bluuebunny/crossref_metadata_2025 huggingface dataset:
Aesthetic Reconstruction of a Facial Defect After Subtotal Resection of the Parotid Gland Using a Superficial Circumflex Iliac Artery Pure Skin Perforator Flap
Authors: Hashimoto Kohei , Lee Haesu , Tashiro Kensuke
Published: June 2022

In the reconstruction of facial defects, thin and flexible coverage of the defect is desirable for cosmetic reasons. A free flap is 1 possible surgical option; however, a flap containing a fatty layer is bulky. in this study, the authors describe the reconstruction of a facial defect after subtotal parotidectomy for right parotid carcinoma using a superficial circumflex iliac artery pure skin perforator flap, with consideration given to facial contour. The superficial circumflex iliac artery pure skin perforator flap is a viable option to achieve the desired clinical and aesthetic outcome.
Maxillary Tuberosity Fractures Following Third Molar Extraction, Prevalence, and Risk Factors
Authors: Shmuly Tom , Winocur-Arias Orit , Kahn Adrian , Findler Mordechai , Adam Iris
Published: June 2022

Objectives:

The aim of this study was to evaluate the prevalence of maxillary tuberosity fractures in an adult population and to examine the different risk factors associated with these fractures.

Materials and Methods:

This is a retrospective study; data was collected from medical records of patients who underwent a non-surgical extraction of a maxillary third molar tooth between January 2017 and March 2019. All extractions were performed by 2 maxillofacial specialists.

Results:

A total of 403 extracted maxillary third molar teeth were included in the study. Out of them 73 cases of tuberosity fractures were recorded (18.1%). No significant difference in the number of recorded fractures was found between the 2 surgeons. The mean age of patients was 32.8 ± 11.5. In the age group of 30 years and under a fractures rate of 12.1% was recorded compared to 25.0% in the age group of over 30 (P = 0.001). Divergent or extremely curved root morphology were associated with a higher risk for fractures (30.7%) compared to convergent root morphology (13.1%) (P < 0.001). Borderline significance (P = 0.069) was observed for extractions of teeth with caries lesions (21.9%) compared to teeth with no caries lesions (14.6%).

Conclusions:

The risk of developing a tuberosity fracture during an extraction of an upper wisdom tooth increases with age by 3.1% per year. Teeth with a caries lesion or teeth with divergent or extremely curved root morphology are associated with a higher risk for tuberosity fractures. Although, distoangular teeth had reduced risk of developing a tuberosity fractures. Data collected in this study may help to evaluate the risk factors associated with tuberosity fractures, and can assist in minimizing complications during extractions.
The Learning Curve and Importance of Collaboration in Endoscopic Thyroidectomy Via Breast Areola Approach: A Single Surgical Team’s Experience of 100 Patients
Authors: Wang Miao-Feng , Xia Heng , Zhao Wei-Jun , Fang Sun-Yang , Liu Zhao
Published: June 2022

Background:

Endoscopic thyroidectomy is popular among young patients because of its excellent cosmetic outcomes. But it takes a long time to become proficient and competent for surgeons. In addition, collaboration plays a critical role in endoscopic thyroidectomy. Our research aims to evaluate the learning curve of endoscopic thyroidectomy via breast areola approach, provide details of this approach, and demonstrate the importance of collaboration.

Methods:

The authors retrospectively analyzed 100 cases of benign and malignant thyroid disease who underwent endoscopic thyroidectomy via breast areola approach between January 2015 and December 2020, which were performed by the same group of surgeons with little experience of endoscopic thyroidectomy. The learning curve was analyzed by moving average method. The mean operation time, blood loss, tumor size, postoperative complications were used to determine learning curve progression.

Results:

The learning curve in the first 30 cases were uplifted, stable at 30 to 60 cases and declined in the following cases. The mean operation time and blood loss decreased significant after the first 30 cases and again after the first 60 cases. And there was no difference in postoperative complications.

Conclusions:

A well-trained surgeon with experience in conventional open thyroidectomy can significantly reduce the total operation time by studying the learning curve. The key steps including establishment of working space and reaching for recurrent laryngeal nerve. A stable level can be achieved after 30 cases. More than 60 cases are required to become proficient. A successful endoscopic thyroid surgery requires a stable team.
Purely Endonasal Endoscopic Approaches for Extracranial Trigeminal Nerve Schwannoma
Authors: Başak Hazan , Mulazimoglu Selcuk , Yucel Levent , Beton Suha , Meco Cem
Published: June 2022

Objective:

The aim of this study is to assess the effectiveness and safety of purely endonasal endoscopic resection of extracranial trigeminal schwannomas (TGSs), with assessment of surgical and clinical outcomes in order to identify optimal candidates for an endonasal endoscopic approach (EEA).

Methods:

A retrospective review of patient’s records operated for TGSs between 2008 and 2021 was conducted. Patients operated with a purely EEA were included in this study. Pictures from a frozen fresh cadaver head dissection were used to demonstrate the surgical approach and to show anatomic relationships, complexity of the surgical area and safe corridors for surgery.

Results:

A total of 5 patients (4 females and 1 male) were operated for TGS. All patients had facial numbness (100%) as a presenting symptom, followed by facial pain in 2 patients (40%), and orbital pain in 1 (20%). Also, 3 patients (60%) had a tumor originating at the level of the foramen ovale and 2 (40%) at the foramen rotundum. The mean tumor diameter was 3,7 ± 2 cm. Gross total resection were achieved in all cases. Postoperatively, 1 patient had severe mastication problems, 1 had blurred vision, and in the long-term follow-up, 1 had frontal sinusitis. The mean follow up was 106.6 (min:49, max:132, SD: 29.82) months. No recurrences were detected.

Conclusions:

In cases with the extradural TGS having limited extension into Posterior Cranial Fossa, or located in the Middle Cranial Fossa, a purely EEA is possible even for tumors bigger in size. Unilateral endonasal corridors are adequate for resection in most cases.
An insula hierarchical network architecture for active interoceptive inference
Authors: Fermin Alan S. R. , Friston Karl , Yamawaki Shigeto
Published: June 2022

In the brain, the insular cortex receives a vast amount of interoceptive information, ascending through deep brain structures, from multiple visceral organs. The unique hierarchical and modular architecture of the insula suggests specialization for processing interoceptive afferents. Yet, the biological significance of the insula's neuroanatomical architecture, in relation to deep brain structures, remains obscure. In this opinion piece, we propose the Insula Hierarchical Modular Adaptive Interoception Control (IMAC) model to suggest that insula modules (granular, dysgranular and agranular), forming parallel networks with the prefrontal cortex and striatum, are specialized to form higher order interoceptive representations. These interoceptive representations are recruited in a context-dependent manner to support habitual, model-based and exploratory control of visceral organs and physiological processes. We discuss how insula interoceptive representations may give rise to conscious feelings that best explain lower order deep brain interoceptive representations, and how the insula may serve to defend the body and mind against pathological depression.
Foraging behaviour, habitat use and population size of the desert horned viper in the Negev desert
Authors: Subach Aziz , Dorfman Arik , Avidov Bar , Domer Adi , Samocha Yehonatan , Scharf Inon
Published: June 2022

The desert horned viper occurs in the dunes of the northwestern Negev desert, Israel. We report on a 2 year study on the viper's behaviour and ecology in its natural habitat. We examined whether the vipers moved faster in a vegetation-dense microhabitat versus an open dune area and detected much slower movement in the former. We nevertheless detected no preference of the vipers for any of the dune areas. We suggest that the vipers trade-off the ease of movement on open areas with prey, which is probably more available in areas with denser vegetation. The activity was higher early in the season and the vipers were mostly active right after sunset, with a second smaller activity peak at sunrise, perhaps searching for burrows to spend the day. Fitting this explanation, movement at the track's end was less directional than at its beginning. We found inter-sexual and between-year differences. For example, females were larger than males in the second year of the study but not in the first one and the population seemed to be smaller in the second year of the study than in its first year. The information we provide on this viper may assist its conservation, as sand dunes are threatened habitats in Israel.
Localization of nanospheres in pheochromocytoma-like cells following exposure to high-frequency electromagnetic fields at 18 GHz
Authors: Tharushi Perera Palalle G. , Linklater Denver P. , Kosyer Erim , Croft Rodney , Ivanova Elena P.
Published: June 2022

Exposure to high-frequency (HF) electromagnetic fields (EMFs) at 18 GHz was previously found to induce reversible cell permeabilization in eukaryotic cells; however, the fate of internalized foreign objects inside the cell remains unclear. Here, silica core–shell gold nanospheres (Au NS) of 20 ± 5 nm diameter were used to study the localization of Au NS in pheochromocytoma (PC 12) cells after exposure to HF EMFs at 18 GHz. Internalization of Au NS was confirmed using fluorescence microscopy and transmission electron microscopy. Analysis based on corresponding scanning transmission electron microscopy energy-dispersive spectroscopy revealed the presence of the Au NS free within the PC 12 cell membrane, cytoplasm, enclosed within intracellular vesicles and sequestered in vacuoles. The results obtained in this work highlight that exposure to HF EMFs could be used as an efficient technique with potential for effective delivery of drugs, genetic material, and nanomaterials into cells for the purpose of cellular manipulation or therapy.
Deciphering the role of residues in the loops nearing the active site of OXA-58 in imparting beta-lactamase activity
Authors: Jain Diamond , Verma Jyoti , Ghosh Anindya S.
Published: June 2022

The existence of OXA-58 carbapenemase alone or in combination with other beta-lactam resistance factors poses significant beta-lactam resistance. The exact mechanism of action of OXA type beta-lactamases is debatable due to the involvement of multiple residues within or outside the active site. In the present work, we have elucidated the relative role of residues present in the putative omega (W169, L170, K171) and β6-β7 (A226 and D228) loops on the activity of OXA-58 by substituting into alanine (and aspartate for A226) through site-directed mutagenesis. E. coli cells harbouring OXA-58, substituted at the putative omega loop, manifest a significant decrease in the beta-lactam resistance profile than that of the cells expressing OXA-58. Further, a reduction in the catalytic efficiency is observed for the purified variants of OXA-58 carrying individual substitutions in the putative omega loop than that of OXA-58. However, the addition of NaHCO3 (for carbamylation of K86) increases catalytic efficiency of the individual protein as revealed by nitrocefin hydrolysis assay and steady state kinetics. Moreover, W169A and K171A substitutions show significant effects on the thermal stability of OXA-58. Therefore, we conclude that the putative omega loop residues W169, L170 and K171, individually, have significant role in the activity and stability of OXA-58, mostly by stabilising carbamylated lysine of active site.
Occurrence, fate, and risk assessment of antibiotics in typical pharmaceutical manufactories and receiving surface waters from different regions
Authors: Liu Yuanfei , Cai Dan , Li Xin , Wu Qingyao , Ding Ping , Shen Liangchen , Yang Jian , Hu Guocheng , Wu Jinhua
Published: June 2022

This study aimed to update information on the presence and persistence of antibiotics in wastewater from four typical pharmaceutical plants in China and the removal of antibiotics by the wastewater treatment process. It also evaluated the environmental impact of antibiotic residues through wastewater discharge into receiving water bodies. The results indicated that 13 antibiotics were detected in wastewater samples with concentrations ranging from 57.03 to 726.79 ng/L. Fluoroquinolones (FQs) and macrolides (MLs) were the most abundant antibiotic classes in wastewater samples, accounting for 42.5% and 38.7% of total antibiotic concentrations, respectively, followed by sulfonamides (SAs) (16.4%) and tetracyclines (TCs) (2.4%). Erythromycin-H2O (ERY), lincomycin (LIN), ofloxacin (OFL), and trimethoprim (TMP) were the most frequently detected antibiotics; among these antibiotics, the concentration of OFL was the highest in most wastewater samples. No significant difference was found in the removal of antibiotics between different treatment processes, and more than 50% of antibiotics were not completely removed with a removal efficiency of less than 70%. The concentration of detected antibiotics in the receiving water was an order of magnitude lower than that in the wastewater due to dilution. Finally, an environmental risk analysis showed that lincomycin and ofloxacin could pose a high risk at the concentrations detected in effluents and a medium risk in their receiving waters, highlighting that they were a potential hazard to the health of the aquatic ecosystem.
Single cell RNA sequencing analysis of mouse cochlear supporting cell transcriptomes with activated ERBB2 receptor, a candidate mediator of cochlear regeneration mechanisms
Authors: Piekna-Przybylska Dorota , Na Daxiang , Zhang Jingyuan , Baker Cameron , Ashton John M. , White Patricia M.
Published: June 2022

Hearing loss caused by the death of cochlear hair cells might be restored through regeneration from supporting cells via dedifferentiation and proliferation, as observed in birds. We recently found that in mice, activation of ERBB2 in supporting cells promoted the differentiation of hair cell-like cells. Here we analyze transcriptomes of neonatal mouse cochlear supporting cells with activated ERBB2 using single-cell RNA sequencing. ERBB2 inductionin vivogenerated a new population of cells expressingde novoSIBLING (small integrin-binding ligand n-linked glycoproteins) proteins and their regulators, particularlySecreted Phosphoprotein 1(SPP1). In other systems, SIBLINGs promote cell survival, proliferation, and differentiation. ERBB2 signaling induced after noise exposure in young adult mice also up-regulated both SPP1 protein and the SPP1 receptor CD44, and drove formation of proliferating stem-like cell aggregates in the organ of Corti. Our results suggest that ectopic activation of ERBB2 signaling in cochlear supporting cells alters the microenvironment, promoting proliferation and cell rearrangements. Together these results suggest a novel mechanism for inducing stem cell-like activity in the adult mammalian cochlea.
Patients with affective disorders profit most from telemedical treatment: Evidence from a naturalistic patient cohort during the COVID-19 pandemic
Authors: Rohrmann Tobias , Praus Peter , Proctor Tanja , Benedyk Anastasia , Tost Heike , Hennig Oliver , Andreas-Meyer-Lindenberg  , Wahl Anna-Sophia
Published: June 2022

Background

During the COVID-19 pandemic telemedicine became essential in maintaining diagnostic procedures and treatment in psychiatry. However, it is still an open question if telemedicine is a feasible treatment option for all groups of psychiatric patients alike. This prospective monocentric observational trial was conducted to assess the general applicability of telemedical treatment in a naturalistic psychiatric outpatient cohort and to identify groups of disorders and clusters of psychopathology that respond particularly well to telemedical treatment considering sociodemographic characteristics and patients’ perspectives.

Methods

Patients were recruited April 2020 - April 2021 and asked to fill out the WHO-5 and the SCL-90R at baseline, after 4-6 and 8-12 weeks and a feedback-survey. Additionally, medical records, psychopathology, psychosocial functioning and sociodemographic data were analyzed. Primary outcomes were well-being, psychopathology and functioning during treatment. Secondly, diagnostic groups and psychopathology linked to a superior treatment-response were determined with respect to patients’ subjective experiences.

Results

Out of 1.385 patients, 254 - mostly with hyperkinetic (35.3%) and depressive disorders (24.6%) - took part. Well-being and SCL-90R total scores improved substantially (both p<0.001). CGI and GAF scores were worse in depressed subjects (both p<0.05). Improvement was mainly seen in depressed patients; chronic disorders experienced a decline in well-being. Sociodemographic characteristics could not explain this difference. Particularly female (r=0.413) patients found telepsychiatry equivalent to conventional treatment. The more virtual sessions participants attended the more likely they were to find telepsychiatry equal to conventional treatment (r=0.231).

Conclusions

Telemedicine is an effective treatment for patients with depression under naturalistic conditions. Telemedical consultations are a simple and reliable way of monitoring symptom severity and directing treatment choices during the treatment of depressive disorders. Patients with depression benefited more from telemedical treatment compared to participants with chronic non episodic psychiatric disorders. Future research needs to concentrate on improving telemedical treatment options suited for the latter conditions. Psychiatric telemedicine yielded overall high degrees of satisfaction among users.
Prots2Net: a PPIN predictor of a proteome or a metaproteome sample
Authors: Alcalá Adrià , Llabrés Mercè
Published: June 2022

Motivation

All molecular functions and biological processes are carried out by groups of proteins that interact to each other. Proteins interactions are modeled by simple networks called Protein-Protein Interaction Networks (PPINs) whose nodes are proteins and whose edges are the protein-protein interactions. PPINs are broadly accepted to model the protein’s functional relations, and their analysis has become a key ingredient in the study of protein functions. New proteins are collected every day from metaproteomic data, and their functional relations must be obtained with high-throughput technology. Retrieving protein-protein interaction data experimentally is a very high time-consuming and labor-intensive task. Consequently, in the last years, the biological community is looking for computational methods to correctly predict PPIs.

Results

We present here Prots2Net, a tool designed to predict the PPIs of a proteome or a metaproteome sample. Our prediction model is a multilayer perceptron neural network that uses protein sequence information only from the input proteins and interaction information from the STRING database. To train the model, Prots2Net explores the PPIs retrieved from the STRING database of two selected species. The tests, reported here on the Yeast and the Human datasets, show that Prots2Net performs better than the previous prediction methods that used protein sequence information only. Therefore, considering the information of PPI data available on the STRING database improves the PPI prediction.

Availability

https://github.com/adriaalcala/prots2net

Contact

merce.llabres@uib.es
Measuring motion-to-photon latency for sensorimotor experiments with virtual reality systems
Authors: Warburton Matthew , Mon-Williams Mark , Mushtaq Faisal , Ryan Morehead J.
Published: June 2022

Consumer virtual reality (VR) systems are increasingly being deployed in research to study sensorimotor behaviours, but properties of such systems require verification before being used as scientific tools. The ‘motion-to-photon’ latency (the lag between a user making a movement and the movement being displayed within the display) is a particularly important metric as temporal delays can degrade sensorimotor performance. Extant approaches to quantifying this measure have involved the use of bespoke software and hardware and produce a single measure of latency and ignore the effect of the motion prediction algorithms used in modern VR systems. This reduces confidence in the generalisability of the results. We developed a novel, system-independent, high-speed camera-based latency measurement technique to co-register real and virtual controller movements, allowing assessment of how latencies change through a movement. We applied this technique to measure the motion-to-photon latency of controller movements in the HTC Vive, Oculus Rift, Oculus Rift S, and Valve Index, using the Unity game engine and SteamVR. For the start of a sudden movement, all measured headsets had mean latencies between 21-42ms. Once motion prediction could account for the inherent delays, the latency was functionally reduced to 2-13ms, and our technique revealed this reduction occurs within ∼25-58ms of movement onset. Our findings indicate that sudden accelerations (e.g. movement onset, impacts and direction changes) will increase latencies and lower spatial accuracy. Our technique allows researchers to measure these factors and determine the impact on their experimental design before collecting sensorimotor data from VR systems.
Holistic inference explains human perception of stimulus orientation
Authors: Mao Jiang , Stocker Alan A.
Published: June 2022

Perception of stimulus features such as orientation is widely considered a Bayesian inference process. In contrast to previous Bayesian observer models, we propose that perception is a holistic inference process that operates across all levels of the representational hierarchy. We test this hypothesis in the context of a typical psychophysical matching task in which subjects are asked to estimate the perceived orientation of a test stimulus by adjusting a probe stimulus (method-of-adjustment). We present a holistic matching model that assumes that subjects’ responses reflect an optimal match between the test and the probe stimulus, both in terms of their inferred feature (orientation) but also their higher-level (category) representation. Validation against multiple existing psychophysical datasets demonstrates that the model provides a quantitatively detailed and accurate description of subjects’ response behavior including data that previous models fail to even qualitatively account for.
Artemisia extracts Differ from Artemisinin Effects on Human Hepatic CYP450s 2B6 and 3A4 in vitro
Authors: Kane Ndeye F. , Kiani Bushra H. , Desrosiers Matthew R. , Towler Melissa J. , Weathers Pamela J.
Published: June 2022

Ethnopharmacological relevance

The Chinese medicinal herb, Artemisia annua L., has been used for >2,000 yr as traditional tea infusions to treat a variety of infectious diseases including malaria, and its use is spreading globally (along with A. afra Jacq. ex Willd.) mainly through grassroots efforts.

Aim of the study

Artemisinin is more bioavailable delivered from the plant, Artemisia annua L. than the pure drug, but little is known about how delivery via a hot water infusion (tea) alters induction of hepatic CYP2B6 and CYP3A4 that metabolize artemisinin.

Materials and Methods

HepaRG cells were treated with 10 μM artemisinin or rifampicin (positive control), and teas (10 g/L) of A. annua SAM, and A. afra SEN and MAL with 1.6, 0.05 and 0 mg/gDW artemisinin in the leaves, respectively; qPCR, and Western blots, were used to measure CYP2B6 and CYP3A4 responses. Enzymatic activity of these P450s was measured using liver microsomes and P450-Glo assays.

Results

All teas inhibited activity of CYP2B6 and CYP3A4. Artemisinin and the high artemisinin-containing tea infusion (SAM) induced CYP2B6 and CYP3A4 transcription, but artemisinin-deficient teas, MAL and SEN, did not. Artemisinin increased CYP2B6 and CYP3A4 protein levels, but none of the three teas did, indicating a post-transcription inhibition by all three teas.

Conclusions

This study showed that Artemisia teas inhibit activity and artemisinin autoinduction of CYP2B6 and CYP3A4 post transcription, a response likely the effect of other phytochemicals in these teas. Results are important for understanding Artemisia tea posology.
A non-destructive approach for measuring rice panicle-level photosynthetic responses using 3D-image reconstruction
Authors: Dharni Jaspinder Singh , Dhatt Balpreet Kaur , Paul Puneet , Gao Tian , Awada Tala , Staswick Paul , Hupp Jason , Yu Hongfeng , Walia Harkamal
Published: June 2022

Our understanding of the physiological response of rice inflorescence (panicle) to environmental stresses is limited by the challenge of accurately determining panicle photosynthetic parameters and their impact on grain yield. This is primarily due to lack of a suitable gas exchange methodology for panicles, as well as non-destructive methods to accurately determine panicle surface area. To address these challenges, we have developed a custom panicle gas exchange cylinder compatible with the LiCor 6800 Infra-red Gas Analyzer. Accurate surface area measurements were determined with a 3D panicle imaging platform to normalize the panicle-level photosynthetic measurements. We observed differential responses in both panicle and flag leaf for two temperate Japonica rice genotypes (accessions, TEJ-1 and TEJ-2) exposed to heat stress during early grain filling. There was a notable divergence in relative photosynthetic contribution of flag leaf and panicles for the genotype tolerant to heat stress (TEJ-2) compared to the less tolerant accession. The novelty of this approach is that it is non-destructive and more accurately determines panicle area and photosynthetic parameters, enabling researchers to monitor temporal changes in panicle physiology during the reproductive development. The method is useful for panicle-level measurements under diverse environmental stresses, and for evaluating genotypic variation for panicle physiology and architecture in other cereals with compact inflorescences.
Three Novel Methods for Determining Motor Threshold with Transcranial Magnetic Stimulation Outperform Conventional Procedures
Authors: Wang Boshuo , Peterchev Angel V. , Goetz Stefan M.
Published: June 2022

Objective

Thresholding of neural responses is central to many applications of transcranial magnetic stimulation (TMS), but the stochastic aspect of neuronal activity and motor evoked potentials (MEPs) challenges thresholding methods. We analyzed existing methods for obtaining TMS motor threshold and their variations, introduced new methods from other fields, and compared their accuracy and speed.

Approach

In addition to existing relative-frequency methods, such as the five-out-of-ten method, we examined adaptive methods based on a probabilistic motor threshold model using maximum-likelihood (ML) or maximuma- posteriori(MAP) estimation. To improve the performance of these adaptive estimation methods, we explored variations in the estimation procedure and inclusion of population-level prior information. We adapted a Bayesian estimation method which iteratively incorporated information of the TMS responses into the probability density function. A family of non-parametric stochastic root-finding methods with different convergence criteria and stepping rules were explored as well. The performance of the thresholding methods was evaluated with an independent stochastic MEP model.

Main Results

The conventional relative-frequency methods required a large number of stimuli, were inherently biased on the population level, and had wide error distributions for individual subjects. The parametric estimation methods obtained the thresholds much faster and their accuracy depended on the estimation method, with performance significantly improved when population-level prior information was included. Stochastic root-finding methods were comparable to adaptive estimation methods but were much simpler to implement and did not rely on a potentially inaccurate underlying estimation model.

Significance

Two-parameter MAP estimation, Bayesian estimation, and stochastic root-finding methods have better error convergence compared to conventional single-parameter ML estimation, and they all require significantly fewer TMS pulses for accurate estimation than conventional relative-frequency methods. Stochastic root finding appears particularly attractive due to the low computational requirements, simplicity of the algorithmic implementation, and independence from potential model flaws in the parametric estimators.
MenDEL: PCR Primer Design as Constrained Optimization Process
Authors: German Sergei , Mitchell Leslie A. , Vela Gartner Antonio , Fenyö David , Boeke Jef D.
Published: June 2022

Motivation

The synthesis of large DNA assemblies has applications in biotechnology, and can help us better understand genome biology. These large DNA assemblies are often constructed from many smaller DNA segments, and it is critical to assess that they are correctly assembled. One low cost and rapid method to ensure that the connection between each segment is correct is to use PCR with primer pairs that span assembly junctions. However, the design of PCR primers for large assemblies consisting of multiple segments, and therefore containing multiple assembly junctions, is a challenging process. Rule-based automation of the process often results in finding primers that satisfy general criteria, but are not necessarily the best fit for every particular junction.

Results

We have developed MenDEL – a web-based DNA design application, that provides a primer pair computation tool for multiple assembly junctions in such a way that for each junction we automatically pick the optimal pair of primers based on user specified constraints.

Availability and Implementation

The MenDEL application is available at https://mendel-isg.nyumc.org to registered users, and the code base for computing junction primers is available at https://github.com/MendelProject/PrimerOptimization.
Position representations of moving objects align with real-time position in the early visual response
Authors: Johnson Philippa A. , Blom Tessel , van Gaal Simon , Feuerriegel Daniel , Bode Stefan , Hogendoorn Hinze
Published: June 2022

Abstract

When localising a moving object, the brain receives outdated sensory information about its position, due to the time required for neural transmission and processing. The brain may overcome these fundamental delays through predictively encoding the position of moving objects using information from their past trajectories. In the present study, we evaluated this proposition using multivariate analysis of high temporal resolution electroencephalographic data. We tracked neural position representations of moving objects at different stages of visual processing, relative to the real-time position of the object. During early stimulus-evoked activity, position representations of moving objects were activated substantially earlier than the equivalent activity evoked by unpredictable flashes, aligning the earliest representations of moving stimuli with their real-time positions. These findings indicate that the predictability of straight trajectories enables full compensation for the neural delays accumulated early in stimulus processing, but that delays still accumulate across later stages of cortical processing.
The assembly yield of complex, heterogeneous structures: A computational toolbox
Authors: Curatolo Agnese I. , Kimchi Ofer , Goodrich Carl P. , Brenner Michael P.
Published: June 2022

The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, we discovered that they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.
Neuronal Population Encoding of Identity in Primate Prefrontal Cortex
Authors: Sharma KK , Diltz MA , Lincoln T , Albuquerque ER , Romanski LM
Published: June 2022

The ventrolateral prefrontal cortex (VLPFC) shows robust activation during the perception of faces and voices. However, little is known about what categorical features of social stimuli drive neural activity in this region. Since perception of identity and expression are critical social functions, we examined whether neural responses to naturalistic stimuli were driven by these two categorial features in the prefrontal cortex. We recorded single neurons in the VLPFC, while two macaques viewed short audiovisual videos of unfamiliar conspecifics making expressions of aggressive, affiliative, and neutral valence. Of the 285 neurons responsive to the audiovisual stimuli, 111 neurons had a main effect (two-way ANOVA) of identity, expression or their interaction in their stimulus related firing rates; however, decoding of expression and identity using single unit firing rates rendered poor accuracy. Interestingly, when decoding from pseudopopulations of recorded neurons, the accuracy for both expression and identity increased with population size, suggesting that the population transmitted information relevant to both variables. Principal components analysis of mean population activity across time revealed that population responses to the same identity followed similar trajectories in the response space, facilitating segregation from other identities. Our results suggest that identity is a critical feature of social stimuli that dictates the structure of population activity in the VLPFC, during the perception of vocalizations and their corresponding facial expressions. These findings enhance our understanding of social behavior beyond the temporal lobe in macaques and humans.

Significance Statement

Primates are unique in their ability to process and utilize complex, multisensory social information. The brain networks that support this are distributed across the temporal and frontal lobes. In this study, we characterize how social variables like identity and expression are encoded in the neural activity of the ventrolateral prefrontal cortex (VLPFC), a prefrontal region of the macaque brain. We found that single neurons do not appear to encode these variables, but populations of neurons display similar activity patterns that are primarily differentiated by the identity of the conspecific that a macaque is attending to. Furthermore, by employing dynamic, multisensory stimuli, our experiment better approximates real world conditions, making our findings more generalizable.
Superior colliculus visual neural sensitivity at the lower limit of natural self-induced image displacements
Authors: Hafed Ziad M. , Chen Chih-Yang , Khademi Fatemeh
Published: June 2022

Visual pattern analysis relies on computations from neurons possessing spatially confined receptive fields. Often, such receptive fields are orders of magnitude larger than the visual pattern components being processed, as well as these components’ minute displacements on the retina, whether due to small object or self motions. Yet, perception effortlessly handles such visual conditions. Here, we show that in the primate superior colliculus, a brain structure long associated with oculomotor control, neurons with relatively large receptive fields are still sensitive to visual pattern displacements as small as 1 min arc. We used real-time gaze-contingent retinal image stabilization to control the instantaneous spatio-temporal luminance modulation of detailed patterns experienced by neurons, probing sensitivity to the lower limit of natural self-induced image displacements. Despite a large difference between pattern displacement amplitudes and receptive field sizes, collicular neurons were strongly sensitive to the visual pattern consequences of the smallest possible image-shifting eye movements.
Vti1a/b support distinct aspects of TGN and cis-/medial Golgi organization
Authors: van Bommel Danique M , Toonen Ruud F , Verhage Matthijs
Published: June 2022

Retrograde trafficking towards the trans-Golgi network (TGN) is important for dense core vesicle (DCV) biogenesis. Here, we used Vti1a/b deficient neurons to study the impact of disturbed retrograde trafficking on Golgi organization and cargo sorting. In Vti1a/b deficient neurons, staining intensity of cis-/medial Golgi proteins (e.g., GM130 and giantin) was increased, while intensity of TGN-resident proteins (e.g., TGN38 and TMEM87A) was decreased. Levels and localization of DCV cargo markers and LAMP1 were altered. This phenotype was not caused by reduced Golgi membrane availability or absence of the TGN compartment. The phenotype was partially phenocopied by disturbing sphingolipid homeostasis, but was not rescued by overexpression of sphingomyelin synthases or the sphingolipid synthesis inhibitor myriocin. We conclude that Vti1a/b are important for distinct aspects of TGN and cis-/medial Golgi organization. Our data underline the importance of retrograde trafficking for Golgi organization, DCV cargo sorting and the distribution of proteins of the regulated secretory pathway.
Model of inverse bleb growth explains giant vacuole dynamics during cell mechanoadaptation
Authors: Cairoli Andrea , Spenlehauer Alice , Overby Darryl R , Lee Chiu Fan
Published: June 2022

Cells can withstand hostile environmental conditions manifest as large mechanical forces such as pressure gradients and/or shear stresses by dynamically changing their shape. Such conditions are realized in the Schlemm’s canal of the eye where endothelial cells that cover the inner vessel wall are subjected to the hydrodynamic pressure gradients exerted by the aqueous humor outflow. These cells form fluid-filled dynamic outpouchings of their basal membrane calledgiant vacuoles. The inverse of giant vacuoles are reminiscent of cellular blebs, extracellular cytoplasmic protrusions triggered by local temporary disruption of the contractile actomyosin cortex. Inverse blebbing has been first observed experimentally during sprouting angiogenesis, but its underlying physical mechanisms are poorly understood. Here, we identify giant vacuole formation as inverse blebbing and formulate a biophysical model of this process. Our model elucidates how cell membrane mechanical properties affect the morphology and dynamics of giant vacuoles and predicts coarsening akin to Ostwald ripening between multiple invaginating vacuoles. Our results are in qualitative agreement with observations from the formation of giant vacuoles during perfusion experiments. Our model not only elucidates the biophysical mechanisms driving inverse blebbing and giant vacuole dynamics, but also identifies universal features of the cellular response to pressure loads that are relevant to many experimental contexts.

Significance statement

Human Schlemm’s canal endothelial cells in physiological conditions are subjected to a pressure gradient caused by the flow of aqueous humor in the basal-to-apical direction across the endothelium leading to the formation of cellular outpouchings called giant vacuoles. The physical mechanisms regulating giant vacuole formation are unknown. By describing giant vacuoles as inward blebs, we formulate a model of their growth and collapse that captures the characteristic features observed experimentally. Our theory reveals that the abrupt increase in surface tension caused by membrane stretching, which is required to accommodate the large areal strains locally induced by inward blebbing, limits giant vacuole growth. The model also predicts a competition between multiple invaginating vacuoles in which big vacuoles win over small vacuoles.
Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture
Authors: Boutet Isabelle , Alves Monteiro Homère J. , Baudry Lyam , Takeuchi Takeshi , Bonnivard Eric , Billoud Bernard , Farhat Sarah , Gonzales-Haraya Ricardo , Salaun Benoit , Andersen Ann , Toullec Jean-Yves , Lallier François , Flot Jean-François , Guiglielmoni Nadège , Guo Ximing , Cui Li , Allam Bassem , Pales-Espinoza Emmanuelle , Hemmer-Hansen Jakob , Marbouty Martial , Koszul Romain , Tanguy Arnaud
Published: June 2022

The European flat oyster (Ostrea edulisL.) is the endemic species of the European coasts. Its exploitation has been reduced during the last decades, because of the appearance of two parasites that have led to the collapse of the stocks and the strong decline of the natural oyster beds.O. edulishas been the subject of numerous studies and programs in population genetics and on the presence of the parasitesBonamia ostreaeandMarteilia refringens. These studies investigated the effects of these parasites mainly on immunity at the molecular and cellular levels. Several genetic selection programs especially related to resistance to the parasite have been initiated. Within the framework of a European project (PERLE 2) which aims to produce genetic lines ofO. eduliswith hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species on the foreshore, obtaining a reference genome has proved to be essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio technology, Illumina, 10X linked and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudo-chromosomes. Annotation of the genome revealed the presence of 35962 protein-coding genes. We analyzed in details the transposable elements (TE) diversity in the flat oyster genome, highlight some specificities in tRNA and miRNA composition and provide first insights in the molecular response ofO. edulistoM. refringens. This genome will serve as a reference for genomic studies onO. edulisto better understand its basic physiology or developing genetic markers in breeding projects for aquaculture or natural reef restoration.
A moonlighting function of a chitin polysaccharide monooxygenase, CWR-1, in allorecognition in Neurospora crassa
Authors: Detomasi Tyler C. , Rico-Ramírez Adriana M. , Sayler Richard I. , Gonçalves A. Pedro , Marletta Michael A. , Glass N. Louise
Published: June 2022

Organisms require the ability to differentiate themselves from organisms of different or even the same species. Allorecognition processes in filamentous fungi are essential to ensure identity of an interconnected syncytial colony to protect it from exploitation and disease. Neurospora crassa has three cell fusion checkpoints controlling formation of an interconnected mycelial network. The locus that controls the second checkpoint, which allows for cell wall dissolution and subsequent fusion between cells/hyphae, cwr, encodes two linked genes, cwr-1 and cwr-2. Previously, it was shown that cwr-1 and cwr-2 show severe linkage disequilibrium with six different haplogroups present in N. crassa populations. Isolates from an identical cwr haplogroup show robust fusion, while somatic cell fusion between isolates of different haplogroups is significantly blocked in cell wall dissolution. The cwr-1 gene encodes a putative polysaccharide monooxygenase (PMO). Herein we confirm that CWR-1 is a C1-oxidizing chitin PMO. We show that the PMO domain of CWR-1 was sufficient for checkpoint function and cell fusion blockage; however, through analysis of active-site, histidine-brace mutants, the catalytic activity of CWR-1 was ruled out as a major factor for allorecognition. Swapping a portion of the PMO domain (V86 to T130) did not switch cwr haplogroup specificity, but rather cells containing this chimera exhibited a novel haplogroup specificity. Allorecognition to mediate cell fusion blockage is likely occurring through a protein-protein interaction between CWR-1 with CWR-2. These data highlight a moonlighting role in allorecognition of the CWR1 PMO domain.
Six-Dimensional Single-Molecule Imaging with Isotropic Resolution using a Multi-View Reflector Microscope
Authors: Zhang Oumeng , Guo Zijian , He Yuanyuan , Wu Tingting , Vahey Michael D. , Lew Matthew D.
Published: June 2022

We report a radially and azimuthally polarized multi-view reflector (raMVR) microscope for precise imaging of the 3D positions and 3D orientations of single molecules (SMs, 10.9 nm and 2.0° precisions using 5000 photons). These precisions are ∼1.5 times better than those of existing methods for SM orientation-localization microscopy. The raMVR microscope achieves 6D super-resolution imaging of Nile red (NR) molecules transiently bound to 150 nm, 350 nm, and 1 µm-diameter lipid-coated spheres, accurately resolving their spherical morphology despite refractive-index mismatch. Simply by observing the rotational dynamics o raMVR images also resolve the infiltration of lipid membranes by amyloid-beta oligomers without covalent labeling. Finally, we demonstrate 6D imaging of HEK-293T cell membranes, where the orientations of merocyanine 540 molecules reveal heterogeneities in membrane fluidity. With its ∼2 µm depth range, nearly isotropic 3D spatial resolution, and superior orientation measurement precision, we expect the raMVR microscope to enable 6D imaging of molecular dynamics within biological and chemical systems with unprecedented detail.