bluuebunny/crossref_metadata_2025 huggingface dataset:
Acute Physical Therapy Competency for Identifying Appropriate Patients for a Physical Therapist Assistant's Caseload
Authors: Powell Debra , Roberts Pamela , Truong Lyna
Published: January 2020

Background:

At an academic medical center, physical therapist assistants (PTAs) were observed spending increased time reviewing charts and collaborating with the physical therapists (PTs) about inappropriate patient caseloads.

Objective:

To develop staff competency through a standardized process for the identification of appropriate patients for a PTA caseload utilizing the APTA's PTA Direction Algorithm and improve PT/PTA relationships in the acute care setting.

Design:

Mixed-methods prospective study.

Methods:

Study consisted of acute care PT staff in an academic medical center using the PTA Direction Algorithm with data collected, pre- and posttraining of the PT staff in the algorithm, and the Mann-Whitney U test was used to determine statistical differences. Focus groups with the PTAs were conducted pre- and posttraining of the PT staff.

Results:

Data were collected from the 2 participating PTA staff for a period of 294 total worked hours both for the pre- and posttraining periods. For the pretraining period, data were collected between April 1, 2018, and April 28, 2018, for 28 days with 302 patient care encounters. The posttraining period occurred between July 1, 2018, and August 11, 2018, for 42 days with 307 patient care encounters. The PTAs' daily average pretraining of 10.79 patient encounters, 40.71 minutes for chart reviews, and 12.89 minutes for PT/PTA collaboration decreased posttraining, to a daily average of 7.31 patient encounters, 6.43 minutes for chart reviews, and 6.76 minutes for PT/PTA collaboration. PTAs spent significantly less time in daily average reviewing of charts posttraining (mean = 6.43, SD 10.98, compared with the pretraining (mean = 40.71, SD 38.96, U = 186.500, P < .001). Collaboration times also significantly decreased posttraining (mean = 6.76, SD 11.14), compared with pretraining (mean = 12.89, SD 11.54, U = 371.00, P = .007); however, the average number of daily encounters unfavorably decreased in the posttraining (mean = 7.31, SD 5.13), compared with the pretraining period (mean = 10.79, SD 5.06, U = 398.5, P = .022).

Limitations:

Small number of participants in one academic medical center.

Conclusions:

The PTA Direction Algorithm tool used in establishing staff competency provided the mechanism for developing a standardized process, significantly improving chart review time, and PT/PTA relationships in the acute care setting.
Health Care Use and Spending of Pediatric Patients With an Intellectual or Developmental Disability
Authors: Kim Jaewhan , Stevens Paul , Carbone Paul S. , Jones Kyle B.
Published: January 2020

Background:

Health care costs and utilization for those with an intellectual or developmental disability (IDD) have been shown to be higher than the general population.

Objective:

To investigate the services that contribute to higher costs and utilization among noninstitutionalized children with an IDD.

Design:

Matched case-control secondary analysis of the 2000–2017 Medical Expenditure Panel Survey. Pediatric (age 0–21) patients with an IDD were matched to non-IDD subjects. Health care utilization and costs were evaluated with zero-inflated negative binomial regressions and generalized linear models, respectively.

Measures:

Outcome measures included high-acuity health care utilization [ie, emergency department (ED) visits and hospital admissions], and cost outcomes for total spending, ED use, hospitalization, medications, office visits, home health, and physical therapy.

Results:

There was no statistical difference in utilization of EDs among the 2 groups though subjects with an IDD showed more hospitalizations than their matched cohort (incidence rate ratios=1.63,P=0.00). Total health care spending was higher among patients with an IDD (coefficient=$5831,P=0.00). Pediatric spending was higher in all measures except for ED. The biggest discrepancies in spending were seen in home health (coefficient=$2558,P=0.00) and outpatient visits (coefficient=$1180,P=0.00).

Conclusions:

Pediatric patients with an IDD had higher health care spending and utilization than non-IDD subjects in all categories except for ED use.
Nurse Continuity at Discharge and Return to Hospital
Authors: Bahr Sarah J. , Bang James , Yakusheva Olga , Bobay Kathleen L. , Krejci Janet , Costa Linda , Hughes Ronda G. , Hamilton Morris , Siclovan Danielle M. , Weiss Marianne E.
Published: January 2020

Background

Promoting continuity of nurse assignment during discharge care has the potential to increase patient readiness for discharge—which has been associated with fewer readmissions and emergency department visits. The few studies that examined nurse continuity during acute care hospitalizations did not focus on discharge or postdischarge outcomes.

Objectives

The aim of this research was to examine the association of continuity in nurse assignment to patients prior to hospital discharge with return to hospital (readmission and emergency department or observation visits), including exploration of the mediating pathway through patient readiness for discharge and moderating effects of unit environment and unit nurse characteristics.

Methods

In a sample of 18,203 adult, medical–surgical patients from 31 Magnet hospitals, a correlational path analysis design was used in a secondary analysis to evaluate the effect of nurse continuity on readmissions and emergency department or observation visits within 30 days after hospital discharge. The mediating pathway through discharge readiness measured by patient self-report and nurse assessments was also assessed. Moderating effects of unit environment and nursing characteristics were examined across quartiles of unit environment (nurse staffing hours per patient day) and unit nurse characteristics (education and experience). Analyses were adjusted for patient characteristics, unit fixed effects, and clustering at the unit level.

Results

Continuous nurse assignment on the last 2 days of hospitalization was observed in 6,441 (35.4%) patient discharges and was associated with a 0.85 absolute percentage point reduction (7.8% relative reduction) in readmissions. There was no significant association with emergency department or observation visits. Sensitivity analysis revealed a stronger effect in patients with higher Elixhauser Comorbidity Indexes. Readiness for discharge was not a mediator of the effect of continuity on return to hospital. Unit characteristics were not associated with nurse continuity. No moderation effect was evident for unit environment and nurse characteristics.

Discussion

Continuity of nurse assignment on the last 2 days of hospitalization can reduce readmissions. Staffing for continuity may benefit patients and healthcare systems, with greater benefits for high-comorbidity patients. Nurse continuity prior to hospital discharge should be a priority consideration in assigning acute care nurses to augment readmission reduction efforts.
Accuracy of Computer-Aided Design/Computer-Aided Manufacturing Surgical Template for Guidance of Dental Implant Distraction in Mandibular Reconstruction With Free Fibula Flaps
Authors: Xingzhou Qu , Wang Zhen , Ong Hui Shan , Chenping Zhang , Abdelrehem Ahmed
Published: January 2020

Purpose:

The direction and orientation of the osteotomized upper segments in dental implant distractor (DID) can be compromised due to an unpredicted vector of distraction. The present study aimed to evaluate the accuracy of computer-aided design/computer-aided manufacturing (CAD/CAM) surgical templates to precisely guide the distraction process in lengthening of the alveolar height for functional mandibular reconstruction.

Patients and Methods:

This retrospective study included all consecutive patients who underwent digitally designed mandibular reconstruction using the fibular flap and DID with the help of CAD/CAM designed surgical templates in a single-stage procedure from 2011 to 2014. First, the preoperative digital planning was performed on 3-dimensional models. Afterward, simulation of the distraction process was made on the virtual model and the resulting new height of the fibula was evaluated. The preoperative simulation was applied to accurately define the exact location and path of the DID device to achieve the suitable vertical height. The preoperative digital planning was used to help the design of the CAD/CAM surgical template, which was then fabricated by means of the 3-dimensional printing technology. The manufactured surgical template-assisted both horizontal and vertical osteotomies of the fibular segments and defining the DID path to lead the distractor into the accurate position. The outcome evaluation was achieved through comparing both preoperative virtual planning with postoperative actual outcomes.

Results:

This study included 14 subjects, 8 were males and 6 were females. The mean age at time of surgery was 31.07 years (range 18–47). All fibular flaps showed 100% success rate. The mean vertical bone height attained with the DID device was 11.35 mm. The vertical and horizontal osteotomies of the fibular segments were completed, then the DID devices were successfully positioned guided by the template. The mean values of the linear and angular deviations for the distractor position and upper segments were calculated and recorded. The maximum linear deviation between the virtual and the postoperative actual distractors was 0.93 mm in the anteroposterior direction, and the greatest in the horizontal plane was 4.64°.

Conclusions:

CAD/CAM surgical templates can accurately guide the direction and orientation of the DID device for functional mandibular reconstruction; therefore, helping to improve the outcomes by accurately transferring the preoperative virtual plan to real surgical procedure.
New Device For Submental Endotracheal Intubation
Authors: Silveira Roger Lanes , Costa Samuel Macedo , Amaral Marcio Bruno Figueiredo
Published: January 2020

The submental intubation is a well-described technique as an alternative for the tracheostomy in the airway management in patients with contraindications for the nasotracheal and cannot remain in the orotracheal position due to the need to maintain the intermaxillary fixation. Residents and young oral and maxillofacial surgeons could have experienced some difficulty performing the technique first described by Altemir (1986). This report aims to describe a new device designed to facilitate and simplify the technique helping surgeons on the submental endotracheal intubation.
Unilateral Cranialization as an Approach for Posterior Table Frontal Sinus Fractures
Authors: Deal Alexandra , Black Jonathan S.
Published: January 2020

Management of posterior table fractures has seen a conservative shift in recent years. Patients who present with CSF leak may be safely monitored, while cranialization is reserved for patients with severe comminuted or displaced posterior table fractures. We report the case of a 20-year-old patient with a comminuted, displaced posterior table fracture that was missing a central segment and was associated with dural injury. The septum and contralateral sinus were unaffected, thus warranting unilateral cranialization. This is a reported case of hemicranialization, which falls on the spectrum of a conservative approach. At 12 months post-op, the patient has not experienced any complications historically associated with cranialization including persistent CSF leak, meningitis, wound infection, alopecia or facial nerve injury at the site of surgery.
The Effects of Maxillary Movements on Nasal Aesthetics Following Orthognathic Surgery
Authors: Üstün Galip Gencay , Konaş Ersoy , El Hakan , Akarsu Güven Bengisu , Dağ Osman , Kamburoğlu Haldun , Mavili Mehmet Emin
Published: January 2020

Improvement of the harmony between facial subunits is the ultimate goal of orthognathic surgery and surgeons must accurately make soft tissue projections for planned bony movements. Yet, few studies have examined the effects’ of orthognathic surgery on aesthetic parameters of nasolabial area on a thorough basis.

This retrospective study included 61 patients that underwent orthognathic surgery. Demographic data, evaluation period, and surgical details were analyzed. Superficial topographical analysis of intercanthal distance, alar width, nasal height, nasal length, nasal tip protrusion, upper lip height, nasal bone angle, supratip break angle, nasal dorsum angle, nasal tip angle, columellar-lobular angle, columellar-labial angle, upper lip angle, and tip-to-midline angle was recorded before and after surgery. Postoperative changes in these parameters and their correlation to maxillary movements were analyzed.

Alar width, upper lip height, columellar-labial angle, supratip break angle, nasal dorsum angle, and upper lip angle increased postsurgery, whereas tip-to-midline angle decreased. Upper lip height and columellar-labial angle were significantly correlated with clockwise/counter-clockwise rotation and anterior re-positioning. Columellar-labial angle increased 2° for each 1 mm of anterior movement and decreased 4° for each 1 mm of counter-clockwise rotation. Novel parameters, such as columellar-lobular angle and tip-to-midline angle, were not associated with any maxillary movement postsurgery.

Orthognathic surgery primarily affected the lower third of the nose and changed alar width, upper lip height, supratip break angle, nasal dorsum angle, columellar-labial angle, upper lip angle, and tip-to-midline angle in this region; however, only columellar-labial angle and upper lip height were found to be correlated solely with maxillary movements.
Assessment of Bone Formation After Secondary Alveolar Bone Grafting With and Without Platelet-Rich Plasma Using Computer-Aided Engineering Techniques
Authors: Chen Shuxiu , Liu Bing , Yin Ningbei , Wang Yongqian , Li Haidong
Published: January 2020

The aim of this study was to analyze the newly formed bone volume (FV), 6 months after secondary alveoloplasty using iliac cancellous bone graft, with and without platelet-rich plasma (PRP). Forty patients with unilateral alveolar cleft were involved in this randomized, prospective, comparative study, with 20 patients each forming the control (group A) and PRP (group B) groups, respectively. The preoperative alveolar defect volume (DV) and the postoperative FV were automatically calculated by the computer-aided engineering software using the patients’ pre and postsurgical computed tomography data. The volume of the actual bone graft (AV) was identical to the DV calculated before surgery. The bone formation ratio (BF%) was calculated as follows: BF% = (FV/AV) × 100%. The mean BF% was 42.54 ± 9.32% in group A and 46.97 ± 18.49% in group B. There was no statistically significant difference between the 2 groups for BF% (P > 0.05). The study presents a fast and accurate method for assessing the effect of PRP in alveolar grafting. However, the study found no conclusive evidence on the effect of PRP on bone growth.
Expression changes of cytotoxicity and apoptosis genes in HTLV-1-associated myelopathy/tropical spastic paraparesis patients from the perspective of system virology
Authors: Ghazvini Kiarash , Youssefi Masoud , Keikha Masoud
Published: January 2020

Although human T-cell lymphotropic virus type-1 (HTLV-1) was the first retrovirus among human pathogens to be identified, insufficient information on the pathogenesis of HTLV-1 infection means that no precise mechanism has yet been provided for HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Based on previous studies, it was found that apoptosis and inflammation stimulation were among the most important mechanisms underlying HAM/TSP. The present study provides an in-silico analysis of the microarray data related to HAM/TSP patients. Expression changes of the genes responsible for cytotoxicity and apoptosis processes of HAM/TSP patients and asymptomatic carriers were investigated. Expression of the genes involved in cytotoxicity and apoptosis in HAM/TSP patients was decreased; hence, a model was proposed indicating that the spread of immune responses in HAM/TSP may be due to expression of HTLV-1 virulence factors and the resistance of HTLV-1-infected cells to apoptosis.
Algoriphagus kandeliae sp. nov., isolated from mangrove rhizosphere soil
Authors: Song Zhi-Man , Wang Kai-Ling , Yin Qi , Chen Cheng-Chun , Xu Ying
Published: January 2020

Strain XY-J91T, a Gram-stain-negative, reddish orange, non-spore-forming and short-rod-shaped marine bacterium, was isolated from rhizosphere soil of the mangrove plant Kandelia candel (L.) Druce in Mai Po Nature Reserve, Hong Kong. The strain showed growth at 15–50 °C (optimum 40 °C), at pH 5.5–9.5 (optimum 7.0–8.0) and with 0–8 % (w/v) NaCl (optimum 1–2 %). The only respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of strain XY-J91T was 40.4 mol%. Strain XY-J91T exhibited highest 16S rRNA gene sequence similarities to the type strains of

Algoriphagus marincola

SW-2T (96.66 %),

Algoriphagus taiwanensis

CC-PR-82T (96.21%),

Algoriphagus ornithinivorans

JC2052T (96.16%),

Algoriphagus confluentis

HJM-2T (95.73%) and

Algoriphagus zhangzhouensis

12C11T (95.52 %). Based on the phylogenetic, phenotypic and chemotaxonomic evidence presented, strain XY-J91T represents a novel species of the genus

Algoriphagus

, for which the name Algoriphagus kandeliae sp. nov. is proposed. The type strain is XY-J91T (=MCCC 1K03612T=KCTC 72216T).
Polyamines produced by Sinorhizobium meliloti Rm8530 contribute to symbiotically relevant phenotypes ex planta and to nodulation efficiency on alfalfa
Authors: Becerra-Rivera Victor A. , Arteaga Alejandra , Leija Alfonso , Hernández Georgina , Dunn Michael F.
Published: January 2020

In nitrogen-fixing rhizobia, emerging evidence shows significant roles for polyamines in growth and abiotic stress resistance. In this work we show that a polyamine-deficient ornithine decarboxylase null mutant (odc2) derived from

Sinorhizobium meliloti

Rm8530 had significant phenotypic differences from the wild-type, including greatly reduced production of exopolysaccharides (EPS; ostensibly both succinoglycan and galactoglucan), increased sensitivity to oxidative stress and decreased swimming motility. The introduction of the odc2 gene borne on a plasmid into the odc2 mutant restored wild-type phenotypes for EPS production, growth under oxidative stress and swimming. The production of calcofluor-binding EPS (succinoglycan) by the odc2 mutant was also completely or mostly restored in the presence of exogenous spermidine (Spd), norspermidine (NSpd) or spermine (Spm). The odc2 mutant formed about 25 % more biofilm than the wild-type, and its ability to form biofilm was significantly inhibited by exogenous Spd, NSpd or Spm. The odc2 mutant formed a less efficient symbiosis with alfalfa, resulting in plants with significantly less biomass and height, more nodules but less nodule biomass, and 25 % less nitrogen-fixing activity. Exogenously supplied Put was not able to revert these phenotypes and caused a similar increase in plant height and dry weight in uninoculated plants and in those inoculated with the wild-type or odc2 mutant. We discuss ways in which polyamines might affect the phenotypes of the odc2 mutant.
Diverse genetic origins of medieval steppe nomad conquerors – a response to Mikheyev et al. (2019)
Authors: Elhaik Eran
Published: January 2020

Recently, Mikheyev et al. (2019) have produced a preprint study describing the genomes of nine Khazars archeologically dated from the 7thto the 9thcenturies found in the Rostov county in modern-day Russia. Skull morphology indicated a mix of “Caucasoid” and “Mongoloid” shapes. The authors compared the samples to ancient and contemporary samples to study the genetic makeup of the Khazars and their genetic legacy and addressed the question of the relationships between the Khazar and Ashkenazic Jews. A careful examination reveals grave concerns regarding all the aspects of the study from the identification of the “Khazar” samples, the choice of environment for ancient DNA sequencing, and the analyses. The authors did not disclose the data used in their study, and their methodology is incoherent. We demonstrate that their analyses yield nonsensical results and argue that none of the claims made in this study are supported by the data unequivocally. Provided the destruction of the bone samples and the irreproducibility of the analyses, even by the forgivable standards of the field, this study is irreplicable, wasteful, and misleading.
Analysis of Plant-derived Phytochemicals as Anti-cancer Agents Targeting Cyclin Dependent Kinase-2, Human Topoisomerase IIa and Vascular Endothelial Growth Factor Receptor-2
Authors: Sarkar Bishajit , Ullah Md. Asad , Islam Syed Sajidul , Rahman Md. Hasanur
Published: January 2020

Cancer is caused by a variety of pathways, involving numerous types of enzymes, among them three enzymes: Cyclin dependent kinase-2 (CDK-2), Human topoisomerase IIα and Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) are three most common enzymes that are involved in the cancer development. Although many chemical drugs are available in the market, plant sources are known to contain a wide variety of agents that are known to possess anticancer activity. In this experiment, total thirty compounds were analysed against the mentioned enzymes using different tools of bioinformatics andin silicobiology like molecular docking study, druglikeness property experiment, ADME/T test, PASS prediction and P450 site of metabolism prediction as well as DFT calculations to determine three best ligands that have the capability to inhibit the mentioned enzymes. Form the experiment, Epigallocatechin gallate was found to be the best ligand to inhibit CDK-2, Daidzein showed best inhibitory activities towards Human topoisomerase IIα and Quercetin was predicted to be the best agent against VEGFR-2. They were also predicted to be quite safe and effective agents to treat cancer. However, morein vivoandin vitroanalysis are required to confirm their safety and efficacy in this regard.
simplePHENOTYPES: SIMulation of Pleiotropic, Linked and Epistatic PHENOTYPES
Authors: Fernandes Samuel B. , Lipka Alexander E.
Published: January 2020

Motivation

Advances in genotyping and phenotyping techniques have enabled the acquisition of a great amount of data. Consequently, there is an interest in multivariate statistical analyses that identify genomic regions likely to contain causal mutations affecting multiple traits (i.e., pleiotropy). As the demand for multivariate analyses increases, it is imperative that optimal tools are available to compare different implementations of these analyses. To facilitate the testing and validation of these multivariate approaches, we developed simplePHENOTYPES, an R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in a wide range of genetic architectures, including additive, dominance and epistatic models.

Results

We illustrate simplePHENOTYPES’ ability to simulate thousands of phenotypes in less than one minute. We then provide a vignette illustrating how to simulate a set of correlated traits in simplePHENOTYPES. Finally, we demonstrate the use of results from simplePHENOTYPES in a standard GWAS software, as well as the numerical equivalence of simulated phenotypes from simplePHENOTYPES and other packages with similar capabilities.

Conclusions

simplePHENOTYPES is a CRAN package that makes it possible to simulate multiple traits controlled by loci with varying degrees of pleiotropy. Its ability to interface with both commonly-used marker data formats and downstream quantitative genetics software and packages should facilitate a rigorous assessment of both existing and emerging statistical GWAS and GS approaches. simplePHENOTYPES is also available athttps://github.coin/sainuelbfernandes/siinplePHENOTYPES.
“Online” modulation of brain hemodynamics despite stereotyped running
Authors: Bergel Antoine , Tiran Elodie , Deffieux Thomas , Demené Charlie , Tanter Mickaël , Cohen Ivan
Published: January 2020

Theta and gamma rhythms coordinate large cell assemblies during locomotion. Their spread across temporal and spatial scales makes them challenging to observe. Additionally, the metabolic cost of these oscillations and their contribution to neuroimaging signals remains elusive. To finely characterize neurovascular interactions in running rats, we monitored brain hemodynamics with functional ultrasound and hippocampal local field potentials in running rats. Theta rhythm and running speed were strongly coupled to brain hemodynamics in multiple structures, with delays ranging from 0.8 seconds to 1.8 seconds. Surprisingly, hemodynamics was also strongly modulated across trials within the same recording session: cortical hemodynamics sharply decreased after 5-10 runs, while hippocampal hemodynamics strongly and linearly potentiated, particularly in the CA regions. This effect occurred while running speed and theta activity remained constant, and was accompanied by increased power in hippocampal high-frequency oscillations (100-150 Hz). Our findings reveal distinct vascular subnetworks modulated across fast and slow timescales and suggest strong adaptation processes despite stereotyped behavior.
Recognition of cellular RNAs by the S9.6 antibody creates pervasive artefacts when imaging RNA:DNA hybrids
Authors: Smolka John A. , Sanz Lionel A. , Hartono Stella R. , Chédin Frédéric
Published: January 2020

The contribution of RNA:DNA hybrid metabolism to cellular processes and disease states has become a prominent topic of study. The S9.6 antibody recognizes RNA:DNA hybrids with a subnanomolar affinity, making it a broadly used tool to detect and study RNA:DNA hybrids. However, S9.6 also binds double-stranded RNAin vitrowith significant affinity. Though frequently used in immunofluorescence microscopy, the possible reactivity of S9.6 with non-RNA:DNA hybrid substratesin situ, particularly RNA, has not been comprehensively addressed. Furthermore, S9.6 immunofluorescence microscopy has been methodologically variable and generated discordant imaging datasets. In this study, we find that the majority of the S9.6 immunofluorescence signal observed in fixed human cells arises from RNA, not RNA:DNA hybrids. S9.6 staining was quantitatively unchanged by pre-treatment with the human RNA:DNA hybrid-specific nuclease, RNase H1, despite experimental verificationin situthat S9.6 could recognize RNA:DNA hybrids and that RNase H1 was active. S9.6 staining was, however, significantly sensitive to pre-treatments with RNase T1, and in some cases RNase III, two ribonucleases that specifically degrade single-stranded and double-stranded RNA, respectively. In contrast, genome-wide maps obtained by high-throughput DNA sequencing after S9.6-mediated DNA:RNA Immunoprecipitation (DRIP) are RNase H1-sensitive and RNase T1- and RNase III-insensitive. Altogether, these data demonstrate that the S9.6 antibody, though capable of recognizing RNA:DNA hybridsin situandin vitro, suffers from a lack of specificity that precludes reliable imaging of RNA:DNA hybrids and renders associated imaging data inconclusive in the absence of controls for its promiscuous recognition of cellular RNAs.
CRISPR-mediated activation of biosynthetic gene clusters for bioactive molecule discovery in filamentous fungi
Authors: Roux Indra , Woodcraft Clara , Hu Jinyu , Wolters Rebecca , Gilchrist Cameron L.M. , Chooi Yit-Heng
Published: January 2020

Accessing the full biosynthetic potential encoded in the genomes of fungi is limited by the low expression of most biosynthetic gene clusters (BGCs) under common laboratory culture conditions. CRISPR-mediated transcriptional activation (CRISPRa) of fungal BGC could accelerate genomics-driven bioactive secondary metabolite discovery. In this work, we established the first CRISPRa system for filamentous fungi. First, we constructed a CRISPR/dLbCas12a-VPR-based system and demonstrated the activation of a fluorescent reporter inAspergillus nidulans. Then, we targeted the native nonribosomal peptide synthetase-like (NRPS-like) genemicAin both chromosomal and episomal contexts, achieving increased production of the compound microperfuranone. Finally, multi-gene CRISPRa led to the discovery of themiccluster product as dehydromicroperfuranone. Additionally, we demonstrated the utility of the variant dLbCas12aD156R-VPR for CRISPRa at room temperature culture conditions. Different aspects that influence the efficiency of CRISPRa in fungi were investigated, providing a framework for the further development of fungal artificial transcription factors based on CRISPR/Cas.
Single-cell transcriptome analysis reveals cell-cell communication and thyrocyte diversity in the zebrafish thyroid gland
Authors: Gillotay Pierre , Shankar Meghna , Haerlingen Benoit , Eski Sema Elif , Pozo-Morales Macarena , Suñer Inés Garteizgogeascoa , Reinhardt Susanne , Kränkel Annekathrin , Bläsche Juliane , Petzold Andreas , Ninov Nikolay , Kesavan Gokul , Lange Christian , Brand Michael , Detours Vincent , Costagliola Sabine , Singh Sumeet Pal
Published: January 2020

The thyroid gland regulates growth and metabolism via production of thyroid hormone in follicles composed of thyrocytes. So far, thyrocytes have been assumed to be a homogenous population. To uncover genetic heterogeneity in the thyrocyte population, and molecularly characterize the non-thyrocyte cells surrounding the follicle, we developed a single-cell transcriptome atlas of the zebrafish thyroid gland. The 6249-cell atlas includes profiles of thyrocytes, blood vessels, lymphatic vessels, immune cells and fibroblasts. Further, the thyrocytes could be split into two sub-populations with unique transcriptional signature, including differential expression of the transcription factorpax2a. To validate thyrocyte heterogeneity, we generated a CRISPR/Cas9-basedpax2aknock-in line, which demonstrated specificpax2aexpression in the thyrocytes. However, a population ofpax2a-low mature thyrocytes interspersed within individual follicles could be distinguished, corroborating heterogeneity within the thyrocyte population. Our results identify and validate transcriptional differences within the nominally homogenous thyrocyte population.

One-line summary

Single-cell analysis uncovers latent heterogeneity in thyroid follicular cells.

Graphical Abstract
Systems level profiling of arginine starvation reveals MYC and ERK adaptive metabolic reprogramming
Authors: Brashears Caitlyn B. , Rathore Richa , Schultze Matthew , Ehrhardt William R. , Tzeng Shin-Chen , Van Tine Brian A. , Held Jason M.
Published: January 2020

Arginine auxotrophy due to the silencing of argininosuccinate synthetase 1 (ASS1) occurs in many cancers, especially sarcomas. Arginine deiminase (ADI-PEG20) therapy exploits this metabolic vulnerability by depleting extracellular arginine, causing arginine starvation. ASS1-negative cells develop resistance to ADI-PEG20 through a metabolic adaptation that includes re-expressing ASS1. As arginine-based multiagent therapies are being developed, further characterization of the changes induced by arginine starvation is needed. In order to develop a systems-level understanding of these changes, activity-based proteomic profiling (ABPP) and phosphoproteomic profiling were performed before and after ADI-PEG20 treatment in ADI-PEG20-sensitive and resistant sarcoma cells. When integrated with previous metabolomic profiling (Kremeret al, 2017a), this multi-omic analysis reveals that cellular response to arginine starvation is mediated by adaptive ERK signaling, driving a Myc-Max transcriptional network. Concomitantly, these data elucidate proteomic changes that facilitate oxaloacetate production by enhancing glutamine and pyruvate anaplerosis, and altering lipid metabolism to recycle citrate for oxidative glutaminolysis. Based on the complexity of metabolic and cellular signaling interactions, these multi-omic approaches could provide valuable tools for evaluating response to metabolically targeted therapies.
Disease mutation study identifies essential residues for phosphatidylserine flippase ATP11A
Authors: Sun Kuanxiang , Tian Wanli , Liu Wenjing , Yang Yeming , Zhu Xianjun
Published: January 2020

PS flippase (P4-ATPase) transports PS from the outer to the inner leaflet of the lipid bilayer in the membrane to maintain PS asymmetry, which is important for biological activity of the cell. ATP11A is expressed in multiple tissues and plays a role in myotube formation. However, detailed cellular function of ATP11A remains elusive. Mutation analysis revealed that I91, L308 and E897 residues in ATP8A2 are important for flippase activity. In order to investigate the roles of these corresponding amino acid residues in ATP11A, we assessed the expression and flippase activity of the respective ATP11A mutant proteins. ATP11A mainly localizes to the Golgi when co-expressed with TMEM30A, the β-subunit of the complex. Y300F and D913K mutations affect correct Golgi localization and PS stimulated flippase activity. In addition, Y300F mutation causes reduced ATP11A expression. Our data provides insight into essential residues for expression and flippase activity of ATP11A.
Function and evolution of B-Raf loop dynamics relevant to cancer recurrence under drug inhibition
Authors: Babbitt Gregory A. , Lynch Miranda L. , McCoy Matthew , Fokoue Ernest P. , Hudson André O.
Published: January 2020

Oncogenic mutations in the kinase domain of the B-Raf protein have long been associated with cancers involving the MAPK pathway. One constitutive MAPK activating mutation in B-Raf, the V600E (valine to glutamate) replacement occurring adjacent to a site of threonine phosphorylation (T599) occurs in many types of cancer, and in a large percentage of certain cancers, such as melanoma. Because ATP binding activity and the V600E mutation are both known to alter the physical behavior of the activation loop in the B-Raf ATP binding domain, this system is especially amenable to comparative analyses of molecular dynamics simulations modeling various genetic and drug class variants. Here, we employ machine learning enabled identification of functionally conserved protein dynamics to compare how the binding interactions of four B-Raf inhibitors impact the functional loop dynamics controlling ATP activation. We demonstrate that drug development targeting B-Raf has progressively moved towards ATP competitive inhibitors that demonstrate less tendency to mimic the functionally conserved dynamic changes associated with ATP activation and leading to the side effect of hyperactivation (i.e. inducing MAPK activation in non-tumorous cells in the absence of secondary mutation). We compare the functional dynamic impacts of V600E and other sensitizing and drug resistance causing mutations in the regulatory loops of B-Raf, confirming sites of low mutational tolerance in these regions. Lastly, we investigate V600E sensitivity of B-Raf loop dynamics in an evolutionary context, demonstrating that while sensitivity has an ancient origin with primitive eukaryotes, it was also secondarily increased during early jawed vertebrate evolution.
A unifying model for the propagation of prion proteins in yeast brings insight into the [PSI+] prion
Authors: Paul Lemarre , Suzanne Sindi S. , Laurent Pujo-Menjouet
Published: January 2020

The use of yeast systems to study the propagation of prions and amyloids has emerged as a crucial aspect of the global endeavor to understand those mechanisms. Yeast prion systems are intrinsically multi-scale: the molecular chemical processes are indeed coupled to the cellular processes of cell growth and division to influence phenotypical traits, observable at the scale of colonies. We introduce a novel modeling framework to tackle this difficulty using impulsive differential equations. We apply this approach to the [PSI+] yeast prion, which associated with the misconformation and aggregation of Sup35. We build a model that reproduces and unifies previously conflicting experimental observations on [PSI+] and thus sheds light onto characteristics of the intracellular molecular processes driving aggregate replication. In particular our model uncovers a kinetic barrier for aggregate replication at low densities, meaning the change between prion or prion-free phenotype is a bi-stable transition. This result is based on the study of prion curing experiments, as well as the phenomenon of colony sectoring, a phenotype which is often ignored in experimental assays and has never been modeled. Furthermore, our results provide further insight into the effect of guanidine hydrochloride (GdnHCl) on Sup35 aggregates. To qualitatively reproduce the GdnHCl curing experiment, aggregate replication must not be completely inhibited, which suggests the existence of a mechanism different than Hsp104-mediated fragmentation. Those results are promising for further development of the [PSI+] model, but also for extending the use of this novel framework to other yeast prion or amyloid systems.

Author summary

In the study of yeast prions, mathematical modeling is a powerful tool, in particular when it comes to facing the difficulties of multi-scale systems. In this study, we introduce a mathematical framework for investigating this problem in a unifying way. We focus on the yeast prion [PSI+] and present a simple molecular scheme for prion replication and a model of yeast budding. In order to qualitatively reproduce experiments, we need to introduce a non-linear mechanism in the molecular rates. This transforms the intracellular system into a bi-stable switch and allows for curing to occur, which is a crucial phenomenon for the study of yeast prions. To the best of our knowledge, no model in the literature includes such a mechanism, at least not explicitly. We also describe the GdnHCl curing experiment, and the propagon counting procedure. Reproducing this result requires challenging hypotheses that are commonly accepted, and our interpretation gives a new perspective on the concept of propagon. This study may be considered as a good example of how mathematical modeling can bring valuable insight into biological concepts and observations.
Influence of the ecological opportunity of interaction on the structure of host-parasite networks
Authors: D’Bastiani Elvira , Campião Karla Magalhães , Boeger Walter Antonio , Araújo Sabrina Borges Lino
Published: January 2020

Despite the great interest to quantify the structure of ecological networks, the influence of morphological, ecological and evolutionary characteristics of the species still remains poorly understood. One of the challenging issues in ecology is how the interaction opportunity influences and provides changes to the associations between species, and which effects these changes have on ecological systems. To explore topological patterns in host-parasite networks, we sampled endoparasites-anurans interactions in South America in order to determine whether the effect of the ecological opportunity affects our understanding of the topological structure of the interaction networks. To identify the effect of the ecological opportunity for interaction, we investigated interactions in environments with and without flood pulse, where presence would promote higher ecological opportunity of interaction. Moreover, we created three theoretical models with filters to test the influence of the ecological opportunity for interaction: random, phylogeny and host body size. We then calculated commonly used binary network metrics (connectance, nestedness and modularity) for the networks generated by the theoretical models. We demonstrated that the interaction ecological opportunity changes the structure of host-parasite networks, and was influenced mainly by phylogeny and body size of the host. Our results indicate that environments that offer greater opportunities for interaction between species present networks with the most connectance/nestedness and less modularity. Networks in environments that do not have such opportunities for interaction depict the opposite pattern. Our results indicate that the ecological opportunity of interaction is reflected in an increase in interaction associations between species and affect/change the organization of these interactive assemblages. From an epidemiological point of view, changes in the composition of parasitic species are associated with risks of invasions and emerging diseases. In part, emerging diseases are the result of processes such as those occurring during the flood pulse, in which climate change, travel, and global trade create opportunities for new species associations. Our results provide insight into the dynamics of incorporating a new resource, considering an evolutionary factor responsible for these changes in species composition.
Assessing the Extent of Structural and Dynamic Modulation of Membrane Lipids due to Pore Forming Toxins: Insights from Molecular Dynamics Simulations
Authors: Varadarajan Vadhana , Desikan Rajat , Ayappa K. G.
Published: January 2020

Infections in many virulent bacterial strains are triggered by the release of pore forming toxins (PFTs), which form oligomeric transmembrane pore complexes on the target plasma membrane. The spatial extent of the perturbation to the surrounding lipids during pore formation is relatively unexplored. Using all-atom molecular dynamics simulations, we investigate the changes in the structure and dynamics of lipids in a 1,2-dimyristoyl-sn-glycero-3-phosphocholine(DMPC) lipid bilayer in the presence of contrasting PFTs. Cytolysin A (ClyA) anαtoxin with its inserted wedge shaped bundle of insertedαhelices induces significant asymmetry across the membrane leaflets in comparison withαhemolysin (AHL) aβtoxin. Despite the differences in hydrophobic mismatch and uniquely different topologies of the two oligomers, perturbation to lipid order as reflected in the tilt angle and order parameters, and membrane thinning is short ranged, lying within ∼ 2.5 nm from the periphery of the either pore complex, commensurate with distances typically associated with van der Waals forces. In contrast, the spatial extent of perturbations to the lipid dynamics extend outward to at least 4 nm for both proteins, and the continuous survival probabilities reveal the presence of a tightly bound shell of lipids in this region. Displacement probability distributions show long tails and the distinctly non-Gaussian features reflect the induced dynamic heterogeneity. A detailed profiling of the protein-lipid contacts with residues tyrosine, tryptophan, lysine and arginine show increased non-polar contacts in the cytoplasmic leaflet for both PFTs, with a higher number of atomic contacts in the case of AHL in the extracellular leaflet due to the mushroom-like topology of the pore complex. The short ranged nature of the perturbations observed in this simple one component membrane suggests an inherent plasticity of membrane lipids enabling recovery of structure and membrane fluidity even in the presence of these large oligomeric trans-membrane protein assemblies. This observation has implications in membrane repair processes such as budding or vesicle fusion events used to mitigate PFT virulence, where the underlying lipid dynamics and fluidity in the vicinity of the pore complex are expected to play an important role.
Convergent evolution and structural adaptation to the deep ocean in the protein folding chaperonin CCTα
Authors: Weber Alexandra A.-T. , Hugall Andrew F. , O’Hara Timothy D.
Published: January 2020

The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including CCTα (Chaperonin Containing TCP-1 subunit α), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examinedin silicolocal protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically-corrected context and found that deep sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed byin silicoglobal protein stability analyses. This suggests that CCTα not only displays structural but also functional adaptations to deep water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as ‘cold-shock’ protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, are key metabolic deep-sea adaptations.
A fast-cooling sample-positioning probe for low-temperature neutron scattering experiments
Authors: Manning Andrew , Avdeev Maxim , Imperia Paolo
Published: January 2020

Top-loading exchange gas cryostats have for a long time been a widely used sample environment device for a variety of neutron scattering experiments. In particular, they allow for simpler and faster changes of samples mounted on sample-positioning probes than is possible with bottom-loading cryostats under vacuum. Here, a new design for sample probes using composite materials is investigated, which significantly decreases the time required to cool a newly installed sample in two different types of closed-cycle exchange gas cryostat.
Impacts of the perceived quality by consumers’ of à la carte restaurants on their attitudes and behavioural intentions
Authors: Souki Gustavo Quiroga , Antonialli Luiz Marcelo , Barbosa Álvaro Alexandre da Silveira , Oliveira Alessandro Silva
Published: January 2020

Purpose

À la carte restaurants have faced increasing challenges in meeting the needs and desires of new food consumers. The purpose of this paper is to propose and test a model for evaluating the consumers’ perceived quality of à la carte restaurants and to review the impact on their attitudes and behavioural intentions.

Design/methodology/approach

A survey was conducted with 508 university students in Brazil, and the data were analysed using structural equation modelling (SEM).

Findings

The results showed that global perceived quality (GPQ), which is a multidimensional construct with nine dimensions, directly impacted emotions, the satisfaction and perceived value by consumers. This satisfaction positively affected word-of-mouth (WOM) communication and the propensity for loyalty. Price did not have a statistically significant impact on customer satisfaction.

Originality/value

This paper, based on the structural model herein proposed and tested, is the most complete of all available articles in the literature about à la carte restaurants, as this study contemplates a greater number of perceived quality factors. In addition, both tangible and intangible perceived quality factors were included in this tested model, which goes beyond what is typically contemplated in other such. Moreover, none of the existing articles in the existing literature simultaneously observed the relationship between perceived quality, positive and negative emotions, price, perceived value, satisfaction, WOM communication and propensity to loyalty. Finally, the questionnaire developed in this study could be used both by academics in future studies and by restaurant managers.