bluuebunny/crossref_metadata_2025 huggingface dataset:
Patterns of Failure After Neoadjuvant Stereotactic Body Radiation Therapy or Fractionated Chemoradiation in Resectable and Borderline Resectable Pancreatic Cancer
Authors: Barrord Michelle , Ahmad Syed , Patel Sameer , Olowokure Olugbenga , Sussman Jeffrey , Smith Milton , Poreddy Sampath , Esslinger Hope , Latif Tahir , Choe Kyuran , Kharofa Jordan
Published: July 2020

Objectives

The goal of this study was to compare outcomes of patients with borderline and resectable pancreatic cancer treated with neoadjuvant stereotactic body radiation therapy (SBRT) versus fractionated chemoradiation.

Methods

Patients with borderline or resectable pancreatic cancer treated with neoadjuvant intent between November 2011 and December 2017 were reviewed. The SBRT volume/dose was 33 Gy in 5 fractions to gross tumor plus abutting vessel with or without 25 Gy in 5 fractions to pancreatic head/body and celiac/superior mesenteric artery. Fractionated chemoradiation volume/dose was 50.4 Gy in 28 fractions to gross tumor, superior mesenteric/celiac arteries, and enlarged lymph nodes with concurrent bolus 5-FU, leucovorin, oxaliplatin, irinotecan or gemcitabine/nab-paclitaxel. Failure patterns, local recurrence-free survival (LRFS), progression-free survival (PFS), and overall survival were assessed.

Results

Forty-three patients were reviewed (18 SBRTs and 25 fractionated). Among patients who underwent resection, patients treated with fractionated chemoradiation had improved LRFS (12-month LRFS, 86% vs 62%, P = 0.003) and PFS (median PFS, 23 months vs 11 months, P = 0.006) compared with SBRT. There was no difference in overall survival.

Conclusions

Stereotactic body radiation therapy may result in inferior LRFS and PFS compared with fractionated chemoradiation, likely because of under coverage of high-risk vascular targets.
Helicobacter pylori Antigen But Not the Organism Is Occasionally Present Within Germinal Centers
Authors: Nelson Nya D. , Tondon Rashmi , Fortuna Danielle , Westerhoff Maria , Swanson Paul E. , Furth Emma
Published: July 2020

Helicobacter pylori infection is present in two thirds of the world’s population and induces a myriad of human diseases, ranging from gastritis to gastric adenocarcinoma and mucosa-associated lymphoid tissue lymphoma. Detection is critical for treatment and may require immunohistochemical (IHC) staining when organisms are not visible on hematoxylin and eosin. We have encountered cases in which IHC for Helicobacter pylori failed to demonstrate curvilinear or coccoid organisms, but did show a reticular pattern of immunoreactivity involving the underlying germinal centers. We performed a systematic retrospective evaluation of the frequency of H. pylori germinal center immunoreactivity over a 54-month period through evaluation of 367 gastric specimens. H. pylori germinal center immunoreactivity was observed in 5% of cases with germinal centers. Nine of 11 (81%) patients with H. pylori germinal center immunoreactivity had concurrent or recent H. pylori infection, in comparison to 36% of patients with germinal centers present but no immunoreactivity (n=9 of 25 patients, P=0.03). None of the patients with germinal center immunoreactivity developed mucosa-associated lymphoid tissue lymphoma. In situ hybridization for H. pylori performed on 3 cases with positive germinal center IHC was negative for H. pylori nucleic acids within those germinal centers, demonstrating that only the antigen is present. This work demonstrates that H. pylori antigen, but not viable organisms, is present in germinal centers in 5% of gastric specimens, and is associated with recent or concurrent H. pylori infection. We advocate for reporting of all H. pylori germinal center immunoreactivity with a recommendation for ancillary H. pylori testing.
Low-density Isolated Intraperitoneal Free Fluid in Pediatric Blunt Trauma Is Not Associated With Abdominal Injury
Authors: Perea Lindsey L. , San Roman Janika , Gaughan John P. , Gefen Ron , Hazelton Joshua P.
Published: July 2020

Objectives

Isolated intraperitoneal free fluid (IIFF) is defined as intraperitoneal fluid seen on computed tomography (CT) without identifiable injury. In a hemodynamically stable patient, this finding creates a challenge for physicians regarding the next steps in management because the clinical significance of this fluid is not completely understood. We hypothesized that pediatric blunt trauma patients with a finding of simple IIFF on CT would not have clinically significant intraabdominal injury.

Methods

A retrospective review (2009–2018) was conducted of all pediatric blunt trauma patients who underwent CT scan of the abdomen/pelvis at our institution. All patients with scans performed at our institution with the finding of IIFF were included. Scans were reviewed to measure the Hounsfield Units (HU) of the intraabdominal fluid. Groups were stratified into HU > 25 and HU ≤ 25, below accepted cutoffs for acute blood, and clinical outcomes were reviewed.

Results

A total of 413 patients had free fluid on CT abdomen/pelvis with 279 (68%) having only the finding of IIFF. The HU was 25 or less in 236 (85%) patients. No patients in the HU ≤ 25 group required operative exploration or had examination findings to indicate they had intraabdominal injury. Four (9%) patients in the HU > 25 required laparotomy (P < 0.0001). No patients in the HU ≤ 25 group required further workup or hospital admission over concern for intraabdominal injury.

Conclusions

Pediatric blunt trauma patients with HU of 25 or less IIFF and a nonperitonitic physical examination did not require operative exploration or further workup for intraabdominal injury. In the absence of other injuries, it is safe to discharge these patients without further workup.
Identifying Jurisdictions at Risk of Containing Housing Units With Deteriorated Paint: Results and Targeting Implications for the US Department of Housing and Urban Development
Authors: Garrison Veronica E. H. , Ashley Peter J.
Published: July 2020

Context:

The US Department of Housing and Urban Development provides millions in annual funding to make low-income housing lead safe, but funds are limited relative to need. To adequately target efforts, local program administrators must identify neighborhoods that are the most “at risk” of residential lead exposure; however, no federal agency currently provides a public data set for this use.

Objectives:

To examine pre-1980 households with large areas of deteriorated paint, a significant and common predictor of lead dust, and identify high-risk jurisdictions. To highlight the potential use of a newly available data set for strategic lead poisoning prevention and targeting.

Design:

Microdata from the 2011 American Housing Survey and the 2009-2013 American Community Survey were used to develop a household-level predicted risk metric that identifies housing units at risk of containing large areas of deteriorated paint. Predicted risk, defined as the mean predicted percentage of occupied housing units at risk of containing deteriorated paint within a given jurisdiction, was summarized by state, county, and tract.

Setting:

National, all occupied housing units.

Participants:

Occupied housing units summarized by household (n = 9 363 000), census tract (n = 72 235), county (n = 3143), and state (n = 51).

Main Outcome Measure:

Housing units built prior to 1980 with a large area of deteriorated paint.

Results:

New York, Rhode Island, New Jersey, Massachusetts, and Pennsylvania had the highest predicted percentage of at-risk households (range: 2.52%-2.90%). County-level and tract-level estimates are the most useful when examining a predefined jurisdiction; New York state was presented as a case study. County-level quartile risk scores revealed Albany as an at-risk jurisdiction. Tract-level quartile risk scores further identified at-risk neighborhoods in northeastern Albany.

Conclusions:

Findings can help housing and health policy makers identify and target geographic areas with a high probability of households at risk of potential exposure to deteriorated lead-based paint.
Microsurgical Resection of a Primary Intraosseous Meningioma Encasing the Superior Sagittal Sinus
Authors: Ene Chibawanye I. , Kurnik Nicole , Vellimana Ananth K. , Liu Yusha , Susarla Srinivas M. , Sekhar Laligam N.
Published: July 2020

Primary intraosseous meningiomas (PIMs) are an infrequent variant of meningiomas characterized by hyperostosis and brain compression. En bloc surgical resection of giant PIMs involving critical structures such as venous sinuses or cranial nerves could be associated with significant morbidity. The objective of this report is to demonstrate the safety and feasibility of piecemeal resection of PIMs involving the superior sagittal sinus and frontal sinus. A 54-year-old female with a large 5 cm thick bifrontal primary intra-osseous meningioma encasing the anterior segment of the superior sagittal sinus and frontal sinus underwent a bifrontal craniotomy with piecemeal microsurgical resection of the lesion, complete frontal sinus exoneration, and a synthetic cranioplasty. Clinical outcome was measured by extent of resection, preservation of cortical draining veins and postoperative course. A Simpson grade I resection of the lesion was achieved following piecemeal resection of the giant PIM without clinical or radiographic evidence of venous infarct or injury. The postoperative course was uncomplicated, and the patient was discharged home 3 days after cranioplasty. A complete resection of a giant bifrontal PIM with superior sagittal sinus encasement and frontal sinus involvement can be achieved safely via a piecemeal approach without significant intra-operative morbidity.
Racial Disparity Between Asian and Caucasian Crouzon Syndrome in Skull Morphology
Authors: Lu Xiaona , Forte Antonio Jorge , Fan Fei , Zhang Zhiyong , Teng Li , Yang Bin , Alperovich Michael , Steinbacher Derek M. , Alonso Nivaldo , Persing John A.
Published: July 2020

Background:

Racial disparity in pathological consequences in skull growth may impact the treatment plan for different patient populations. This study attempts to explore the differences between Asian and Caucasian cranial morphology in Crouzon syndrome.

Method:

Ninety-one computed tomographic scans were included (Asian Crouzon syndrome, n = 12; Asian controls, n = 22; Caucasian Crouzon syndrome, n = 16; Caucasian controls, n = 41), and measured using Mimics and 3-matics software.

Results:

The entire cranial base length was reduced 11.92 mm (P = 0.004) in Asian Crouzon patients, and 14.58 mm (P < 0.001) in Caucasian Crouzon patients, compared to respective controls. The cranial base angle on the facial side of basicranium was more narrowed in Crouzon syndrome in both races, with similar changes of degrees (9.61°, P = 0.002, in Asian Crouzon; 9.20°, P = 0.019, in Caucasian Crouzon). However, the intracranial side was statistically more narrowed only in the Asian group (9.86°, P = 0.003). Both Asian and Caucasian Crouzon patients developed reduced posterior fossa volume, by 15% (P = 0.034) and 17% (P = 0.004), respectively. However, Caucasian Crouzon patients developed a more shortened anterior and middle cranial base, than that of Asian patients. The separation of lateral pterygoids was only significantly increased in Caucasian patients (5.49°, P < 0.001).

Conclusion:

Crouzon syndrome causes a shortened, widened, and kyphotic cranial base across both races. It also restricts the development of the posterior cranial fossa. However, the skull malformation is not the same between populations: Asian Crouzon patients developed more narrowed cranial base angulation on the intracranial side of basicranium, while Caucasian Crouzon patients developed more widened lateral pterygoids.
Study of the Anatomical Structure of the Nasopharyngeal Cavity and Distribution of the Air Flow Field
Authors: Tang Yuanyuan , Bie Xu , Yu Shen , Sun Xiuzhen
Published: July 2020

To build a biomechanical numerical model of the nasopharynx, construct an accurate computerized numerical description of its specific anatomical structures, analyze the distribution of air flow field, starting with the anatomical structure of the pharyngeal recess, correlate its anatomical characteristics with the occurrence and development of nasopharyngeal carcinoma from the perspective of biomechanics. In this study, the nasal and nasopharyngeal cavities of healthy male adult, with the pharyngeal recess in an open state, were scanned by CT to obtain DICOM imaging data. Then, they were imported into Mimics 20.0 to build a model which was recorded in binary STL format. Each file was imported into Geomagic studio 12.0 to construct a 3D model saved in an IGES format. Then, it was imported into ANSYS Workbench for numerical simulation of air flow field. The authors found that:

Above all, the causes and pathogenesis of nasopharyngeal carcinoma can be identified from the perspective of biomechanics through the construction of a 3D model and analysis of the characteristics of air flow field. With more in-depth research, it is expected that a more solid scientific foundation will be created for related quantitative analysis.
Three-Dimensional Planning and Surgical Technique for Modified Le Fort I and Le Fort III Osteotomy in Non-Syndromic Patients
Authors: Goulart Douglas Rangel , Huentequeo-Molina Claudio , Alister Juan Pablo , Olate Sergio
Published: July 2020

Total midface deficiency, to include the orbits, nose, zygomas, and maxilla, can occur in both syndromic and non-syndromic individuals. The treatment with combination of Le Fort III and I osteotomy could be used and it is few reported in the literature. The aim of the study is to present how technology can make the procedure for the correction of hypoplasia of the middle third more predictable and safer. The 2 clinical cases were managed under submental intubation and using VSP that generated 3D printing of oclusal splints and cutting guides. Modified oblique Le Fort III osteotomy (MOLFIIIO) and Le Fort I osteotomy were used due to patients present large sagittal discrepancy between maxilla and mandible (18 and 17 mm). The patients presented good outcomes without complications. In this study, the authors demonstrate that non-syndromic patient could be managed safety with MOLFIII and Le Fort I osteotomies for the correction of midfacial deformities using virtual surgical planning (VSP) associated with 3D printing technique and piezoelectric surgery.
Radiographic Evaluation in the Diagnosis of Alveolar Bone Quality in Implant Rehabilitation
Authors: Oliveira Marina Reis , Gonçalves Andréa , Gabrielli Marisa Aparecida Cabrini , Pereira-Filho Valfrido Antonio
Published: July 2020

This study evaluated the optical bone density of the maxilla and mandible and correlate with the classification of bone quality of the Lekholm and Zarb (L & Z). Sixty edentulous areas were evaluated. Panoramic and periapical radiographs were performed with an aluminum scale to evaluate the optical bone density. L & Z classification was also applied. By using periapical radiographs, a statistically significant difference was observed in the optical bone density of the posterior maxilla (2.38 ± 1.06) and the posterior mandible (3.84 ± 0.68), when compared to the other regions (P ≤ 0.015). However, with panoramic radiographs, no differences were observed in the optical bone density (P = 0.6322). A negative correlation was observed between the L & Z classification and the optical bone density obtained by the periapical radiographs (rho = −0.463; P < 0.001), that is, the worse the bone quality, the lower the bone density. However, there was no significant correlation with the bone density obtained by panoramic radiographs (rho = −0.009; P = 0.948). As for gender, a correlation between aging and the presence of medullary bone was observed in females, assessed by the L & Z classification (rho = 0.398; P = 0.006). However, there was a correlation between aging and a denser and less medullary presence in males, both assessed by the L & Z classification (rho = −650; P = 0.016), as well as the optical density assessed by periapical (rho = 0.621; P = 0.023) and panoramic (rho = 0.588; P = 0.035) radiographs. These results suggest that gender and age interfere with the bone quality and periapical radiographs are an acceptable method for evaluating bone density. However, a panoramic radiograph was not found to be a reliable method.
Black esophagus and diabetes: a close relationship
Authors: Rodriguez Fernandez Laura , García Sánchez María Concepción , Prieto de Paula José María , Miramontes González José Pablo
Published: July 2020

The black esophagus is a rare clinical entity, down to 0.2% in autopsy series and 0.001–0.2% in series of endoscopies. Although it is an entity that has already been reported in the literature, its etiopathogenesis is not completely known. Different theories have been proposed to clarify their cause. One of these theories makes a hypothesis of a viral infection as the underlying cause; this theory can be seen in the literature extensively, but only two cases were reported. The first case is a case with histopathological confirmation of Herpes virus infection. The second is a case in which vascular deterioration has been the main cause of esophageal necrosis. In both cases, diabetes is the factor that determines a bad evolution of the disease.
A Survey of Electroconvulsive Therapy in Finland
Authors: Sumia Petri , Seppälä Niko , Ritschkoff Jukka , Tammentie-Sarèn Tarja , Leinonen Esa , Järventausta Kaija
Published: July 2020

Objectives

The purpose of this study was to explore the use of electroconvulsive therapy (ECT) in Finland in 2013. This included the rate of use, patient ages, sex, number of treatments, patient diagnoses, regional distribution, and availability of ECT.

Methods

A structured electronic questionnaire was used to collect data regarding the use of ECT from 21 Finnish hospital districts' 29 psychiatric ECT units. Data for comparison were collected from scientific publications concerning the use of ECT in Sweden, Norway, Denmark, and Estonia.

Results

Of 29 psychiatric ECT units, 25 (86%) responded. Electroconvulsive therapy was available in all except 1 hospital district, which used the services of another hospital district. Electroconvulsive therapy was administered to 1023 patients in total. The mean number of treatments per patient was 9.7. Twenty-three persons per 100,000 inhabitants received ECT. The ECT rate between hospital districts varied from 7.5 to 53.0 per 100,000 inhabitants. The mean number and median were 24.9 and 21.7 per 100,000 inhabitants, respectively. Maintenance therapy was administered to 27.1% of patients. Most (75%) of the ECT units indicated the capability to administer ECT to all patients who required it. The most common indications for ECT were major depression (38.4%), psychotic depression (30.9%), and bipolar disorder with depressive episodes (14.2%).

Conclusions

Electroconvulsive therapy was available in every hospital district in Finland. In Finland, ECT was administered at approximately the same level as in Norway, Denmark, and Estonia (24, 32, and 28 per 100,000 inhabitants, respectively), but less than in Sweden (41 per 100,000 inhabitants).
A Pilot Study of Cognitive Impairment in Longstanding Electroconvulsive Therapy–treated Schizophrenia Patients Versus Controls
Authors: Danenberg Renana , Ruimi Liad , Shelef Assaf , Paleacu Kertesz Diana
Published: July 2020

Background

Electroconvulsive therapy (ECT), though reliable and effective, is controversial due to its media portrayal as a treatment with severe side effects. Electroconvulsive therapy is mainly given to patients suffering from affective disorders and treatment-resistant schizophrenia. Although past research assessed the amount and duration of memory loss due to ECT, little is known about its influence on cognition for patients suffering from schizophrenia, whose cognitive decline is an inherent part of their illness. We aimed to test whether maintenance ECT causes cognitive decline among elderly schizophrenia patients.

Methods

Twenty elderly (age >65 years) patients suffering from schizophrenia and schizoaffective disorder who received maintenance ECT were matched with 20 controls suffering from the same illnesses that have never been treated with ECT. The match was based on age, sex, and illness duration. The participants were evaluated using the Montreal Cognitive Assessment for cognitive decline and a Positive and Negative Syndrome Scale (PANSS) for illness severity.

Results

A lower score in the abstraction subscale was found in the maintenance ECT population (P = 0.002), without significant differences in the total Montreal Cognitive Assessment and the delayed-recall subscale scores. In the treatment group, a correlation was found between an impairment in naming and positive symptoms in the PANSS score (r = −0.45) and between abstraction impairment and negative symptoms (r = −0.56) and total PANSS score (r = −0.497).

Conclusions

Maintenance ECT does not worsen existing global cognitive deficits or delayed recall in elderly schizophrenia patients. The abstraction impairment was possibly due to the higher disease burden of the patients referred to ECT.
Nitrogen deposition is negatively related to species richness and abundance of threatened species in Swiss butterflies
Authors: Roth Tobias , Kohli Lukas , Rihm Beat , Meier Reto , Amrhein Valentin
Published: July 2020

Nitrogen (N) deposition caused by agriculture and combustion of fossil fuels is a major threat to plant diversity, but the effects on higher trophic levels are less clear. In this study we investigated how N deposition may affect species richness and abundance (number of individuals per species) in butterflies. We started with reviewing the literature and found that vegetation parameters might be as important as climate and habitat variables in explaining variation in butterfly species richness. It thus seems likely that increased N deposition indirectly affects butterfly communities via its influence on plant communities. We then analysed data from the Swiss biodiversity monitoring program surveying species diversity of vascular plants and butterflies in 383 study sites of 1 km2 that are regularly distributed over Switzerland, covering a modelled N deposition gradient from 2 to 44 kg N ha −1 yr−1. Using traditional linear models and structural equation models, we found that high N deposition was consistently linked to low butterfly diversity, suggesting a net loss of butterfly diversity through increased N deposition. At low elevations, N deposition may contribute to a reduction in butterfly species richness via microclimatic cooling due to increased plant biomass. At higher elevations, negative effects of N deposition on butterfly species richness may also be mediated by reduced plant species richness. In most butterfly species, abundance was negatively related to N deposition, but the strongest negative effects were found for species of conservation concern. We conclude that in addition to factors such as intensified agriculture, habitat fragmentation and climate change, N deposition is likely to play a key role in negatively affecting butterfly diversity and abundance.

Article Impact Statement

Nitrogen deposition negatively affects butterfly species richness and butterfly abundance, particularly in species of conservation concern.

Data accessibility and reproducibility of results

Data and R-scripts to reproduce the results of this manuscript including figures and tables are provided at https://github.com/TobiasRoth/NDep_butterflies. Raw data for analyses are provided in the folder “data”, and the folder “R” contains the R-Script that was used to export the data from the BDM database and to produce the figures and tables of the manuscript.
CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase
Authors: Lu Yang Young , Bai Jiaxing , Wang Yiwen , Wang Ying , Sun Fengzhu
Published: July 2020

Motivation

Rapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, one primary step is sequence comparison. Alignment-free sequence comparison based onk-mer frequencies offers a computationally efficient solution, yet in practice, thek-mer frequency vectors for largekof practical interest lead to excessive memory and storage consumption.

Results

We report CRAFT, a general genomic/metagenomic search engine to learn compact representations of sequences and perform fast comparison between DNA sequences. Specifically, given genome or high throughput sequencing (HTS) data as input, CRAFT maps the data into a much smaller embedding space and locates the best matching genome in the archived massive sequence repositories. With 102– 104-fold reduction of storage space, CRAFT performs fast query for gigabytes of data within seconds or minutes, achieving comparable performance as six state-of-the-art alignment-free measures.

Availability

CRAFT offers a user-friendly graphical user interface with one-click installation on Windows and Linux operating systems, freely available athttps://github.com/jiaxingbai/CRAFT.

Contact

wangying@xmu.edu.cn;fsun@usc.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes
Authors: McClenaghan Beverly , Fahner Nicole , Cote David , Chawarski Julek , McCarthy Avery , Rajabi Hoda , Singer Greg , Hajibabaei Mehrdad
Published: July 2020

The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here, we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea water samples. We found that deep sea water samples (> 1400 m depth) had significantly lower DNA concentrations than surface or mid-depth samples necessitating a refined protocol with a larger sampling volume. We recovered significantly more DNA in large volume water samples (1.5 L) filtered at sea compared to small volume samples (250 mL) held for lab filtration. Furthermore, the number of unique sequences (exact sequence variants; ESVs) recovered per sample was higher in large volume samples. Since the number of ESVs recovered from large volume samples was less variable and consistently high, we recommend the larger volumes when sampling water from the deep ocean. We also identified three primer sets which detected the most fish taxa but recommend using multiple markers due the variability in detection probabilities and taxonomic resolution among fishes for each primer set. Overall, fish diversity results obtained from metabarcoding were comparable to conventional survey methods. While eDNA sampling and processing need be optimized for this unique environment, the results of this study demonstrate that eDNA metabarcoding can be employed to facilitate biodiversity surveys in the deep ocean, require less dedicated survey effort per unit identification and are capable of simultaneously providing valuable information on other taxonomic groups.
Loss of Circadian Protection in Adults Exposed to Neonatal Hyperoxia
Authors: Issah Yasmine , Naik Amruta , Tang Soon Y , Forrest Kaitlyn , Brooke Thomas G , Lahens Nicholas , Theken Katherine N. , Sehgal Amita , Worthen George S. , FitzGerald Garret A. , Sengupta Shaon
Published: July 2020

Adverse early life exposures having a lasting negative impact on health. For examples, neonatal hyperoxia which is a risk factor for chronic lung disease of prematurity or bronchopulmonary dysplasia (BPD) confers susceptibility to respiratory infections like Influenza A (IAV) later in life. Given our previous findings that the circadian clock exerts a protective effect on injury from IAV, we asked if the long-term impact of neonatal hyperoxia includes disruption of circadian rhythms. We show here that neonatal hyperoxia abolishes the circadian clock mediated time of day protection from IAV, not through the regulation of viral burden, but through host tolerance pathways. We further discovered that that this dysregulation is mediated through the intrinsic clock in the lung, rather than through central or immune system clocks. Loss of circadian protein,Bmal1, in AT2 cells of the lung recapitulates the increased mortality, loss of temporal gating and other key features of hyperoxia-exposed animals. Taken together, our data suggest a novel role for the circadian clock in AT2 clock in mediating long-term effects of early life exposures to the lungs.

Brief Summary

Neonatal hyperoxia abrogates the circadian protection from Influenza infection in recovered adults.
Forensic analysis of Soil Microbiomes: Linking Evidence to a Geographic Location
Authors: Cocking Jill Hager , Turley Sgt. Ryan , Fofanov Viacheslav Y. , Samuels-Crow Kimberly , Hungate Bruce , Mau Rebecca L. , Keim Paul S. , Caporaso J. Gregory , Hepp Crystal
Published: July 2020

Over the past two decades, advances in molecular biology have greatly expanded our understanding of microbiomes – the diverse assemblages of microorganisms that inhabit the human body as well as the world around us, and applications in microbiome science have become an active area of research. Differences in the diversity (i.e., richness) and composition of microbiomes has been found to be informative in varied areas of science, including human health, agronomy, and forensic science. Soil harbors microbiomes that vary based on many factors, including the geology of the soil (e.g., sand, silt, or clay), climate, and use of the soil. As a result, the microbiological composition of any two soil samples will never be exactly alike. This inherent variation between microbiomes of different locations has proven to be specific enough to be potentially useful in forensic investigations to associate a person or piece of evidence to a source site.

In this study, a soil microbiome was extracted from the sock of a criminal suspect and compared to the microbiome of soil samples taken from locations traveled to by the suspect. The locations analyzed varied in their soil microbiome composition, and the microbiome profiled from the sock was found to be most similar to the location where the suspect was thought to have left the body of a murder victim. These results provide a case study illustrating that information contained in a soil microbiome may be applied to link evidence to the location where a crime took place, potentially serving as an investigative tool in law enforcement.
Abandonment and restoration of Mediterranean meadows: long-term effects on a butterfly-plant network
Authors: Colom Pau , Traveset Anna , Stefanescu Constantí
Published: July 2020

Both the intensification and abandonment of traditional agricultural practices are known to be major threats to biodiversity worldwide, above all in industrialized countries. Although land abandonment in particular has a negative effect on the diversity of both plant and insect communities, few studies have ever analysed these two groups together and none has yet examined the effect on plant-insect interactions using a network approach. In view of the notable decline of pollinator insects reported in past decades, it is essential to understand how the structure of a plant-pollinator network changes during the ecological succession that occurs as traditionally managed habitats are abandoned, and to what extent this network is re-established when habitats are restored. We monitored a butterfly-plant network for 22 years in habitats where land abandonment and restoration have taken place and were able to compare restoration by grazing with restoration combining mowing and grazing. Abandonment leads to significant reductions in the cover of typical grasslands plants and, in turn, rapidly provokes changes in butterfly assemblages and plant interactions. Specifically, it caused a replacement of multivoltine by monovoltine species, increasing network specialization due to the great specificity in the interactions that monovoltine species established with plants. Changes in butterfly communities were also recorded in a nearby unaltered habitat due to the metapopulation structure of some species. A highly dynamic source-sink system was established between managed and unmanaged habitat patches, which ultimately allowed the metapopulations to persist. Restoration combining mowing and grazing promoted a quick return to the pre-abandonment situation in the butterfly community, and also increased generality and nestedness, two network descriptors that are known to enhance community stability.
An orthogonal differentiation platform for genomically programming stem cells, organoids, and bioprinted tissues
Authors: Skylar-Scott Mark A. , Huang Jeremy Y. , Lu Aric , Ng Alex H.M. , Duenki Tomoya , Nam Lucy L. , Damaraju Sarita , Church George M. , Lewis Jennifer A.
Published: July 2020

Simultaneous differentiation of human induced pluripotent stem cells (hiPSCs) into divergent cell types offers a pathway to achieving tailorable cellular complexity, patterned architecture, and function in engineered human organoids and tissues. Recent transcription factor (TF) overexpression protocols typically produce only one cell type of interest rather than the multitude of cell types and structural organization found in native human tissues. Here, we report an orthogonal differentiation platform for genomically programming stem cells, organoids and bioprinted tissues with controlled composition and organization. To demonstrate this platform, we orthogonally differentiated endothelial cells and neurons from hiPSCs in a one-pot system containing neural stem cell-specifying media. By aggregating inducible-TF and wildtype hiPSCs into pooled and multicore-shell embryoid bodies, we produced vascularized and patterned cortical organoids within days. Using multimaterial 3D bioprinting, we patterned 3D neural tissues from densely cellular, matrix-free stem cell inks that were orthogonally differentiated on demand into distinct layered regions composed of neural stem cells, endothelium, and neurons, respectively. Given the high proliferative capacity and patient-specificity of hiPSCs, our platform provides a facile route for programming cells and multicellular tissues for drug screening and therapeutic applications.
Does the Preferred Walk-Run Transition Speed on Inclines Minimize Energetic Cost, Heart Rate or Neither?
Authors: Brill Jackson W. , Kram Rodger
Published: July 2020

Humans prefer to walk at slow speeds and to run at fast speeds. In between, there is a speed at which people choose to transition between gaits, the Preferred Transition Speed (PTS). At slow speeds, it is energetically cheaper to walk and at faster speeds, it is cheaper to run. Thus, there is an intermediate speed, the Energetically Optimal Transition Speed (EOTS). Our goals were to determine: 1) how PTS and EOTS compare across a wide range of inclines and 2) if the EOTS can be predicted by the heart rate optimal transition speed (HROTS). Ten healthy, high-caliber, male trail/mountain runners participated. On day 1, subjects completed 0° and 15° trials and on day 2, 5° and 10°. We calculated PTS as the average of the walk-to-run transition speed (WRTS) and the run-to-walk transition speed (RWTS) determined with an incremental protocol. We calculated EOTS and HROTS from energetic cost and heart rate data for walking and running near the expected EOTS for each incline. The intersection of the walking and running linear regression equations defined EOTS and HROTS. We found that PTS, EOTS, and HROTS all were slower on steeper inclines. PTS was slower than EOTS at 0°, 5°, and 10°, but the two converged at 15°. PTS and EOTS were only moderately correlated. Although EOTS correlated with HROTS, EOTS was not predicted accurately by heart rate on an individual basis.
Prostaglandin E2 promotes intestinal inflammation via inhibiting microbiota-dependent regulatory T cells
Authors: Crittenden Siobhan , Goepp Marie , Pollock Jolinda , Robb Calum T. , Smyth Danielle J. , Zhou You , Andrews Robert , Tyrrell Victoria , Adima Alexander , O’Connor Richard A. , Davies Luke , Li Xue-Feng , Yao Hatti X. , Ho Gwo-Tzer , Zheng Xiaozhong , Mair Amil , Vermeren Sonja , Qian Bin-Zhi , Mole Damian J. , Schwarze Jürgen K.J. , Breyer Richard M. , Arends Mark J. , O’Donnell Valerie B. , Iredale John P. , Anderton Stephen M. , Narumiya Shuh , Maizels Rick M. , Rossi Adriano G. , Howie Sarah E. , Yao Chengcan
Published: July 2020

The gut microbiota fundamentally regulates intestinal homeostasis and disease partially through mechanisms that involve modulation of regulatory T cells (Tregs), yet how the microbiota-Treg crosstalk is physiologically controlled is incompletely defined. Here, we report that prostaglandin E2 (PGE2), a well-known mediator of inflammation, inhibits mucosal Tregs in a manner depending on the gut microbiota. PGE2 through its receptor EP4 diminishes Treg-favorable commensal microbiota. Transfer of the gut microbiota that was modified by PGE2-EP4 signaling modulates mucosal Treg responses and exacerbates intestinal inflammation. Mechanistically, PGE2-modified microbiota regulates intestinal mononuclear phagocytes and type I interferon signaling. Depletion of mononuclear phagocytes or deficiency of type I interferon receptor contracts PGE2-dependent Treg inhibition. Taken together, our findings provide emergent evidence that PGE2-mediated disruption of microbiota-Treg communication fosters intestinal inflammation.
Cancer-associated fibroblasts in pancreatic ductal adenocarcinoma determine response to SLC7A11 inhibition
Authors: Sharbeen George , McCarroll Joshua A. , Akerman Anouschka , Kopecky Chantal , Youkhana Janet , Holst Jeff , Boyer Cyrille , Erkan Mert , Goldstein David , Timpson Paul , Cox Thomas R. , Pereira Brooke A. , Chitty Jessica L. , Fey Sigrid , Najumudeen Arafath K. , Campbell Andrew D. , Sansom Owen J. , Ignacio Rosa Mistica C. , Naim Stephanie , Liu Jie , Russia Nelson , Lee Julia , Chou Angela , Johns Amber , Gill Anthony , Gonzales-Aloy Estrella , Kokkinos John , Gebski Val , Turner Nigel , Apte Minoti , Davis Thomas P. , Morton Jennifer P. , Haghighi Koroush ,   Australian Pancreatic Cancer Genome Initiative, Phillips Phoebe A.
Published: July 2020

Cancer-Associated Fibroblasts (CAFs) are major contributors to pancreatic ductal adenocarcinoma (PDAC) progression, through pro-tumour cross-talk and the generation of fibrosis (physical barrier to drugs). CAF inhibition is thus an ideal component of any therapeutic approach for PDAC. SLC7A11 is a cystine transporter that has been identified as a potential therapeutic target in PDAC cells. However, no prior study has evaluated the role of SLC7A11 in PDAC tumour stroma and its prognostic significance. Herein we show that high expression of SLC7A11 in PDAC tumour stroma (but not tumour cells) is independently prognostic of poorer overall survival. We demonstrate using orthogonal approaches that PDAC-derived CAFs are highly dependent on SLC7A11 for cystine uptake and glutathione synthesis, and that SLC7A11 inhibition significantly decreases their proliferation, reduces their resistance to oxidative stress and inhibits their ability to remodel collagen and support PDAC cell growth. Importantly, our paradigm-shifting work demonstrates the need to inhibit SLC7A11 in the PDAC stroma, as genetic ablation of SLC7A11 in PDAC cells alone is not enough to reduce tumour growth. Finally, our work validates that a nano-based gene-silencing drug against SLC7A11, developed by our group, reduces PDAC tumour growth, CAF activation and fibrosis in a mouse model of PDAC.
The role of musical priming in brand recall
Authors: Levrini Gabriel , Schaeffer Cristian Luis , Nique Walter
Published: July 2020

Purpose

The purpose of this paper is twofold: first, to analyze whether musical priming induces greater recall of brands and, second, to study the emotional priming effects of music, in comparison with non-emotional music, including gender comparison.

Design/methodology/approach

Through the utilization of neuromarketing tools and protocols (quantitative and qualitative), the study explores facial eltromyography (EMG) capabilities and skin conductance responses (SCR) measuring consumers’ emotional responses.

Findings

The findings show that at least, 40 percent of the total sample recognized a musical priming effect. The study measures the emotional response to musical priming as positive. Emotional video recognition was much higher in females. Both the self-report and physiological measures support the notion that emotional background music can elicit emotional responses in consumers.

Research limitations/implications

The research measured emotional response to musical priming without testing how these responses influence consumers’ attention and overall behavior.

Practical implications

The five senses, especially hearing, play an important role in the purchasing decision process and in the individual customer experience. People become aware of the products and brands that surround them and make their choice. In terms of digital trading activities and online sales, increasing physiological understanding of musical priming reactions may mean that, for companies, selling low-end online goods may be economically worthwhile to cooperate with platforms such as Spotify or iTunes to select individual users.

Social implications

More research is needed in priming process techniques in order to better understand how primes activate knowledge in the consumer’s mind. Understanding this process will inform marketers how close a prime needs to be to a target to have an effective influence, as well as when marketers should be concerned about negative priming effects.

Originality/value

At the best of our knowledge, it is the first time that music priming is analyzed in terms of self-report and physiological measures From the measurement’s perspective, the results reaffirm that physiological and self-report measures capture different levels of information. While SCR and EMG capture real-time subconscious responses, MAN scale self-report data provide information regarding how cognitive effort, in terms of intensity and valence, affects brand recall.
New boundary conditions for simulating the filling stage of the injection molding process
Authors: Galuppo Wagner de Campos , Magalhães Ana , Ferrás Luís Lima , Nóbrega João Miguel , Fernandes Célio
Published: July 2020

Purpose

The purpose of this paper is to develop new boundary conditions for simulating the injection molding process of polymer melts.

Design/methodology/approach

The boundary conditions are derived and implemented to simulate real-life air vents (used to allow the air escape from the mold). The simulations are performed in the computational library OpenFOAM® by considering two different fluid models, namely, Newtonian and generalized Newtonian (Bird–Carreau model).

Findings

A detailed study on the accuracy of the solver interFoam for simulating the filling stage is presented, by considering simple geometries and adaptive mesh refinement. The verified code is then used to study the three-dimensional filling of a more complex geometry.

Originality/value

The results obtained showed that the numerical method is stable and allows one to model the filling process, simulating the real injection molding process.
Construction project productivity evaluation framework with expanded system boundaries
Authors: Zhan Wenting , Pan Wei , Chen Le
Published: July 2020

Purpose

While the investment in construction projects has increased over the past few decades, low construction project productivity (CPP) appeared to be persistent, thereby reflecting an “investment-in-failure” paradox between the investment and CPP. Hence, this paper aims to develop a systematic and holistic CPP evaluation framework to explain the apparent paradox in the construction industry.

Design/methodology/approach

The paper first reviews the literature about the theories of system, production, principal–agent and project success evaluation to re-conceptualise the CPP and proposes a two-stage CPP evaluation framework. The framework is subsequently explored through a sequential qualitative mixed-methods design within the context of the Hong Kong construction industry by combining 32 semi-structured interviews with senior industry experts and exploratory case studies, with three real-life construction projects.

Findings

The paper identifies three system boundaries for CPP evaluation, that is, parameter, timeframe and stakeholder, and develops a two-stage CPP evaluation framework to indicate site efficiency and utilisation effectiveness, thereby accessing the productivity of both the construction and post-construction stages. The “investment-in-failure” paradox associated with current CPP evaluation approaches is primarily attributed to the narrowly defined CPP boundaries.

Research limitations/implications

The qualitative exploration of the evaluation framework only focusses on the Hong Kong construction industry. Further case studies within other urban contexts could be used to improve the generalisability of the findings. Quantitative research is also necessary to advance theoretical development of the two-stage CPP evaluation.

Practical implications

The systemic CPP conceptualisation and the two-stage CPP evaluation framework support the systems thinking of industry stakeholders and enable them to formulate holistic strategies for long-term CPP enhancement.

Originality/value

The research demonstrates the needs to expand the system boundaries of CPP to reflect its systemic value and to shift the paradigm of CPP evaluation from being output-orientated and quantity-focussed to being outcome-orientated and value-focussed.
What constitutes risk for a theatrical film distributor? Evidence from the Hindi film industry
Authors: Dyondi Rashmi , Jha Shishir Kumar , Haldar Arunima
Published: July 2020

Purpose

This paper aims to examine the strategic issues of risk for independent theatrical film distributors in the Hindi film industry in India.

Design/methodology/approach

The study adopted qualitative grounded theory approach to explore contextually relevant strategic issues of risk for independent theatrical film distributors. Semi-structured in-depth interviews with Hindi film distributors helped to gain explorative insights about the risk behaviour of film distributors operating in Mumbai “circuit”.

Findings

The findings suggest that risk faced by distributors is a function of product (film content) features, contractual terms, resources such as finance and strength of strategic alliances with the producers. The study develops a business risk model for the film distributors from a series of propositions.

Originality/value

The paper contributes to the literature on motion picture industry by highlighting the importance of distribution risk in the film value chain.