson Juliet K , Maher Toby M , Marshall Richard P , Lukey Pauline T , Fahy William A , Jenkins Gisli , Saini Gauri
Published: November 2018

Idiopathic pulmonary fibrosis is a progressive and fatal interstitial lung disease. We aimed to determine if patient response to a palliative assessment survey could predict disease progression or death.

We undertook a cross-sectional study in a UK clinical cohort of incident cases. Rasch-based methodology provided a disease distress value from an abridged 11 item model of the original 45 item survey. Distress values were compared with measures of lung function. Disease progression or mortality alone was predicted at twelve months from survey completion, with risk of death assessed at three, six and twelve months.

Disease distress values were negatively correlated with lung function (r=-0.275 percent predicted DLCO). Expected survey scores computed from distress values could distinguish disease progression, 8.8 (p=0.004), and people who died, 10.2 (p=0.002), from those who did not progress, 6.9. Actual survey scores predicted disease progression and mortality with an area under the curve of 0.60 and 0.64, respectively. Each point increment in actual score increased risk of twelve-month mortality by 10%, almost 43% of people scoring above 18 did not survive beyond 105 days.

We define a short questionnaire that can score disease distress and predict prognosis, assisting clinical decision making in progressive fibrosis.
Prenatal exposure to particulate matter (PM2.5) and low birth weight in a Sri Lankan birth cohort
Authors: Tipre Meghan , Wickremesinghe Rajitha , Nandasena Sumal , Kasturiratne Anuradhini , Larson Rodney , Meleth Sreelatha , Wimalasiri Udaya , Lungu Claudiu , Smith Tamika , Sathiakumar Nalini
Published: November 2018

Background

About 74% of the Sri Lankan population use biomass in the form of unprocessed wood as the primary cooking fuel. A growing body of evidence from meta-analyses and individual studies although limited by few prospective studies, report that prenatal exposure to particulate matter of size 2.5 µm (PM2.5) emissions from biomass fuel burning may be associated with low birth weight (LBW) (<2500 grams). We present results examining the association between PM2.5 and LBW in context of a birth cohort study in Sri Lanka.

Methods

We followed 545 pregnant women from their first trimester until delivery and assessed outcomes at birth. Exposure to household air pollution (HAP) from biomass smoke was assessed using detailed questionnaire about fuel type, kitchen characteristics and cooking practices; two-hour measurements of kitchen PM2.5 were collected in a subset of households (n=304, 56%). Data from questionnaires and measured PM2.5 were used to estimate two-hour kitchen PM2.5 concentrations in unmeasured households. Data on covariates related to household characteristics, socio-demographic, maternal health and lifestyle factors were collected from baseline interviews. We performed linear and logistic regression analysis to evaluate the association between HAP exposure, and birth weight and LBW.

Results

Of the total, 78% of the households used wood as primary or secondary fuel (n=425); households using wood had four-fold higher PM2.5 levels compared to those using LPG. In linear regression models, we found an inverse association between a 10-unit increase in PM2.5 and birth weight (β,-0.03; SE, 0.02; p, 0.06) adjusted for covariates. Similarly, categorical HAP exposure (>50% wood use) was significantly associated with birth weight as compared to LPG users (β, −0.13; SE, 0.06; p, 0.0331). In logistic regression models, a 10-unit increase in PM2.5 was associated with increased odds for LBW (OR, 1.26; 95%CI, 1.02-1.55; p, 0.0355), while the prevalence of LBW was highest among >50% wood users (OR, 2.82; 95%CI, 1.18-6.73; p, 0.0124), as compared to those using >50% LPG with wood and only LPG users. The association between HAP exposure and birth weight/LBW were consistent among term births (n=486).

Conclusions

The finding of a significant association between prenatal PM2.5 exposure and LBW in a low-middle income country (LMIC) setting where competing risk factors are minimal fills a gap in the body of evidence linking HAP from biomass smoke to LBW. These results underscore the crucial need to implement prevention and reduction of HAP exposure in LMICs where the HAP burden is high.
Particulate Matter fractions and kitchen characteristics in Sri Lankan households using solid fuel and LPG
Authors: Nandasena Sumal , Wickremasinghe Rajitha , Kasturiratne Anuradhani , Wimalasiri Udaya , Tipre Meghan , Larson Rodney , Levitan Emily , Sathiakumar Nalini
Published: November 2018

Introduction

Use of solid fuel for cooking is a major source of household air pollution in developing countries. Of the many pollutants emitted during solid fuel combustion, Particulate Matter (PM)is considered to be one of the most hazardous pollutants. We monitored PM fractions emitted during solid fuel and Liquefied Petroleum Gas(LPG) combustion in kitchens of Sri Lankan households.

Methods

Households of children in a longitudinal study in Ragama, Sri Lanka was the study population. At the age of 36 months of children, a sample of households were visited and different aerodynamic diameters of PM (PM1, PM2.5, PM10) were monitored during the main cooking session for 3 hours. Basic characteristics of kitchen (e.g., availability of chimney, functionality of chimney, etc.) were assessed by a questionnaire. Cooking energy, other sources of household air pollution, size of open spaces in the kitchen (e.g., windows), etc. were assessed at the time of PM monitoring.

Results

Questionnaire was administered for mothers in 426 households. Out of them, 245 (57.5%)and 116 (27.2%) households used LPG and wood as the primary cooking fuel respectively. During the cooking period, PM2.5 concentrations of households uses only wood fuel and cook inside the main housing building were 344.1 μg/m3(Inter Quartile Range(IQR) = 173.2-878.0μg/m3), 88.7 μg/m3(54.8- 179.2 μg/m3); 91.7 μg/m3 (56.0- 184.9 μg/m3) and 115.1 μg/m3(83.4 - 247.9 μg/m3) in kitchen, sleeping room, living room and immediate outdoor respectively. Immediate outdoor PM2.5 concentrations in wood burning households was higher among households not having chimney (n = 8)compare to those having a chimney (n = 8) (245.9μg/m3 (IQR = 72.5 – 641.7μg/m3)) VS. (105.7μg/m3 (83.4– 195.8μg/m3)).Fuel type and stove type, availability of a chimney and their functional status, ratio between open space and total space of kitchen, PM2.5 concentration at the non-cooking time (i.e., baseline PM2.5concentration) were the determinants of PM2.5 in wood using kitchens during cooking period.

Conclusions

PM concentrations were higher in kitchen and other microenvironments of the households use wood for cooking as compared to LPG use for cooking. Immediate outdoor PM concentration was higher than the sleeping and living room PM concentrations. Several factors determine the PM2.5concentrationsduring the cooking including the fuel type.
The specificity of ParR binding determines the compatibility of conjugative plasmids inClostridium perfringens
Authors: Watts Thomas D. , Traore Daouda A.K. , Atkinson Sarah C. , Lao Carmen , Caltabiano Natalie , Rood Julian I. , Adams Vicki
Published: November 2018

Plasmids that encode the same replication machinery are generally unable to coexist in the same bacterial cell. However,Clostridium perfringensstrains often carry multiple conjugative toxin or antibiotic resistance plasmids that are closely related and encode similar Rep proteins. In many bacteria, plasmid partitioning upon cell division involves a ParMRC system and there are ~10 different ParMRC families inC. perfringens, with differences in amino acid sequences between each ParM family (15% − 54% identity). Since plasmids encoding genes belonging to the same ParMRC family are not observed in the same strain, these families appear to represent the basis for plasmid compatibility inC. perfringens. To understand this process, we examined the key recognition steps between ParR DNA-binding proteins and theirparCbinding sites. The ParR proteins bound to sequences within aparCsite from the same ParMRC family, but could not interact with aparCsite from a different ParMRC family. These data provide evidence that compatibility of the conjugative toxin plasmids ofC. perfringensis mediated by theirparMRC-like partitioning systems. This process provides a selective advantage by enabling the host bacterium to maintain separate plasmids that encode toxins that are specific for different host targets.
Long-distance dispersal, ice sheet dynamics, and mountaintop isolation underlie the genetic structure of glacier ice worms
Authors: Hotaling Scott , Shain Daniel H. , Lang Shirley A. , Bagley Robin K. , Tronstad Lusha M. , Weisrock David W. , Kelley Joanna L.
Published: November 2018

Disentangling the contemporary and historical factors underlying the spatial distributions of species is a central goal of biogeography. For species with broad distributions but little capacity to actively disperse, disconnected geographic distributions highlight the potential influence of passive, long-distance dispersal (LDD) on their evolutionary histories. However, dispersal alone cannot completely account for the biogeography of any species, and other factors–e.g., habitat suitability, life history–must also be considered. North American ice worms (Mesenchytraeus solifugus) are ice-obligate annelids that inhabit coastal glaciers from Oregon to Alaska. Previous studies identified a complex biogeographic history for ice worms, with evidence for genetic isolation, unexpectedly close relationships among geographically disjunct lineages, and contemporary migration across large (> 1,500 km) areas of unsuitable habitat. In this study, we analyzed genome-scale sequence data for most of the known ice worm range. We found clear support for divergence between populations along the Pacific Coast and the inland flanks of the Coast Mountains (mean FST= 0.60), likely precipitated by episodic ice sheet expansion and contraction during the Pleistocene. We also found support for LDD of ice worms from Alaska to Vancouver Island, perhaps mediated by migrating birds. Our results highlight the power of genomic data for disentangling complex biogeographic patterns, including the presence of LDD.
Holobiont Evolution: Mathematical Model with Verticalvs.Horizontal Microbiome Transmission
Authors: Roughgarden Joan
Published: November 2018

A holobiont is a composite organism consisting of a host together with its microbiome, such as a coral with its zooxanthellae. Hosts and their microbiomes are often intimately integrated in behavior, physiology, anatomy, and development. To explain this integration, some investigators contend that selection operates on holobionts as a unit and view the microbiome’s genes as extending the host’s nuclear genome to jointly comprise a hologenome. Holobiont selection then operates on holobionts with their hologenomes by analogy to how ordinary natural selection operates on individuals with their genes. Other investigators point out that vertical transmission of microbiomes is uncommon. They contend that holobiont selection cannot be effective because a holobiont’s microbiome is an acquired condition rather than an inherited trait. The disagreement between these positions invites a simple mathematical model to see how holobiont selection might operate and to assess its plausibility as an evolutionary force.

Here I present two variants of such a model. In one variant, juvenile hosts obtain microbiomes from their parents (vertical transmission). In the other variant, microbiomes of juvenile hosts are assembled from source pools containing the combined microbiomes of all parents (horizontal transmission). According to both variants, holobiont selection indeed causes evolutionary change in holobiont traits. Therefore, holobiont selection is plausibly an effective evolutionary force with either mode of microbiome transmission.

Furthermore, the modeling employs two distinct concepts of inheritance, depending on the mode of microbiome transmission: collective inheritance whereby juveniles inherit a sample of the collected genomes from all parents as contrasted with lineal inheritance whereby juveniles inherit the genomes from only their own parents. Collective inheritance may also apply to the evolution of soil and other microbes that feature large amounts of horizontal gene transfer and may underlie cultural evolution wherein each generation inherits a sample from the collected knowledge of the preceding generation. A distinction between collective and lineal inheritance also features in theories of multilevel selection.
Dynamic-parameter movement models reveal drivers of migratory pace in a soaring bird
Authors: Eisaguirre Joseph M. , Auger-Méthé Marie , Barger Christopher P. , Lewis Stephen B. , Booms Travis L. , Breed Greg A.
Published: November 2018

Astract

Long distance migration can increase lifetime fitness, but can be costly, incurring increased energetic expenses and higher mortality risks. Stopover and other en route behaviors allow animals to rest and replenish energy stores and avoid or mitigate other hazards during migration. Some animals, such as soaring birds, can subsidize the energetic costs of migration by extracting energy from flowing air. However, it is unclear how these energy sources affect or interact with behavioral processes and stopover in long-distance soaring migrants. To understand these behaviors and the effects of processes that might enhance use of flight subsidies, we developed a flexible mechanistic model to predict how flight subsidies drive migrant behavior and movement processes. The novel modelling framework incorporated time-varying parameters informed by environmental covariates to characterize a continuous range of behaviors during migration. This model framework was fit to GPS satellite telemetry data collected from a large soaring and opportunist foraging bird, the golden eagle (Aquila chrysaetos), during migration in western North America. Fitted dynamic model parameters revealed a clear circadian rhythm in eagle movement and behavior, which was directly related to thermal uplift. Behavioral budgets were complex, however, with evidence for a joint migrating/foraging behavior, resembling a slower paced fly-and-forage migration, which could facilitate efficient refueling while still ensuring migration progress. In previous work, ecological and foraging conditions are normally considered to be the key aspects of stopover location quality, but taxa that can tap energy sources from moving fluids to drive migratory locomotion, such as the golden eagle, may pace migration based on both foraging opportunities and available flight subsidies.
Structural basis of hypoxic gene regulation by the Rv0081 transcription factor ofMycobacterium tuberculosis
Authors: Kumar Ashwani , Phulera Swastik , Rizvi Arshad , Sonawane Parshuram , Panwar Hemendra Singh , Banerjee Sharmistha , Sahu Arvind , Mande Shekhar C.
Published: November 2018

The transcription factor Rv0081 ofM. tuberculosiscontrols the hypoxic gene expression and acts as a regulatory hub in the latent phase of tuberculosis infection. We report here the crystal structure of Rv0081 at 3.3 Å resolution revealing that it belongs to the well-known ArsR/SmtB family proteins. ArsR/SmtB family transcriptional repressors exert gene regulation by reversible metal binding. Hypoxia in general is sensed by bacterial transcriptional regulators via metals or Cys-mediated thiol switches. Oxygen sensing typically leads to transcriptional repressor changing its conformational state with altered DNA-binding property under different oxygen levels. Surprisingly Rv0081 neither has a metal binding domain nor does it possess Cys residues suggesting an alternate mechanism of gene regulation. Our structural analysis identified Ser 48, Ser 49, Ser 52 and Gln 53 as potential residues of Rv0081 involved in DNA binding. We probed DNA-binding of Rv0081 with electrophoretic mobility shift assay (EMSA) as well as surface plasmon resonance (SPR), where the Alanine mutants of these residues showed diminished DNA binding. Similarly, Aspartate mutants of these Ser residues was shown to fail to bind to DNA. Since, phosphorylation of various regulatory proteins is one of the important controlling mechanisms, we expected the role of Ser-phosphorylation of Rv0081 in hypoxic condition. Probing Rv0081 with anti-phosphoserine antibodies inM. tuberculosiscell lysate showed marked enhancement in the phosphorylation of Rv0081 protein under hypoxia. Overall, our structural and biochemical analysis provides the molecular basis for the regulation of Rv0081 in the latent phase of tuberculosis infection.

IMPORTANCE

Tuberculosis is one of the deadliest infectious diseases caused by the bacteriumMycobacterium tuberculosis. In about 90% of the infected people,M. tuberculosisexists in a dormant or a latent stage which can be reactivated in favorable conditions. Hypoxia (low oxygen pressure) is one of causes of dormancy. Understanding hypoxic gene regulation inM. tuberculosisis therefore an important step to understand latency. Rv0081 is a transcriptional regulator of genes expressed during hypoxia. In order to understand the mechanism by which Rv00081 regulates gene expression during hypoxia, we have solved the crystal structure of Rv0081 and identified amino acid residues which are critical in its transcriptional regulator activity. The crystal structure is suggestive of mechanism of gene regulation under hypoxia.
Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia
Authors: Kerr Peter J. , Eden John-Sebastian , Di Giallonardo Francesca , Peacock David , Liu June , Strive Tanja , Read Andrew F. , Holmes Edward C.
Published: November 2018

Myxoma virus (MYXV) has been evolving in a novel host species – European rabbits – in Australia since 1950. Previous studies of viruses sampled from 1950 to 1999 revealed a remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 2008 and 2017 we show that MYXV evolution in Australia can be characterized by three lineages, one of which exhibited a greatly elevated rate of evolutionary change and a dramatic break-down of temporal structure. Phylogenetic analysis revealed that this apparently punctuated evolutionary event occurred between 1996 and 2012. The branch leading to the rapidly evolving lineage contained a relatively high number of non-synonymous substitutions, and viruses in this lineage reversed a mutation found in the progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the reading frame of theM005L/Rgene. Analysis of genes encoding proteins involved in DNA synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. Although there was some evidence for recombination across the MYXV phylogeny, this was not associated with the increase in evolutionary rate. The period from 1996 to 2012 saw significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic disease and prolonged drought in south-eastern Australia, followed by the partial recovery of populations. We therefore suggest that a rapidly changing environment for virus transmission changed the selection pressures faced by MYXV and altered the course of virus evolution.

IMPORTANCE

The co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural ‘experiments’ in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a break-down in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple non-synonymous and indel mutations. We suggest that this punctuated evolutionary event likely reflects a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.
Global Quantitative Mapping of Enhancers in Rice Genome by STARR-seq
Authors: Sun Jialei , He Na , Niu Longjian , Huang Yingzhang , Shen Wei , Zhang Yuedong , Li Li , Hou Chunhui
Published: November 2018

Identification of enhancers has been a challenge in plants. STARR-seq measures enhancer activity of millions fragments in parallel. Here we present a global map of rice enhancers quantitatively determined using STARR-seq. Most enhancers are mapped within genes, especially at the 5’ untranslated regions (5’ UTR) and the coding sequences. Silent and low expressed genes in genomic regions enriched with transposable elements (TEs) are frequently found containing proximal enhancers. Analysis of enhancer epigenetic features at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and are lack of H3K4me1. Clustering enhancers by their epigenetic modifications revealed that about 40% of identified enhancers carry one or more epigenetic marks. Repressive H3K27me3 is frequently enriched with positive marks of H3K4m3 and/or H3K27ac, which together may bookmark poised enhancers. Intergenic enhancers were predicted based on the location of DHS relative to genes, which overlap poorly with functionally identified enhancers. In summary, enhancers were quantitatively identified by functional analysis in a model plant genome, which provides a valuable resource for further mechanistic studies in different biological contexts.
The concerted action of E2-2 and HEB is critical for early lymphoid specification
Authors: Bouderlique Thibault , Perez Lucia Peña , Kharazi Shabnam , Hils Miriam , Li Xiaoze , Krstic Aleksandra , De Paepe Ayla , Schachtrup Christian , Gustafsson Charlotte , Holmberg Dan , Schachtrup Kristina , Månsson Robert
Published: November 2018

The apparition of adaptive immunity inGnathostomatacorrelates with the expansion of the E-protein family to encompass E2-2, HEB and E2A. Within the family, E2-2 and HEB are more closely evolutionarily related but their concerted action in hematopoiesis remains to be explored. Here we show that the combined disruption of E2-2 and HEB results in failure to express the early lymphoid program in CLPs and a near complete block in B-cell development. In the thymus, ETPs were reduced and T-cell development perturbed, resulting in reduced CD4 T- and increased γδ T-cell numbers. In contrast, HSCs, erythro-myeloid progenitors and innate immune cells were unaffected showing that E2-2 and HEB are dispensable for the ancestral hematopoietic lineages. Taken together, this E-protein dependence suggests that the appearance of the fullGnathostomataE-protein repertoire was critical to reinforce the gene regulatory circuits that drove the emergence and expansion of the lineages constituting humoral immunity.
Subdivision of light signalling networks contributes to cellular partitioning of C4photosynthesis in maize
Authors: Hendron Ross-W. , Kelly Steven
Published: November 2018

Plants coordinate the expression of genes required to conduct photosynthesis in response to growth and environmental changes. In species that conduct two-cell C4photosynthesis, the expression of photosynthesis genes is partitioned such that leaf mesophyll and vascular sheath cells accumulate different components of the photosynthetic pathway. The identity of the regulatory networks that facilitate this partitioning are unknown. Here we show that differences in light perception between mesophyll and bundle sheath cells facilitate differential regulation and accumulation of photosynthesis genes in the C4cropZea mays(maize). We show that transcripts encoding photoreceptors differentially accumulate in mesophyll and bundle sheath cells in a manner that is consistent with biophysical light filtration. We further show the blue light (but not red) is necessary and sufficient to activate photosystem II assembly in etiolated maize mesophyll cells, while both red and blue produce the same effect in C3Hordeum vulgare(barley). Finally, we demonstrate that changes in abundance of >20% of genes that differentially accumulate between mesophyll and bundle sheath cells can be recapitulated by spectrum specific deetiolation of maize seedlings. These findings provide evidence that subdivision of light signalling networks is a key component of cellular partitioning of C4photosynthesis in maize.
Enhanced cell-cell contact stability and decreased N-cadherin-mediated migration upon Fibroblast Growth Factor Receptor-N-cadherin cross-talk
Authors: Nguyen Thao , Duchesne Laurence , Sankara Narayana Gautham Hari Narayana , Boggetto Nicole , Fernig David D. , Murade Chandrashekhar Uttamrao , Ladoux Benoit , Mège René-Marc
Published: November 2018

N-cadherin adhesion has been reported to enhance cancer and neuronal cell migration either by mediating actomyosin-based force transduction or initiating Fibroblast Growth Factor Receptor (FGFR)-dependent biochemical signalling. Here we show that FGFR1 reduces N-cadherin-mediated cell migration. Both proteins are co-stabilised at cell-cell contacts through direct interaction. As a consequence, cell adhesion is strengthened, limiting the migration of cells on N-cadherin. Both the inhibition of migration and the stabilisation of cell adhesions require the FGFR activity stimulated by N-cadherin engagement. FGFR1 stabilises N-cadherin at the cell membrane through a pathway involving Src and p120. Moreover, FGFR1 stimulates the anchoring of N-cadherin to actin. We found that the migratory behaviour of cells depends on an optimum balance between FGFR-regulated N-cadherin adhesion and actin dynamics. Based on these findings we propose a positive feedback loop between N-cadherin and FGFR at adhesion sites limiting N-cadherin-based single cell migration.