bluuebunny/crossref_metadata_2025 huggingface dataset:
The Fremantle Neck Awareness Questionnaire in Chronic Neck Pain Patients
Authors: Onan Dilara , Gokmen Derya , Ulger Ozlem
Published: August 2019

Study Design.

Cross-cultural adaptation and psychometric analysis.

Objective.

The aim of this study wad to develop “Fremantle Neck Awareness Questionnaire Turkish (FreNAQ-T)” and to investigate the validity, reliability, and psychometric properties of FreNAQ-T in the Turkish population with chronic neck pain (CNP).

Summary of Background Data.

As the different beliefs about the nature of the problem in chronic pain (CP) and its future consequences lead to mis-stimulated neuroplastic changes, the perceptual level and proprioceptive-awareness should be examined in CP. The perceptual level and propriceptive awareness in individuals with chronic low back pain and in knee osteoarthritis were evaluated, whereas the neck version has not been studied.

Methods.

The neck version was conducted using forward-backward method to translate the FreBAQ from English to Turkish. The number of the included patients was 111. The FreNAQ-T was applied to 37 patients after 3 days for test–retest reliability. Validity of the FreNAQ-T was assessed using Rasch analysis and Spearman correlation coefficient. Reliability of the FreNAQ-T's internal consistency was tested by Person Separation Index (PSI) and Cronbach Alpha. Test–retest reliability was tested by differential item functioning (DIF) by time.

Results.

All items of FreNAQ-T were found to fit Rasch Model (given Bonferroni adjustment fit level of 0.006 and χ
2: 6 (df = 9), P = 0.739). Internal construct validity evaluation was good, overall mean item fit residual was 0.141 (SD 1.089), and mean person fit residual was −0.211 (SD 1.173). In reliability evaluation, the PSI was 0.69 (good) and Cronbach alpha was 0.70 (acceptable). When the test–retest was examined via DIF by time, none of the items showed DIF.

Conclusion.

The FreNAQ-T is a valid, reliable, unidimensional scale in CNP and suitable for the assessment of neck-specified awareness-perception in Turkish population with CNP.

Level of Evidence: 3
Neurofibromatosis type 2 and related disorders
Authors: Halliday Dorothy , Parry Allyson , Evans D. Gareth
Published: August 2019

Purpose of review

Neurofibromatosis type 2 (NF2) is a schwannoma predisposition syndrome, alongside schwannomatosis related to germline LZTR1 and SMARCB1 pathogenic variants. This review highlights their overlapping phenotypes, new insight into NF2 phenotype and treatment outcomes.

Recent findings

Mosaic NF2 is more prevalent than previously thought. Use of next-generation sequencing and tumour testing is needed to differentiate mosaic NF2 and schwannomatosis. Developing NF2 phenotypic insights include vasculopathy with brainstem infarction and vessel stenosis; focal cortical dysplasia in severe phenotypes; swallowing/speech difficulties and continued debate into malignancy in NF2. Proposed are: use of visual evoked potentials to monitor optic nerve sheath meningioma; potential routine magnetic resonance angiogram in adolescence and a genetic score to cohort patients with similar pathogenic_variants, for natural history/treatment outcome studies. Cohort studies found survival analysis to hearing loss and unilateral visual loss in severe mutation groups was 32 and 38 years; active management gave better outcomes than surveillance in spinal ependymoma; gamma knife, bevacizumab and hearing preservation surgery maintained or improved short-term hearing in selected patients, and gamma knife had a good long-term tumour control in mild patients with small tumours.

Further long-term outcome studies are needed comparing similar severity patients to allow informed decision making.
Validation of dabrafenib-trametinib prognostic groups in patients treated with vemurafenib and cobimetinib for advanced BRAF-mutated melanoma
Authors: Sorich Michael J. , Rowland Andrew , Hopkins Ashley M.
Published: August 2019

Prognostic groups defined by lactate dehydrogenase concentration and number of organ sites containing metastases have been reported for patients treated with dabrafenib and trametinib for advanced melanoma. We aimed to validate these prognostic groups for patients treated with vemurafenib and cobimetinib in the coBRIM and BRIM-3 clinical studies. Eight hundred nine patients were included, 240 treated with vemurafenib plus cobimetinib and 569 with vemurafenib. For patients treated with vemurafenib and cobimetinib, both overall survival (P < 0.001, c-statistic = 0.72) and progression-free survival (P < 0.001, c-statistic = 0.65) differed markedly between prognostic groups. Two-year progression-free survival ranged from 3 (lactate dehydrogenase ≥2 times the upper limit of normal) to 50% (normal lactate dehydrogenase and ≤3 sites), and two-year overall survival ranged from 7 to 71%. For patients treated with vemurafenib monotherapy, overall survival (P < 0.001, c-statistic = 0.66) and progression-free survival (P < 0.001, c-statistic = 0.62) also differed significantly between prognostic groups. In conclusion, prognostic groups identified for patients treated with dabrafenib and trametinib are also applicable to patients treated with vemurafenib and cobimentinib.
Neoadjuvant intravitreal ranibizumab treatment in high-risk ocular melanoma patients: a two-stage single-centre phase II single-arm study
Authors: Hussain Rumana N. , Heimann Heinrich , Damato Bertil
Published: August 2019

Despite an established history of intraocular antivascular endothelial growth factor (anti-VEGF) agents therapy in a variety of ocular pathologies as well as other cancer forms, use in the primary treatment of uveal melanoma has not been well assessed. This was a two-stage therapeutic and exploratory phase II, non-randomised, single centre trial involving intraocular treatment with 0.5 mg in 0.05 ml of ranibizumab via six intravitreous injections over 6 months in patients with primary ocular melanoma that otherwise required radical surgery because of tumour size. Seven patients were recruited with a median age of 66 years. At baseline, the longest basal diameter was 15.1 mm (mean, range 10–20.4 mm) with a height measured by ultrasonography of 9.2 mm (mean, range 6.6–12.7 mm). No patients achieved complete or partial response at any visit. All required enucleation. Histopathological analysis revealed mixed cell melanoma in 5/7 (71%) and spindle cell morphology in 2/7 (29%) with ciliary body involvement in 4/7 (57%) and the presence of closed loops also in 4/7 (57%). Genetic analysis demonstrated loss of chromosome 3 in 5/7 (71%) but abnormalities in chromosome 1,6 or 8 in all cases. Our study was terminated early as alternative treatments were clearly superior for local tumour control. There continues to be a role of intravitreal anti-VEGF for the treatment of the sequelae of local radiotherapy in the form of radiation retinopathy and so these agents may be used as adjuncts in the treatment of uveal melanoma rather than as a primary treatment.
What is the Likelihood of Subsequent Arthroplasties after Primary TKA or THA? Data from the Osteoarthritis Initiative
Authors: Santana Daniel C. , Anis Hiba K. , Mont Michael A. , Higuera Carlos A. , Piuzzi Nicolas S.
Published: August 2019

Background

Osteoarthritis is common and debilitating, in part because it often affects more than one large weightbearing joint. The likelihood of undergoing more than one total joint arthroplasty has not been studied in a heterogeneous, multicenter population in the United States.

Questions/purposes

We used prospectively collected data of patients with osteoarthritis from the multicenter Osteoarthritis Initiative (OAI) project to ask (1) What is the likelihood of a subsequent THA or TKA after primary TKA or THA? (2) What risk factors are associated with undergoing contralateral TKA after primary TKA?

Methods

Longitudinally maintained data from the OAI were used to identify 332 patients who underwent primary TKA and 132 patients who underwent primary THA for osteoarthritis who did not have a previous TKA or THA in this retrospective study. OAI was a longitudinal cohort study of knee osteoarthritis conducted at five centers in the United States (Columbus, OH, USA; Pittsburgh, PA, USA; Baltimore, MD, USA; Pawtucket, RI, USA; and San Francisco, CA, USA). In this study, the mean follow-up time was 4.0 ± 2.3 years, with 24% (112 of 464) followed for less than 2 years. The primary outcome was the cumulative incidence of subsequent arthroplasty calculated using the Kaplan-Meier method. Age, BMI, gender, and contralateral Kellgren-Lawrence grade, medial joint space width, and hip-knee-ankle angles were modeled as risk factors of contralateral TKA using Cox proportional hazards.

Results

Using the Kaplan-Meier method, at 8 years the cumulative incidence of contralateral TKA after the index TKA was 40% (95% CI 31 to 49) and the cumulative incidence of any THA after index TKA was 13% (95% CI 5 to 21). The cumulative incidence of contralateral THA after the index THA was 8% (95% CI 2 to 14), and the cumulative incidence of any TKA after index THA was 32% (95% CI 15 to 48). Risk factors for undergoing contralateral TKA were younger age (HR 0.95 for each year of increasing age [95% CI 0.92 to 0.98]; p = 0.001) and loss of medial joint space width with a varus deformity (HR 1.26 for each 1 mm loss of joint space width at 1.6o varus [1.06 to 1.51]; p = 0.005).

Conclusion

Patients who underwent TKA or THA for osteoarthritis had a high rate of subsequent joint arthroplasties in this study conducted at multiple centers in the United States. The rate of subsequent joint arthroplasty determined in this study can be used to counsel patients in similar settings and institutions, and may serve as a benchmark to assess future osteoarthritis disease-modifying interventions.

Level of Evidence

Level III, therapeutic study.
Treatment of Horizontal Neck Wrinkles with Hyaluronic Acid Filler: A Retrospective Case Series
Authors: Tseng Fangwen , Yu Hsiaoen
Published: August 2019

Background:

Horizontal neck wrinkles are a common aesthetic deficiency but limited treatment options exist and none have been studied with follow-ups of over 2 months.

Methods:

This dual-center, retrospective case series (Apr 2016–Jan 2017) included adult patients receiving CPM-HA to treat horizontal neck wrinkles. Patients were followed up for 40 weeks. CPM-HA treatment efficacy was evaluated through the Horizontal Neck Wrinkle Severity Scale and Global Aesthetic Improvement Scale (GAIS). Adverse events (AEs) and pain on injection, as assessed on the visual analogue scale, were documented.

Results:

Sixty-four lateral neck halves from 32 women (23–61 years) were analyzed. Significant improvement in wrinkle intensity, as assessed by Horizontal Neck Wrinkle Severity Scale, was observed from the second week onwards (1.352 ± 0.682, P<0.05). This improvement was sustained throughout the study duration and remained statistically significant at week 36 (1.423 ± 0.796, P<0.05). Patient GAIS (92.3%–100% through 36 weeks) and physician GAIS (100% through 24 weeks) were both excellent. Visual analogue scale scores revealed more pain associated with blunt cannula use (2.72 ± 1.71) than with sharp needle use (1.75 ± 1.39). AEs included erythema (62.5%), pruritus (43.7%), ecchymosis (43.7%), and localized swelling (25%).

Conclusions:

Subdermal injection of CPM-HA is safe and effective for treating horizontal neck wrinkles. Sustained improvement of wrinkle intensity up to 36 weeks and minimal AEs with no Tyndall effect were observed.
A Rare Case of Persistent Unilateral Gestational Gigantomastia
Authors: Rutherford Claire L. , Hsieh Michael K.H. , Tan Hui-Min , Twoon Mark , Kong Tze-Yean
Published: August 2019

A 34-year-old para 2 + 0 Indonesian woman presented with persistent right-sided gestational gigantomastia some 24 months following delivery. This was severely debilitating her activities of daily living, including caring for her children. On examination, she was found to have extreme hypertrophy of her right breast, which was nodular throughout on palpation. Biochemical investigations were unremarkable and revealed no obvious etiology. Magnetic resonance imaging identified grossly enlarged right breast tissue with prominent vessels. Given the minimal involution of her breast over the 24 months postpartum, she elected for a breast reduction with free nipple grafting following appropriate counseling. This was performed through excision of breast parenchyma preserving superior-medial tissue, followed by a free nipple graft.
Withdrawal from an opioid induces a transferable memory trace in the cerebrospinal fluid
Authors: Drdla-Schutting Ruth , Heinl Céline , Hadschieff Viktoria , Sandkühler Jürgen
Published: August 2019

Opioids are the most powerful analgesics available to date. However, they may also induce adverse effects including paradoxical opioid-induced hyperalgesia. A mechanism that might underlie opioid-induced hyperalgesia is the amplification of synaptic strength at spinal C-fibre synapses after withdrawal from systemic opioids such as remifentanil (“opioid-withdrawal long-term potentiation [LTP]”). Here, we show that both the induction as well as the maintenance of opioid-withdrawal LTP were abolished by pharmacological blockade of spinal glial cells. By contrast, the blockade of TLR4 had no effect on the induction of opioid-withdrawal LTP. D-serine, which may be released upon glial cell activation, was necessary for withdrawal LTP. D-serine is the dominant coagonist for neuronal NMDA receptors, which are required for the amplification of synaptic strength on remifentanil withdrawal. Unexpectedly, opioid-withdrawal LTP was transferable through the cerebrospinal fluid between animals. This suggests that glial-cell-derived mediators accumulate in the extracellular space and reach the cerebrospinal fluid at biologically active concentrations, thereby creating a soluble memory trace that is transferable to another animal (“transfer LTP”). When we enzymatically degraded D-serine in the superfusate, LTP could no longer be transferred. Transfer LTP was insensitive to pharmacological blockade of glial cells in the recipient animal, thus representing a rare form of glial cell-independent LTP in the spinal cord.
Driving Simulator Performance After Administration of Analgesic Doses of Ketamine With Dexmedetomidine or Fentanyl
Authors: Hayley Amie C. , Downey Luke A. , Green Maja , Shiferaw Brook , Kenneally Michaela , Keane Michael , Adams Mark , Shehabi Yahya
Published: August 2019

Purpose/Background

As a sole agent, ketamine acutely compromises driving ability; however, performance after coadministration with the adjuvant sedating agents dexmedetomidine or fentanyl is unclear.

Methods/Procedures

Using a randomized within-subject design, 39 participants (mean ± SD age, 28.4 ± 5.8 years) received 0.3 mg/kg bolus followed by 0.15 mg kg−1 h−1 infusion of ketamine (3-hour duration), in addition to either (i) 0.7 μg kg−1 h−1 infusion of dexmedetomidine for 1.5 hours (n = 19; KET/DEX) or (ii) three 25 μg fentanyl injections for 1.5 hours (n = 20; KET/FENT). Whole blood drug concentrations were determined during ketamine only, at coadministration (KET/DEX or KET/FENT) and at 2 hours after treatment. Subjective effects were determined using a standardized visual analog scale. Driving performance was assessed at baseline and at posttreatment using a validated computerized driving simulator. Primary outcomes included SD of lateral position (SDLP) and steering variability (SV).

Findings/Results

Administration of ketamine with dexmedetomidine but not fentanyl significantly increased SDLP (F
1,18 = 22.60, P < 0.001) and reduced SV (F1,18 = 164.42, P < 0.001) 2 hours after treatment. These deficits were comparatively greater for the KET/DEX group than for the KET/FENT group (t
37 = −5.21 [P < 0.001] and t
37 = 5.22 [P < 0.001], (respectively). For the KET/DEX group, vehicle control (SV) and self-rated performance (visual analog scale), but not SDLP, was inversely associated with ketamine and norketamine blood concentrations (in nanograms per milliliter). Greater subjective effects were moderately associated with driving deficits.

Implications/Conclusions

Driving simulator performance is significantly compromised after coadministration of analgesic range doses of ketamine with dexmedetomidine but not fentanyl. An extended period of supervised driver abstinence is recommended after treatment, with completion of additional assessments to evaluate home readiness.
Meritorious Academic Partnership Designation
Authors: Harper Mary G. , Burke Kathleen G. , Keim Susan K. , Morgan Larissa , Maloney Patsy
Published: August 2019

Graduate nursing education programs’ focus on preparation for academia results in many graduate nurses being unprepared to function as nursing professional development (NPD) practitioners in the practice environment. This article describes the development of an innovative collaborative partnership designation program and how a specialty organization, health system, and academia partnered to create an educational program to prepare NPD practitioners. The designation program provides a practical tool for use by NPD departments to advocate for the NPD specialty.
Therapeutic advances in SMA
Authors: Ludolph Albert C. , Wurster Claudia D.
Published: August 2019

Purpose of review

To review the advent of novel therapies and their impact on the field of chromosome 5q-associated spinal muscular atrophy (SMA).

Recent findings

Antisense oligonucleotides (ASOs) enhancing SMN2 function are delivered intrathecally and small molecules will also be available soon delivered by the oral route; alternatively, systemic injection of viral vectors in order to replace the SMN gene are likely to be available in the future. In summer 2019, it remains the core finding that intrathecally delivered ASOs convincingly change the natural history of the disease in children and that the treatment effect is the better, the earlier ASO treatment is started. Therefore, postnatal screening for deletions and mutations in the SMN gene is presently discussed. Much has to be learnt, however, both on the challenges of the intrathecal mode of delivery and the efficacy of ASOs in adolescent and adult patients. Therapeutic outcome measures mirroring this phenotype are difficult to assess in this group of patients.

Therapeutic advances in 5q-associated SMA have been convincing in the previous years and change the field. This includes newborn screening, changing phenotypes in the treated children, challenges for drug administration in adolescents and adults and the comparison of drug effects. Long-term studies are required.
Iclaprim reduces the incidence and severity of Staphylococcus aureus-induced septic arthritis in a murine model
Authors: Huang D. B. , Noviello S. , Gemmell C. G.
Published: August 2019

Staphylococcus aureus

is the most common non-gonococcal aetiology of septic arthritis. The efficacy of iclaprim against

S. aureus

LS-1, a clinical strain identified from a patient with septic arthritis, was studied in MF1 mice to evaluate the activity of iclaprim, which is in clinical development, in preventing joint infections. Iclaprim (2.5–80 mg kg−
1) administered as a single dose via the tail vein reduced the incidence of

S. aureus

septic arthritis and mortality in an experimental murine model of septic arthritis.
Carbonic anhydrase VII regulates dendritic spine morphology and density via actin filament bundling
Authors: Bertling Enni , Blaesse Peter , Seja Patricia , Kremneva Elena , Gateva Gergana , Virtanen Mari A. , Summanen Milla , Spoljaric Inkeri , Blaesse Michael , Paavilainen Ville , Vutskits Laszlo , Kaila Kai , Hotulainen Pirta , Ruusuvuori Eva
Published: August 2019

Intracellular pH is a potent modulator of neuronal functions. By catalyzing (de)hydration of CO2, intracellular carbonic anhydrase (CAi) isoforms CAII and CAVII contribute to neuronal pH buffering and dynamics. The presence of two highly active isoforms suggests that they form spatially distinct CAipools enabling subcellular modulation of pH. Here we show that CAVII, unlike CAII, is localized to the filamentous actin network, and its overexpression induces formation of thick actin bundles and membrane protrusions in fibroblasts. In neurons, CAVII is enriched in dendritic spines, and its over-expression causes aberrant spine morphology. We identified amino acids unique to CAVII that are required for direct actin interactions, promoting actin filament bundling and spine targeting. Lack of CAVII in neocortical neurons leads to reduced spine density and increased proportion of small spines. Thus, our work demonstrates highly distinct subcellular expression patterns of CAII and CAVII, and a novel, structural role of CAVII.
Detecting selection from linked sites using an F-model
Authors: Galimberti Marco , Leuenberger Christoph , Wolf Beat , Szilágyi Sándor Miklós , Foll Matthieu , Wegmann Daniel
Published: August 2019

Allele frequencies vary across populations and loci, even in the presence of migration. While most differences may be due to genetic drift, divergent selection will further increase differentiation at some loci. Identifying those is key in studying local adaptation, but remains statistically challenging. A particularly elegant way to describe allele frequency differences among populations connected by migration is theF-model, which measures differences in allele frequencies by population specificFSTcoefficients. This model readily accounts for multiple evolutionary forces by partitioningFSTcoefficients into locus and population specific components reflecting selection and drift, respectively. Here we present an extension of this model to linked loci by means of a hidden Markov model (HMM) that characterizes the effect of selection on linked markers through correlations in the locus specific component along the genome. Using extensive simulations we show that our method has up to two-fold the statistical power of previous implementations that assume sites to be independent. We finally evidence selection in the human genome by applying our method to data from the Human Genome Diversity Project (HGDP).
Growing old too early, automated assessment of skeletal muscle single fiber biomechanics in ageing R349P desmin knock-in mice using the MyoRobot technology
Authors: Meyer Charlotte , Haug Michael , Reischl Barbara , Prölß Gerhard , Pöschel Thorsten , Rupitsch Stefan J , Clemen Christoph S , Schröder Rolf , Friedrich Oliver
Published: August 2019

Muscle biomechanics is determined by active motor-protein assembly and passive strain transmission through cytoskeletal structures. The extrasarcomeric desmin filament network aligns myofibrils at the z-discs, provides nuclear-sarcolemmal anchorage and may also serve as memory for muscle repositioning following large strains. Our previous analyses of R349P desmin knock-in mice, an animal model for the human R350P desminopathy, already depicted pre-clinical changes in myofibrillar arrangement and increased fiber bundle stiffness compatible with a pre-aged phenotype in the disease. Since the specific effect of R349P desmin on axial biomechanics in fully differentiated muscle fibers is unknown, we used our automated MyoRobot biomechatronics platform to compare passive and active biomechanics in single fibers derived from fast- and slow-twitch muscles from adult to senile mice hetero- or homozygous for this desmin mutation with wild-type littermates. Experimental protocols involved caffeine-induced Ca2+-mediated force transients, pCa-force curves, resting length-tension curves, visco-elasticity and ‘slack-tests’. We demonstrate that the presence of R349P desmin predominantly increased single fiber axial stiffness in both muscle types with a pre-aged phenotype over wild-type fibers. Axial viscosity was unaffected. Likewise, no systematic changes in Ca2+-mediated force properties were found. Notably, mutant single fibers showed faster unloaded shortening over wild-type fibers. Effects of ageing seen in the wild-type always appeared earlier in the mutant desmin fibers. Impaired R349P desmin muscle biomechanics is clearly an effect of a compromised intermediate filament network rather than secondary to fibrosis.
Fork Pausing Complex Engages Topoisomerases at the Replisome
Authors: Shyian Maksym , Albert Benjamin , Zupan Andreja Moset , Ivanitsa Vitalii , Charbonnet Gabriel , Dilg Daniel , Shore David
Published: August 2019

Replication forks temporarily or terminally pause at hundreds of hard-to-replicate regions around the genome. A conserved pair of budding yeast replisome components Tof1-Csm3 (fission yeast Swi1-Swi3 and human TIMELESS-TIPIN) acts as a ‘molecular brake’ and promotes fork slowdown at proteinaceous replication fork barriers (RFBs), while the accessory helicase Rrm3 assists the replisome in removing protein obstacles. Here we show that Tof1-Csm3 complex promotes fork pausing independently of Rrm3 helicase by recruiting topoisomerase I (Top1) to the replisome. Topoisomerase II (Top2) partially compensates for the pausing decrease in cells when Top1 is lost from the replisome. The C-terminus of Tof1 is specifically required for Top1 recruitment to the replisome and fork pausing but not for DNA replication checkpoint (DRC) activation. We propose that forks pause at proteinaceous RFBs through a ‘sTOP’ mechanism (‘slowing down with TOPoisomerases I-II’), which we show also contributes to protecting cells from topoisomerase-blocking agents.
A Custom Microcontrolled and Wireless-Operated Chamber for Auditory Fear Conditioning
Authors: Júnior Paulo Aparecido Amaral , Mourão Flávio Afonso Gonçalves , Amâncio Mariana Chamon Ladeira , Pinto Hyorrana Pereira , Carvalho Vinícius Rezende , de Oliveira Guarnieri Leonardo , Magalhães Hermes Aguiar , Moraes Márcio Flávio Dutra
Published: August 2019

Animal behavioral paradigms, such as classical conditioning and operant conditioning, are an important tool to study the neural basis of cognition and behavior. These paradigms involve manipulating sensory stimuli in a way that learning processes are induced under controlled experimental conditions. However, the majority of the commercially available equipment did not offer flexibility to manipulate stimuli. Therefore, the development of most versatile devices would allow the study of more complex cognitive functions. The purpose of this work is to present a low-cost, customized and wireless-operated chamber for animal behavior conditioning, based on the joint operation of two microcontroller modules: Arduino Due and ESP8266-12E. Our results showed that the auditory stimulation system allows setting the carrier frequency in the range of 1 Hz up to more than 100 kHz and the sound stimulus can be modulated in amplitude, also over a wide range of frequencies. Likewise, foot-shock could be precisely manipulated regarding its amplitude (from ~200 μA to ~1500 μA) and frequency (up to 20 pulses per second). Finally, adult rats exposed to a protocol of cued fear conditioning in our device showed consistent behavioral response and electrophysiological evoked responses in the midbrain auditory pathway. Furthermore, the device developed in the current study represents an open source alternative to develop customized protocols to study fear memory under conditions of varied sensory stimuli.
Tonic GABAAconductance favors temporal over rate coding in the rat hippocampus
Authors: Dembitskaya Yulia , Wu Yu-Wei , Semyanov Alexey
Published: August 2019

Synaptic plasticity is triggered by different patterns of neuronal network activity. Network activity leads to an increase in ambient GABA concentration and tonic activation of GABAAreceptors. How tonic GABAAconductance affects synaptic plasticity during temporal and rate-based coding is poorly understood. Here, we show that tonic GABAAconductance differently affects long-term potentiation (LTP) induced by different stimulation patterns. The LTP based on a temporal spike - EPSP order (spike-timing-dependent [st] LTP) was not affected by exogenous GABA application. Backpropagating action potential, which enables Ca2+entry through N-methyl-D-aspartate receptors (NMDARs) during stLTP induction, was only slightly reduced by the tonic conductance. In contrast, GABA application impeded LTP dependent on spiking rate (theta-burst-induced [tb] LTP) by reducing the EPSP bust response and, hence, NMDAR-mediated Ca2+entry during tbLTP induction. Our results may explain the changes in different forms of memory under physiological and pathological conditions that affect tonic GABAAconductance.
dsRNA-Seq: Identification of viral infection by purifying and sequencing dsRNA
Authors: Decker Carolyn J. , Steiner Halley R. , Hoon-Hanks Laura L. , Morrison James H. , Haist Kelsey C. , Stabell Alex C. , Poeschla Eric M. , Morrison Thomas E. , Stenglein Mark D. , Sawyer Sara L. , Parker Roy
Published: August 2019

RNA viruses are a major source of emerging and re-emerging infectious diseases around the world. We developed a method to identify RNA viruses that is based on the fact that all RNA viruses produce dsRNA while replicating. Purifying and sequencing dsRNA from total RNA isolated from infected tissue allowed us to recover replicating viral sequences. We refer to this approach as dsRNA-Seq. By assembling dsRNA sequences into contigs we identified full length RNA viruses of varying genome types infecting mammalian culture samples, identified a known viral disease agent in laboratory infected mice, and successfully detected naturally occurring RNA viral infections in reptiles. Here we show that dsRNA-Seq is a preferable method for identifying viruses in organisms that don’t have sequenced genomes and/or commercially available rRNA depletion reagents. Similar to other metagenomic strategies, dsRNA-Seq has the potential to identify unknown viral disease agents that share little to no similarity to known viruses. However, the significant advantage of this method is the ability to identify replicated viral sequences, which is useful for distinguishing infectious viral agents from potential noninfectious viral particles or contaminants.
Smad4 signaling establishes the somatosensory map of basal vomeronasal sensory neurons
Authors: Naik Ankana S. , Lin Jennifer M. , Taroc Ed Zandro M. , Katreddi Raghu R. , Frias Jesus A. , Sammons Morgan , Forni Paolo E.
Published: August 2019

The accessory olfactory system is a unique model that can give insights on how the neurons can establish and maintain their identity, and connectivity. The vomeronasal organ (VNO) contains two distinct populations of vomeronasal sensory neurons (VSNs) each with specific innervation patterns to the accessory olfactory bulb (AOB). Though morphogenic signals are critical in defining various neuronal populations, the morphogenic signaling profiles that influence each VSN population remains unknown. Here, we found a pronounced BMP signaling gradient within the basal VSNs. By generating Smad4 conditional mutants, we disrupted canonical TGF-β/BMP signaling in maturing basal VSNs and in all mature VSNs. We show that Smad4 loss-of-function in immature basal neurons leads to a progressive loss of basal VSNs, reduced activation of the remnant basal VSNs, and aberrant glomeruli formation in posterior AOB. However, Smad4 ablation in all mature VSNs does not affect neuronal activity nor survival but causes aberrant glomeruli formation only in the posterior AOB. Our study reveals that Smad4 signaling plays a critical role in mediating development, function, and circuit formation of basal VSNs.
Inhibition of ErbB kinase signalling promotes resolution of neutrophilic inflammation
Authors: Rahman A. , Henry K. M. , Herman K. D. , Thompson A. A. R , Isles H. M. , Tulotta C. , Sammut D. , Rougeot J. J. Y. , Khoshaein N. , Reese A. E. , Higgins K. , Tabor C. , Sabroe I. , Zuercher W. J. , Savage C. O. , Meijer A. H. , Whyte M. K. B. , Dockrell D. H. , Renshaw S. A. , Prince L. R.
Published: August 2019

Neutrophilic inflammation with prolonged neutrophil survival is common to many inflammatory conditions, including chronic obstructive pulmonary disease (COPD). There are few specific therapies that reverse neutrophilic inflammation, but uncovering mechanisms regulating neutrophil survival is likely to identify novel therapeutic targets. Screening of 367 kinase inhibitors in human neutrophils and a zebrafish tail fin injury model identified ErbBs as common targets of compounds that accelerated inflammation resolution. The ErbB inhibitors gefitinib, CP-724714, erbstatin and tyrphostin AG825 significantly accelerated apoptosis of human neutrophils, including neutrophils from people with COPD. Neutrophil apoptosis was also increased in Tyrphostin AG825 treated-zebrafishin vivo. Tyrphostin AG825 decreased peritoneal inflammation in zymosan-treated mice, and increased lung neutrophil apoptosis and macrophage efferocytosis in a murine acute lung injury model. Tyrphostin AG825 and knockdown ofegfraanderbb2by CRISPR/Cas9 reduced inflammation in zebrafish. Our work shows that inhibitors of ErbB kinases have therapeutic potential in neutrophilic inflammatory disease.
Protein-protein docking using learned three-dimensional representations
Authors: Derevyanko Georgy , Lamoureux Guillaume
Published: August 2019

Protein-protein interactions are determined by a number of hard-to-capture features related to shape complementarity, electrostatics, and hydrophobicity. These features may be intrinsic to the protein or induced by the presence of a partner. A conventional approach to protein-protein docking consists in engineering a small number of spatial features for each protein, and in minimizing the sum of their correlations with respect to the spatial arrangement of the two proteins. To generalize this approach, we introduce a deep neural network architecture that transforms the raw atomic densities of each protein into complex three-dimensional representations. Each point in the volume containing the protein is described by 48 learned features, which are correlated and combined with the features of a second protein to produce a score dependent on the relative position and orientation of the two proteins. The architecture is based on multiple layers of SE(3)-equivariant convolutional neural networks, which provide built-in rotational and translational invariance of the score with respect to the structure of the complex. The model is trained end-to-end on a set of decoy conformations generated from 851 nonredundant protein-protein complexes and is tested on data from the Protein-Protein Docking Benchmark Version 4.0.
Advanced paternal age diversifies individual trajectories of vocalization patterns in neonatal mice
Authors: Mai Lingling , Inada Hitoshi , Kimura Ryuichi , Kanno Kouta , Matsuda Takeru , Tachibana Ryosuke O. , Tucci Valter , Komaki Fumiyasu , Hiroi Noboru , Osumi Noriko
Published: August 2019

Infant crying is an innate communicative behavior that is frequently impaired in certain neurodevelopmental disorders (NDDs). Since advanced paternal age is a reported risk factor for NDDs in offspring, we evaluated the impact of a father’s age on early vocal development in C57BL/6J mice. We recorded and applied a unique combination of computational analyses to ultrasonic vocalizations (USVs) emitted by mouse pups sired by young and aged fathers. Our data showed that advanced paternal age reduced the number and duration of USVs, and altered the syllable composition in pups. Moreover, pups born to young fathers showed convergent vocal characteristics with a rich repertoire during postnatal development, while those born to aged fathers exhibited more divergent vocal patterns with limited repertoire. Principal component analysis in conjunction with clustering analysis demonstrated that pups from aged fathers deviated from typical trajectories of vocal development, which were considered as atypical individuals. Thus, our study indicates that advanced paternal age has a significant effect on offspring’s early vocal development. It is suggested that the trajectories of vocal development could be a useful marker of the NDD-like phenotype associated with the advanced paternal age. In addition, our comprehensive computational analysis described here is an effective approach to characterize the altered individual diversity relevant to neurodevelopmental disorders.

One Sentence Summary

Advanced paternal age affects vocal development in early postnatal mice, with more pups showing atypical developmental trajectories.
The effect of habitat choice on evolutionary rescue in subdivided populations
Authors: Czuppon Peter , Blanquart François , Uecker Hildegard , Débarre Florence
Published: August 2019

Evolutionary rescue is the process by which a population, in response to an environmental change, successfully avoids extinction through adaptation. In spatially structured environments, dispersal can affect the probability of rescue. Here, we model an environment consisting of patches that degrade one after another, and we investigate the probability of rescue by a mutant adapted to the degraded habitat. We focus on the effects of dispersal and of immigration biases. We find that the probability of evolutionary rescue can undergo up to three phases: (i) starting from low dispersal rates, it increases with dispersal; (ii) at intermediate dispersal rates, it decreases; (iii) finally, at large dispersal rates, the probability of rescue increases again with dispersal, except if mutants are too counter-selected in not-yet-degraded patches. The probability of rescue is generally highest when mutant and wild-type individuals preferentially immigrate into patches that have already undergone environmental change. Additionally, we find that mutants that will eventually rescue the population most likely first appear in non-degraded patches, and that the relative contribution of standing genetic variation vs. de-novo mutations declines with increasing emigration rates. Overall, our results show that habitat choice, when compared to the often studied unbiased immigration scheme, can substantially alter the dynamics of population survival and adaptation to new environments.
Developing a rapid and highly efficient cowpea regeneration and transformation system using embryonic axis explants
Authors: Che Ping , Chang Shujun , Simon Marissa K. , Zhang Zhifen , Shaharyar Ahmed , Ourada Jesse , O’Neill Dennis , Torres-Mendoza Mijael , Guo Yinping , Marasigan Kathleen M. , Vielle-Calzada Jean-Philippe , Ozias-Akins Peggy , Albertsen Marc C. , Jones Todd J.
Published: August 2019

Cowpea is one of the most important legume crops planted worldwide, especially in Sub-Saharan Africa and Asia. Despite decades of effort, genetic engineering of cowpea is still challenging due to inefficient in vitro shoot regeneration, Agrobacterium-mediated T-DNA delivery and transgenic selection. Here, we report a rapid and highly efficient cowpea transformation system using embryonic axis explants isolated from imbibed mature seeds. We found that removal of the shoot apical meristem by cutting through the middle of the epicotyl stimulated direct multiple shoot organogenesis from the cotyledonary node tissue. Furthermore, the application of a ternary transformation vector system using an optimized pVIR accessory plasmid provided high levels of Agrobacterium-mediated gene delivery. The utilization of spectinomycin as the selection agent enabled more efficient transgenic selection and plant recovery. Transgenic cowpea shoots developed exclusively from the cotyledonary nodes at high frequencies of 4.5 to 37% across a wide range of cowpea genotypes. We believe that the transformation principles established in this study could also be applied to other legumes to increase transformation efficiencies.
Aging induces aberrant state transition kinetics in murine muscle stem cells
Authors: Kimmel Jacob C. , Hwang Ara B. , Marshall Wallace F. , Brack Andrew S.
Published: August 2019

Murine muscle stem cells (MuSCs) experience a transition from quiescence to activation that is required for regeneration, but it remains unclear if the transition states and rates of activation are uniform across cells, or how features of this process may change with age. Here, we use timelapse imaging and single cell RNA-seq to measure activation trajectories and rates in young and aged MuSCs. We find that the activation trajectory is conserved in aged cells, and develop effective machine learning classifiers for cell age. Using cell behavior analysis and RNA velocity, we find that activation kinetics are delayed in aged MuSCs, suggesting that changes in stem cell dynamics may contribute to impaired stem cell function with age. Intriguingly, we also find that stem cell activation appears to be a random walk like process, with frequent reversals, rather than a continuous, linear progression. These results support a view of the aged stem cell phenotype as a combination of differences in the location of stable cell states and differences in transition rates between them.

Summary Statement

We find that aged muscle stem cells display delayed activation dynamics, but retain a youthful activation trajectory, suggesting that changes to cell state dynamics may contribute to aging pathology.
Shuttling of Dorsal by Cactus: mechanism and implications
Authors: Schloop Allison E. , Carrell-Noel Sophia , Reeves Gregory T.
Published: August 2019

In a developing animal, morphogen gradients act to pattern tissues into distinct domains of cell types. However, despite their prevalence in development, morphogen gradient formation is a matter of debate. In our recent publication, we showed that the Dorsal/NF-κB morphogen gradient, which patterns the DV axis of the early Drosophila embryo, is partially established by a mechanism of facilitated diffusion. This mechanism, also known as “shuttling,” occurs when a binding partner of the morphogen facilitates the diffusion of the morphogen, allowing it to accumulate at a given site. In this case, the inhibitor Cactus/IκB facilitates the diffusion of Dorsal/NF-κB. In the fly embryo, we used computation and experiment to not only show that shuttling occurs in the embryo, but also that it enables the viability of embryos that inherit only one copy ofdorsalmaternally. Here we further discuss our evidence behind the shuttling mechanism, the previous literature data explained by the mechanism, and how it may also be critical for robustness of development. Finally, we describe an interaction between Dorsal and BMP signaling that is likely affected by shuttling.
A probabilistic framework for cellular lineage reconstruction using single-cell 5-hydroxymethylcytosine sequencing
Authors: Wangsanuwat Chatarin , Aldeguer Javier F. , Rivron Nicolas C. , Dey Siddharth S.
Published: August 2019

Lineage reconstruction is central to understanding tissue development and maintenance. While powerful tools to infer cellular relationships have been developed, these methods typically have a clonal resolution that prevent the reconstruction of lineage trees at an individual cell division resolution. Moreover, these methods require a transgene, which poses a significant barrier in the study of human tissues. To overcome these limitations, we report scPECLR, a probabilistic algorithm to endogenously infer lineage trees at a single cell-division resolution using 5-hydroxymethylcytosine. When applied to 8-cell preimplantation mouse embryos, scPECLR predicts the full lineage tree with greater than 95% accuracy. Further, scPECLR can accurately extract lineage information for a majority of cells when reconstructing larger trees. Finally, we show that scPECLR can also be used to map chromosome strand segregation patterns during cell division, thereby providing a strategy to test the “immortal strand” hypothesis in stem cell biology. Thus, scPECLR provides a generalized method to endogenously reconstruct lineage trees at an individual cell-division resolution.
Identification and mapping of central pair proteins by proteomic analysis
Authors: Dai Daniel , Ichikawa Muneyoshi , Peri Katya , Rebinsky Reid , Bui Khanh Huy
Published: August 2019

Cilia or flagella of eukaryotes are small micro-hair like structures that are indispensable to single-cell motility and play an important role in mammalian biological processes. Cilia or flagella are composed of nine doublet microtubules surrounding a pair of singlet microtubules called the central pair (CP). Together, this arrangement forms the canonical and highly conserved 9+2 axonemal structure. The CP, which is a unique structure exclusive to motile cilia, is a pair of structurally dimorphic singlet microtubules decorated with numerous associated proteins. Mutations of CP-associated proteins cause several different physical symptoms termed ciliopathies. Thus, it is crucial to understand the architecture of the CP. However, the protein composition of the CP was poorly understood. This was because identification of CP proteins was mostly limited by availableChlamydomonasmutants of CP proteins. In this study, we conducted a comprehensive CP proteome analysis using several CP mutants and identified 37 novel CP protein candidates. By usingChlamydomonasstrains lacking specific CP sub-structures, we also present a more complete model of localization of known and newly identified CP proteins. This work has established a new foundation for CP protein analysis for future studies.
CRISPR/Cas9 interrogation of the mouse Pcdhg gene cluster reveals a crucial isoform-specific role for Pcdhgc4
Authors: Garrett Andrew M. , Bosch Peter J. , Steffen David M. , Fuller Leah C. , Marcucci Charles G. , Koch Alexis A. , Bais Preeti , Weiner Joshua A. , Burgess Robert W.
Published: August 2019

The mammalian Pcdhg gene cluster encodes a family of 22 cell adhesion molecules, the gamma-Protocadherins (γ-Pcdhs), critical for neuronal survival and neural circuit formation. The extent to which isoform diversity–aγ-Pcdh hallmark–is required for their functions remains unclear. We used a CRISPR/Cas9 approach to reduce isoform diversity, targeting each Pcdhg variable exon with pooled sgRNAs to generate an allelic series of 26 mouse lines with 1 to 21 isoforms disrupted via discrete indels at guide sites and/or larger deletions/rearrangements. Analysis of 5 mutant lines indicates that postnatal viability and neuronal survival do not require isoform diversity. Surprisingly, as it is the only γ-Pcdh that cannot independently engage in homophilic trans-interactions, we find that γC4, encoded by Pcdhgc4, is the only critical isoform. Because the human orthologue is the only PCDHG gene constrained in humans, our results indicate a conserved γC4 function that likely involves distinct molecular mechanisms.
TAL1-mediated epigenetic modifications down-regulate the expression of GIMAP family in non-small cell lung cancer
Authors: Tang Zhongxiang , Wang Lili , Dai Pei , Ruan Pinglang , Liu Dan , Tan Yurong
Published: August 2019

Backgroud

The study was designed to explore the role of GIMAP family in non-small cell lung cancer (NSCLC) and its possible expression regulation mechanisms using existing biological databases including encyclopedia of DNA elements (ENCODE), gene expression omnibus (GEO), and the cancer genome atlas (TCGA).

Methods

Lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) were used to evaluate the expression of GIMAPs in TCGA. Five NSCLC datasets were then selected from GEO for validation. RNA-seq and Chip-seq data from ENCODE and GEO were used to observe epigenetic modifications on the chromosomes of GIAMPs in NSCLC. We constructed protein-protein interaction (PPI) network to reveal the main interacting proteins of GIMAPs. We then analyzed the correlation and regulatory mechanism between TAL1 and the expression of GIMAP family. We also used Kaplan-Meier for survival analysis.

Results

All 7 genes in the GIMAP family were down-regulated in NSCLC. H3K4me3 and H3K27ac disappeared, while H3K27me3 increased on the chromosome of this family. The expression of TAL1 was positively correlated with the expression of GIMAPs. sh-TAL1 significantly down-regulated the expression of GIMAP family through epigenetic modification. High expression of GIMAPs and TAL1 was found to be associated with a good prognosis of NLCSC.

Conclusion

The downregulation of TAL1 caused the disappearance of H3K27ac and H3K4me3. It also caused an increase in H3K27me3 on the GIMAPs gene, eventually leading to the overall downregulation of the GIMAP family genes.