bluuebunny/crossref_metadata_2025 huggingface dataset:
Insufficient vaccination and inadequate immunization rates among Korean patients with inflammatory bowel diseases
Authors: Ryu Han Hee , Chang Kiju , Kim Nayoung , Lee Ho-Su , Hwang Sung Wook , Park Sang Hyoung , Yang Dong-Hoon , Byeon Jeong-Sik , Myung Seung-Jae , Yang Suk-Kyun , Ye Byong Duk
Published: November 2021

This study aimed to evaluate self-reported vaccination rates, immunity, knowledge of and attitudes toward vaccination among Korean patients with inflammatory bowel disease (IBD) as well as to identify factors associated with proper vaccination.

Between November 2013 and February 2015, consecutive patients with IBD were invited to complete a standardized questionnaire on vaccination. Moreover, immune status for common vaccine-preventable diseases was evaluated via serologic tests.

A total of 310 patients with IBD were invited to the questionnaire survey and 287 patients (92.6%) who completed the questionnaires were finally enrolled (men, 188 [65.5%], median age at survey, 29.9 years [interquartile range, 22.3–39.2], ulcerative colitis: Crohn disease = 165:122]. Self-reported vaccine uptake rates were as follows: hepatitis A virus (HAV; 13.2%), hepatitis B virus (HBV; 35.2%), seasonal influenza (43.2%), pneumococcus (4.9%). Most of the patients (87.1%) did not know that proper vaccination has been recommended for patients with IBD. Up to 64.8% and 32.8% of patients were negative for IgG anti-HAV antibody and IgG HBV surface antibody, respectively. In a multivariable analysis, newspaper subscription (aOR [adjusted odds ratio] 2.185, 95% confidence interval [CI] 1.136–4.203, P = .019), ever recommendation of vaccination by a physician (aOR 2.456, 95% CI 1.240–4.862, P = .010), and use of anti-tumor necrosis factor agents (aOR 4.966, 95% CI 1.098–22.464, P = .037) showed a significant association with uptake of adult vaccines recommended for patients with IBD.

Vaccine uptake rates, positivity of antibody to HAV and HBV, and knowledge of patients with IBD regarding vaccination were not sufficient. Proper educational information and recommendation from physicians could enhance awareness among patients with IBD about the need for vaccination and thereby improve vaccination rates.

Trial registration number: NCT01984879.
An HIV elite controller patient carrying the homozygous H63D variant in the homeostatic iron regulator gene
Authors: Zanella Isabella , Focà Emanuele , Degli-Antoni Melania , Castelli Francesco , Quiros-Roldan Eugenia
Published: November 2021

Rationale:

HIV elite controllers represent a rare subset of persons living with HIV, able to spontaneously control viral replication without antiviral therapy. HLA-B∗57 and HLA-B∗27 alleles are associated to efficient polyfunctional CD8+ T-cell response and are overrepresented in elite controllers but these alleles alone incompletely explain spontaneous HIV replication control in these subjects. Further mechanisms involved in innate and adaptive immune response and host genetics may contribute to this control. In this context, the homeostatic iron regulator (HFE) gene encodes a major histocompatibility complex-class-I-like molecule involved in both innate immunity, acting also through autophagy regulation, and iron homeostasis, strictly related to immune functions and susceptibility to infections.

Patient concerns:

Homozygousity for the p.His63Asp (H63D) variant in the HFE gene was identified in an 80-year-old HIV-infected woman with spontaneous control of viral replication.

Diagnosis:

HIV-1 RNA was undetectable in patient's serum with a routine assay and an ultra-sensitive assay (<1 copy/mL) during the 30 years follow-up. CD4+ and CD8+ T cell counts were stable and normal during all this period.

Interventions:

The patient had a history of absence of any physical ailment and no antiviral therapy has been prescribed during the 30 years of follow-up. The subject did not harbor HLA-B∗57 and HLA-B∗27 alleles. HFE gene was sequenced by Sanger, as part of a larger study on a cohort of HIV infected patients, aged >65 years and screened for polymorphisms in genes belonging to several pathways involved in neuroinflammation.

Outcomes:

The woman had CD4+ and CD8+ T cell normal values and spontaneously controlled serum HIV-1 RNA levels for 30 years.

Lessons:

We assume that the interplay between the HFE H63D variant in homozygosity and innate immunity, perhaps through autophagy regulation, could play a role in HIV-1 replication control in our patient. This hypothesis needs to be explored in in vitro and in vivo studies. Understanding mechanisms involved in spontaneous control of HIV-1 replication remains indeed a challenge due to its possible implications for HIV cure research.
Awake nasotracheal intubation under bronchoscopic guidance and anesthetic management in a patient undergoing excision of an endotracheal mass
Authors: Kim Jonghae , Park Bum Young , Lim Jung A.
Published: November 2021

Rationale:

The main challenge facing anesthesiologists during endotracheal mass resection is securing effective airway management during surgery. It is important to select an airway intubation and airway maintenance method according to the patient's condition and the characteristics of the mass.

Patient concerns:

A 74-year-old woman with aggravated dyspnea for 1 year was scheduled to undergo endotracheal mass excision under general anesthesia.

Diagnosis:

The mass was 4 × 3 × 3 cm ovoid-shaped, and located 4 cm above the carina, occupying 41% of the tracheal lumen in a preoperative chest computed tomography and bronchoscopy.

Interventions:

After preparing extracorporeal membrane oxygenation in case of the inability to ventilate and intubate, we attempted awake bronchoscopy-guided nasotracheal intubation using a reinforced endotracheal tube with an inner diameter of 5.5 mm and outer diameter of 7.8 mm after a translaryngeal block. The tube was passed around the mass without resistance and placed right above the carina. With the tube pulled back above the mass, another tube was introduced from the opened trachea below the mass to the right main bronchus. Following the resection of the tracheal portion containing the mass, the posterior wall of the remaining trachea was reconstructed. The tube placed in the right main bronchus was removed and the tube in the upper trachea was introduced right above the carina. The patient's head was kept flexed once the anastomosis of the trachea was completed, and the surgery ended uneventfully.

Outcomes:

The mass was confirmed as schwannoma by histopathological finding. The patient was discharged from the hospital on the 6th postoperative day without complication.

Lessons:

Awake bronchoscopy-guided intubation is a safe airway management method in patients with an endotracheal mass. Close cooperation between anesthesiologist and surgeon, and preparation for airway management before surgery is essential. It is necessary to establish alternative plans that can be implemented in the case that intubation and ventilation are not possible.
Peripheral neuropathy after extra-corporeal membrane oxygenation therapy in children
Authors: Ko Jun Young , Lee Mi rim , Ha Eun-Hye , Kim Aram
Published: November 2021

Rationale:

In recent years, the use of extracorporeal membrane oxygenation (ECMO) treatment for pediatric patients with cardiorespiratory failure has increased, with emphasis being given to the prevention of complications in ECMO-treated patients. Several studies have reported ECMO-related central nervous system complications, such as intracranial hemorrhage, cerebral infarction, and seizure. However, few cases of peripheral nerve injury have been reported in ECMO-treated adults; there have also been no reported cases of peripheral nerve injury in the pediatric population.

Patient Concerns:

Two pediatric patients aged 16 and 6 experienced motor weakness in the extremities after the insertion of ECMO equipment.

Diagnoses:

They were diagnosed with peripheral nerve injuries through an electrodiagnostic study that showed femoral/sciatic neuropathies and brachial plexopathy. Arteriography and doppler sonography was performed to find the cause of peripheral nerve injury, and this may be the results of vascular compromise and compressive injuries, respectively.

Interventions:

Surgical embolectomy was performed to remove thrombus in one patient. Two patients received orthosis, and physical therapy and occupational therapy were performed to prevent contracture and improve strength and functional use.

Outcomes:

Two pediatric patients showed a gradual improvement in motor power and function.

Lessons:

Through this case report, we present rare ECMO-related complications and emphasize the importance of early diagnosis and monitoring of peripheral nerve injury in ECMO-treated children.
The role of rehabilitation and vitamin D supplementation on motor and psychological outcomes in poststroke patients
Authors: Torrisi Michele , Bonanno Lilla , Formica Caterina , Arcadi Francesca Antonia , Cardile Davide , Cimino Vincenzo , Bramanti Placido , Morini Elisabetta
Published: November 2021

Post-Stroke depression affects between 12% and 72% of patients who have suffered a stroke. The association between low serum levels of 25-hydroxyvitamin D (25(OH) D) and increased risk of depression is reported in both stroke and non-stroke patients. Similarly, high 25(OH) D levels might be associated with greater functional improvement during rehabilitation program.

We wanted to investigate the effects of an intensive rehabilitation on poststroke outcomes. We wondered if the daily rehabilitation of motor and cognitive functions could also have an effect on mood and functional abilities in addition to or as an alternative to vitamin D supplementation.

We conducted a 12-week, randomized trial, double blind, parallel, monocentric clinical trial of 40 patients undergoing intensive neuro-rehabilitation treatment at a specialized care facility for ischemic or hemorrhagic brain stroke. Participants were randomly assigned, in a 1:1 ratio, to 1 of 2 parallel groups: in the experimental group, 2000 IU/day of oral cholecalciferol was administered; in the control group patients were not taking vitamin D supplementation. Patients underwent a text evaluation to investigate psychological and motor outcomes.

Significant intra-group difference in outcomes measures was found but not between control group and experimental group. In the vitamin D group, we highlighted significant differences between T0 and T1 in calcium (P < .001), vitamin D (P < .001), in Montgomery Aasberg Depression Rating Scale (P = .001), and in Functional Independent Measures (P < .001). In the health control group, we found a significant difference in calcium (P = .003), vitamin D (P < .001), Montgomery Aasberg Depression Rating Scale (P = 0.006), in general self-efficacy (P = .009), and in Functional Independent Measures (P < .001).

Our results show that the beneficial effect on mood and functional recovery is mainly due to neurorehabilitation rather than vitamin D supplementation.
Cardiogenic shock caused by Takotsubo syndrome complicated with severe anxiety
Authors: Fang Shu , Wang Yu , He Peng-Kang , Han Xiao-Ning , Yang Ying , Hong Tao , Gong Yan-Jun
Published: November 2021

Rationale:

Takotsubo syndrome (TTS) is characterized by transient and reversible left ventricular systolic dysfunction, which are often associated with acute physical or emotional stressors. Cancer is one of the comorbidities in TTS, and TTS is even considered as a paraneoplastic syndrome, but its mechanism remains unclear. We report a patient in whom cancer and untreated mental disorders triggered TTS.

Patient concerns:

A 59-year-old man was transferred to the Department of Cardiology because of acute onset of severe chest pain and dyspnea before cystoscopy. He presented with hematuria, had been diagnosed with a high-grade urothelial bladder cancer, and underwent transurethral resection of bladder tumors 4 months previously. He had severe anxiety regarding recurrence and death from cancer, especially after the hematuria recurred.

Diagnosis:

TTS and severe anxiety.

Interventions:

The results of coronary angiography, a left ventriculogram, echocardiography, and the clinical outcome led to the diagnosis of TTS. The patient was treated with extracorporeal membrane oxygenation support, mechanical ventilation, and drugs for heart failure and anxiety.

Outcomes:

Echocardiography showed normal wall motion on day 6 of symptom onset. Six months after symptom onset, the anxiety score was reduced from 12 to 11, and the patient had no episodes of any discomfort, and no evidence of cancer recurrence was observed.

Lessons:

Patients with cancer and TTS have a higher level of stress, and physicians need to pay more attention to early screening and early treatment of mental disorders in these patients. Prompt and effective multidisciplinary treatment, including psychological counseling and antianxiety drugs, can improve the prognosis in such cases.
Pulmonary sarcomatoid carcinoma mimicking pleural mesothelioma
Authors: Wang Le , Zhang Jing , Chen Xing , Liang Maoli , Li Shuo , Zhou Wei , Cao Jie
Published: November 2021

Introduction:

Pulmonary sarcomatoid carcinoma (PSC) is an extremely rare biphasic tumor characterized by a mixture of malignant epithelial and mesenchymal cells. Owing to the rarity, as well as the lack of typical manifestations and imaging signs, the rate of misdiagnosis is high. Herein, we present a case of PSC misdiagnosed as pleural mesothelioma in a 59-year-old man.

Patient concerns:

A 59-year-old man presented with recurrent coughing, fever, and chest pain.

Diagnosis:

Chest computed tomography showed 2 large and dense masses involving the inferior lobes of right lung, along with slight irregular pleural thickening and a small amount of effusion.

Interventions:

Chest computed tomography-guided tumor biopsy was performed. PSC was confirmed based on histopathology and immunohistochemistry. The patient refused treatment due to economic reasons.

Outcomes:

The patient developed adrenal, multiple lung and brain metastasis. The overall survival time was 11 months.

Conclusions:

PSC, despite its rarity, should be considered in the differential diagnosis of lung cancer. Besides, biopsy, histopathology, and specific immunohistochemical staining of larger tissue specimens can be contributing to the accurate diagnosis of PSC.
Totally thoracoscopic surgery for treating left atrial myxoma
Authors: Zhao Feng , Chen Tongyun , Tang Yipeng , Chen Qingliang , Jiang Nan , Guo Zhigang
Published: November 2021

We aimed to summarize the experience of totally thoracoscopic surgery for left atrial myxoma, together with analyzing the safety and feasibility. We retrospectively analyzed the clinical data of 15 patients with left atrial myxoma admitted to our hospital from October 2016 to October 2018. The auxiliary hole was located at the midline of the 5th intercostal space of the right chest. The endoscope hole was located at the front position of the fourth intercostal space. Specimens were sent to the pathology department for pathological examination. All the procedures were completed successfully. Extracorporeal circulation time was 46.5 ± 18.6 minute, cross-clamping time was 20.6 ± 6.7 minute, thoracic drainage fluid was 89+60.2 ml, ventilator assist time was 4.3 ± 2.6 hour, intensive care unit stay time was 14.5 ± 4.2 hour, the average postoperative hospital stay was 5.2 ± 1.2 day. There was no death, or red blood cell transfusion during and after surgery. No postoperative complications were reported by the patients. No recurrence of myxoma, residual shunt in the atrial septum and valvular lesions were found after 3months of postoperative cardiac ultrasound examination. Total thoracoscopic surgery for left atrial myxoma was less invasive with satisfactory cosmetic appearance with feasibility and safety. Besides, it caused no serious complications.
Risk factors for the histologic discrepancy of gastric adenomatous lesions and long-term outcome
Authors: Joo Jong Seok , Park Jae Ho , Kim Ju Seok , Kang Sun Hyung , Moon Hee Seok , Sung Jae Kyu , Jeong Hyun Yong
Published: November 2021

Although endoscopic forceps biopsies (EFB) have a significant role in diagnosing gastric adenoma, there are still discrepancies between EFBs and finalized pathology results.

Therefore, the objective of this study was to find the risk factors that cause this discrepancy and to analyze the effects of this discrepancy on the long-term outcome.

In this study patients that had received endoscopic resection due to low-grade gastric adenoma diagnosis from EFB between January of 2011 and January of 2018 at the Chungnam National University Hospital were retrospectively analyzed. According to whether there was histological discrepancy the cumulative incidence of the metachronous lesions were analyzed.

A total of 745 lesions diagnosed as low-grade gastric adenoma at EFB were enrolled, and the final pathology results were confirmed to be non-neoplastic (n = 19), low-grade adenoma (n = 614), High-grade adenoma (n = 63), and carcinoma (n = 49), and with the exception of non-neoplastic lesion, the results confirmed 84.6% (n = 614) for the concordant group and 15.4% (n = 112) for the discordant. The results of the multivariate analysis confirmed that depressed lesion (odds ratio [OR]: 2.056; 95% confidence interval [CI]: 1.130–3.451; P = .011), erythema (OR: 2.546; 95% CI: 1.604–4.030; P = .004), and a size >1.5 cm (OR: 1.903; 95% CI: 1.102–3.172; P = .018) were risk factors for discrepancy. The results also confirmed that for the average observation period of (SD) 39.12 (12.31) months, the cumulative incidence of metachronous neoplasm had a higher significance (P = 0.001) in the discordant group when compared to that of the concordant group.

The factors related to the histologic discrepancy of low-grade gastric adenoma were depressed lesion, erythema and size >1.5 cm. In the groups with histological discrepancy, the cumulative incidence of the metachronous neoplasm was significantly higher and therefore closer observation of such patients after performing endoscopic resection is necessary.
The efficacy of 5 rehabilitation treatments after anterior cruciate ligament reconstruction
Authors: Wang Congxiao , Ji Zhonglei , Wang Luyi , Zhang Qiaorong , Wang Hujun , Qie Shuyan
Published: November 2021

Background:

The efficacy of traditional rehabilitation, proprioceptive training, and neuromuscular training after anterior cruciate ligament (ACL) reconstruction is also controversial. In order to help medical staff better choose the rehabilitation treatment plan after ACL reconstruction, we conducted this network meta-analysis.

Methods:

Chinese and English databases such as Wanfang, Weipu, China Zhiwang, and PubMed, Cochrane Library, Embase were retrieved. We collected clinical controlled trial papers on traditional rehabilitation therapy, proprioceptive training and neuromuscular training after ACL reconstruction for meta-analysis.

Results:

In this meta-analysis, 12 studies were included, including 486 patients who received rehabilitation treatment after ACL reconstruction. Based on network meta-analysis, it was found that 4 groups of direct comparison and 6 groups of indirect comparison were formed for 5 rehabilitation treatment schemes after ACL reconstruction. The curative effect of traditional rehabilitation training combined with proprioception training is better than that of traditional rehabilitation training (mean difference value of traditional rehabilitation training combined with proprioception training vs traditional rehabilitation training was 8.00, 95% confidence interval: 2.61,13.39). The efficacy of proprioceptive training is better than that of traditional rehabilitation training (mean difference value of proprioceptive training vs traditional rehabilitation training is 11.01, 95% confidence interval: 0.62,21.39). There was no statistical significance between the other rehabilitation trainings. According to the surface under cumulative ranking curve, the therapeutic effects of the 5 rehabilitation treatment programs after ACL reconstruction were ranked as follows: proprioceptive training (72%) > traditional rehabilitation training combined with neuromuscular training (70.8%) > traditional rehabilitation training combined with proprioception training (57.1%) > neuromuscular training (45.5%) > traditional rehabilitation training (4.6%). No publication bias was found in the funnel plot.

Conclusion:

Combined with the results of meta-analysis and surface under cumulative ranking efficacy sequence diagram, it can be seen that traditional rehabilitation training combined with proprioceptive training and traditional rehabilitation training combined with neuromuscular training have significant efficacy. Due to the limitations of this study, the conclusions of this network meta-analysis still need to be further confirmed by a large sample size and well-designed randomized controlled trials.
Posterior fossa transient ischemic attack in the setting of bilateral persistent hypoglossal arteries
Authors: Ren Xiaolu
Published: November 2021

Rationale:

Persistent hypoglossal artery (PHA) is the second rare abnormal anastomosis of the internal carotid and vertebrobasilar arteries, and bilateral persistent hypoglossal arteries in particular have rarely been reported. This is the first case of bilateral persistent hypoglossal arteries presenting with posterior fossa transient ischemic attack (TIA).

Patient concerns:

We reported a 54-year old female with posterior fossa TIA due to the coexisting bilateral persistent hypoglossal arteries and left internal carotid artery stenosis.

Diagnosis:

The patient was diagnosed with posterior fossa TIA, bilateral persistent hypoglossal arteries and left internal carotid artery stenosis.

Interventions:

The patient was given aspirin 100 mg/qd and advised to avoid excessive neck movement.

Outcomes:

Symptoms of intermittent subjective dizziness accompanied by nausea were relieved.

Lessons:

Although requires no special treatment, PHA could be accompanied by hypoplasia of vertebral arteries and posterior communicating arteries and becomes the main blood supply pathway for the posterior circulation. Accurate identification and evaluation of PHA is important of ensuring the safety of carotid interventions and identifying specific types of stroke.
Therapeutic Risk Management and Firearm-related Lethal Means Safety
Authors: Simonetti Joseph A. , Wortzel Hal S. , Matarazzo Bridget B.
Published: November 2021

Safety planning to reduce suicide or other-directed violence risk involves efforts toward “making the environment safe,” including working collaboratively with at-risk patients to encourage voluntary changes in their firearm storage decisions [ie, lethal means safety (LMS) counseling]. This column provides a conceptual framework and real-world evidence to support the delivery of LMS counseling to at-risk patients, as well as guidance on asking about firearm access and making individualized safety recommendations. It also reviews important elements related to documenting LMS discussions and legal considerations related to these conversations.
Genome-wide selection signatures reveal widespread synergistic effects of culture conditions and temperature stress in Drosophila melanogaster
Authors: Claire Burny , Viola Nolte , Marlies Dolezal , Christian Schlötterer
Published: November 2021

Experimental evolution combined with whole-genome sequencing is a powerful approach to study the adaptive architecture of selected traits, in particular when replicated experimental populations evolving in opposite selective conditions (e.g. hot vs. cold temperature) are compared. Nevertheless, such comparisons could be affected by environmental effects shared between selective regimes (e.g. laboratory adaptation), which complicate the interpretation of selection signatures. Here, we used an experimental design, which takes advantage of the simplicity of selection signatures from founder populations with reduced variation, to study the fitness consequences of the laboratory environment (culture conditions) at two temperature regimes. After 20 generations of adaptation at 18°C and 29°C, strong genome-wide selection signatures were observed. About one third of the selection signatures can be either attributed to temperature effects, laboratory adaptation or the joint effects of both. The fitness consequences reflecting the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions, fitting the pattern of larger expression differences between founders at 29°C. We propose that evolve and resequence (E&R) with reduced genetic variation allows to study genome-wide fitness consequences driven by the interaction of multiple environmental factors.
Improving Neural Networks for Genotype-Phenotype Prediction Using Published Summary Statistics
Authors: Cui Tianyu , Mekkaoui Khaoula El , Havulinna Aki , Marttinen Pekka , Kaski Samuel
Published: November 2021

Phenotype prediction is a necessity in numerous applications in genetics. However, when the size of the individual-level data of the cohort of interest is small, statistical learning algorithms, from linear regression to neural networks, usually fail due to insufficient data. Fortunately, summary statistics from genome-wide association studies (GWAS) on other large cohorts are often publicly available. In this work, we propose a new regularization method, namely, main effect prior (MEP), for making use of GWAS summary statistics from external datasets. The main effect prior is generally applicable for machine learning algorithms, such as neural networks and linear regression. With simulation and real-world experiments, we show empirically that MEP improves the prediction performance on both homogeneous and heterogeneous datasets. Moreover, deep neural networks with MEP outperform standard baselines even when the training set is small.
Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not
Authors: Fataftah Nazeer , Edlund Erik , Lihavainen Jenna , Bag Pushan , Björkén Lars , Näsholm Torgny , Jansson Stefan
Published: November 2021

Fertilization with nitrogen (N)-rich compounds leads to increased growth, but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treatingPopulussaplings with high or low levels of inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream ofPopulustrees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−1) delayed senescence but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids (TCA), arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3−1and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in any of the treatments. Taken together, metabolomic rearrangement under different N forms or experimental setups could modulate senescence process, but not initiation and progression inPopulus. We propose that the different regulation of C and N status through direct molecular signaling of NO3−1could account for the contrasting effects of NO3−1and Arg on senescence.

One sentence summary

Nitrate, administered by precision fertilization through injection into the trunk, may delay autumn senescence and change metabolism inPopulusleaves, while the same amount of amino acids does not have the same effect.
Contribution of linear and nonlinear mechanisms to predictive motion estimation
Authors: Liu Belle , Hong Arthur , Rieke Fred , Manookin Michael B.
Published: November 2021

Successful behavior relies on the ability to use information obtained from past experience to predict what is likely to occur in the future. A salient example of predictive encoding comes from the vertebrate retina, where neural circuits encode information that can be used to estimate the trajectory of a moving object. Predictive computations should be a general property of sensory systems, but the features needed to identify these computations across neural systems are not well understood. Here, we identify several properties of predictive computations in the primate retina that likely generalize across sensory systems. These features include calculating the derivative of incoming signals, sparse signal integration, and delayed response suppression. These findings provide a deeper understanding of how the brain carries out predictive computations and identify features that can be used to recognize these computations throughout the brain.
4DPhenoMVS: A Low-Cost 3D Tomato Phenotyping Pipeline Using a 3D Reconstruction Point Cloud Based on Multiview Images
Authors: Zhai Ruifang , Wang Yinghua , Hu Songtao , Yang Wanneng
Published: November 2021

Manual phenotyping of tomato plants is time consuming and labor intensive. Due to the lack of low-cost and open-access 3D phenotyping tools, the dynamic 3D growth of tomato plants during all growth stages has not been fully explored. In this study, based on the 3D structural data points generated by employing structures from motion algorithms on multiple-view images, we proposed a dynamic 3D phenotyping pipeline, 4DPhenoMVS, to calculate and analyze 14 phenotypic traits of tomato plants covering the whole life cycle. The results showed that the R2 values between the phenotypic traits and the manual measurements stem length, plant height, and internode length were more than 0.8. In addition, to investigate the environmental influence on tomato plant growth and yield in the greenhouse, eight tomato plants were chosen and phenotyped during 7 growth stages according to different light intensities, temperatures, and humidities. The results showed that stronger light intensity and moderate temperature and humidity contribute to a higher growth rate and higher yield. In conclusion, we developed a low-cost and open-access 3D phenotyping pipeline for tomato plants, which will benefit tomato breeding, cultivation research, and functional genomics in the future.

Highlights

Based on the 3D structural data points generated by employing structures from motion algorithms on multiple-view images, we developed a low-cost and open-access 3D phenotyping tool for tomato plants during all growth stages.
High-frequency changes in single-trial visual evoked potentials for unattended stimuli in chronic schizophrenia
Authors: Kipiński Lech , Maciejowski Andrzej , Małyszczak Krzysztof , Pilecki Witold
Published: November 2021

Background

Patients with schizophrenia reveal changes in information processing associated with external stimuli, which is reflected in the measurements of brain evoked potentials. We discuss actual knowledge on electro- (EEG) and magnetoencephalographic (MEG) changes in schizophrenia.

New method

The commonly used averaging technique entails the loss of information regarding the generation of evoked responses. We propose a methodology to describe single-trial (non-averaged) visual evoked potentials (VEP) using spectral and statistical analyses. We analysed EEG data registered in the O1-Cz and O2-Cz leads during unattended pattern-reversal stimulation, collected from a group of adult patients with chronic schizophrenia, and compared them to those of healthy individuals. Short-time single-trial VEP were transformed to the frequency domain using the FFT algorithm. Changes of the spectral power were visualized using spectrograms which were created by stacking single-trial spectra across all trials. Measures of the absolute and the relative spectral power were calculated and compared statistically.

Results

In schizophrenia, the energy density of VEP oscillations is shifted towards higher (gamma) frequencies, compared to healthy individuals. These differences are statistically significant in all analysed frequency bands for the relative power. This indicates distorted early processing of visual stimuli in schizophrenia.

Comparison with existing methods

The main advantage of the presented methodology is its simplicity and ease of interpretation of obtained results. The presented observations complement the knowledge on gamma oscillations acquired from computationally more complex methods of time–frequency analysis.

Conclusions

High-frequency changes for single-trial VEPs are detected in chronic schizophrenia.
Reliability of quantitative multiparameter maps is high for MT and PD but attenuated for R1 and R2* in healthy young adults
Authors: Wenger Elisabeth , Polk Sarah E. , Kleemeyer Maike M. , Weiskopf Nikolaus , Bodammer Nils C. , Lindenberger Ulman , Brandmaier Andreas M.
Published: November 2021

We investigate the reliability of individual differences of four quantities measured by magnetic resonance imaging based multiparameter mapping (MPM): magnetization transfer (MT), proton density (PD), longitudinal relaxation rate (R1), and effective transverse relaxation rate (R2*). A total of four MPM datasets, two on each of two consecutive days, were acquired in healthy young adults. On Day 1, no repositioning occurred; on Day 2, participants were repositioned between MPM datasets. Using intra-class correlation effect decomposition (ICED), we assessed the contributions of session-specific, day-specific, and residual sources of measurement error. For whole-brain gray and white matter, all four MPM parameters showed high reproducibility and high reliability, as indexed by the coefficient of variation (CoV) and the intra-class correlation (ICC). However, MT, PD, R1, and R2* differed markedly in the extent to which reliability varied across brain regions. MT and PD showed high reliability in almost all regions. In contrast, R1 and R2* showed low reliability in some regions outside the basal ganglia, such that the sum of the measurement error estimates in our structural equation model was higher than estimates of between-person differences. In sum, in this sample of healthy young adults, the four MPM parameters showed very little variability over four measurements over two days but differed in how well they could assess between-person differences. We conclude that R1 and R2* might carry only limited person-specific information in samples of healthy young adults, and, by implication, might be of restricted utility for studying associations to between-person differences in behavior.
The roles of distinct Ca2+ signaling mediated by Piezo and inositol triphosphate receptor (IP3R) in the remodeling of E-cadherin during cell dissemination
Authors: Cabrera Alejandra J.H. , Gumbiner Barry M. , Kwon Young V.
Published: November 2021

Given the role of E-cadherin (E-cad) in holding epithelial cells together, the inverse relationship between E-cad levels and cell invasion has been perceived as a principle underlying the invasiveness of tumor cells. In contrast, our study employing the Drosophila model of cell dissemination demonstrates that E-cad is necessary for the invasiveness of Rasv12-transformed cells in vivo. Drosophila E-cad/β-catenin disassembles at adherens junctions and assembles at invasive protrusions—the actin- and cortactin-rich invadopodia-like protrusions associated with breach of the extracellular matrix (ECM)—during cell dissemination. Loss of E-cad attenuates dissemination of Rasv12-transformed cells by impairing their ability to compromise the ECM. Strikingly, the remodeling of E-cad/β-catenin subcellular distribution is controlled by two discrete intracellular calcium signaling pathways: Ca2+ release from endoplasmic reticulum via the inositol triphosphate receptor (IP3R) disassembles E-cad at adherens junctions while Ca2+ entry via the mechanosensitive channel Piezo assembles E-cad at invasive protrusions. Thus, our study provides molecular insights into the unconventional role of E-cad in cell invasion during cell dissemination in vivo and describes the discrete roles of intracellular calcium signaling in the remodeling of E-cad/β-catenin subcellular localization.
Chromosome scale assembly of allopolyploid genome of the diatom Fistulifera solaris
Authors: Maeda Yoshiaki , Watanabe Kahori , Kobayashi Ryosuke , Yoshino Tomoko , Bowler Chris , Matsumoto Mitsufumi , Tanaka Tsuyoshi
Published: November 2021

Microalgae including diatoms are of interest for environmentally-friendly manufacturing such as biofuel production. However, only a very few of their genomes have been elucidated owing to their diversified and complex evolutionary history. The genome of the marine oleaginous diatom Fistulifera solaris, an allopolyploid diatom possessing two subgenomes, has been analyzed previously by pyrosequencing. However, many unsolved regions and unconnected scaffolds remained. Here we report the entire chromosomal structure of the genome of F. solaris strain JPCC DA0580 using a long-read nanopore sequencing platform. From just one single run using a MinION flow-cell, the chromosome scale assembly with telomere-to-telomere resolution was achieved for 41 out of 44 chromosomes. Centromere regions were also predicted from the chromosomes, and we discovered conserved motifs in the predicted regions. The function of the motifs was experimentally confirmed by successful transformation of the diatom via bacterial conjugation. This discovery provides insights into chromosome replication, facilitating the rational design of artificial chromosomes for large-scale metabolic engineering of diatoms. The chromosome scale assembly also suggests the potential existence of multi-copy mini-chromosomes and tandemly repeated lipogenesis genes related to the oleaginous phenotype of F. solaris. The nanopore sequencing also solved the sequential arrangement of the repeat region in the F. solaris mitochondrial genome. Findings of this study will be useful to understand and further engineer the oleaginous phenotype of F. solaris.
GutMicroNet: an interactive platform for gut microbiome interaction exploration
Authors: Arif Muhammad , Portlock Theo , Güngör Cem , Koç Elif , Özcan Berkay , Subaş Oğuzhan , Çakmak Buğra , Turkez Hassan , Uhlén Mathias , Mardinoglu Adil , Shoaie Saeed
Published: November 2021

The human gut microbiome data has been proven to be a powerful tool to understand the human body in both health and disease conditions. However, understanding their complex interactions and impact on the human body remains a challenging task. Unravelling the species-level interactions could allow us to study the causality of the microbiome. Moreover, it could lead us to better understand the underlying mechanisms of complex diseases and, subsequently, the discovery of new therapeutic targets. Given these challenges and benefits, it has become evident that a freely accessible and centralized platform for presenting gut microbiome interaction is essential to untangle the complexity and open multiple new paths and opportunities in disease- and drug-related research. Here, we present GutMicroNet, an interactive visualization platform of human gut microbiome interaction networks. We generated 45 gut microbiome co-abundance networks from various geographical origins, gender, and diseases based on the data presented in the Human Gut Microbiome Atlas. This interactive platform includes more than 1900 gut microbiome species and allows users to query multiple species at the same time based on their interests and adjust it based on the statistical properties. Moreover, users can download publication-ready figures or network information for further analysis. The platform can be accessed freely onhttps://gutmicro.netwithout any login requirements or limitations, including access to the full networks data.
Realistic alpha oscillations and transient responses in a cortical microcircuit model
Authors: Kiani Andres A. , Netoff Theoden I. , Ghose Geoffrey M.
Published: November 2021

Neural-mass modeling of neural population data (EEG, ECoG, or LFPs) has shown promise both in elucidating the neural processes underlying cortical rhythms and changes in brain state, as well as offering a framework for testing the interplay between these rhythms and information processing. Models of cortical alpha rhythms (8 - 12 Hz) and their impact in visual sensory processing have been at the forefront of this effort, with the Jansen-Rit being one of the more popular models in this domain. The Jansen-Rit model, however, fails in reproducing key physiological observations including the level of inputs that cortical neurons receive and their responses to visual transients. To address these issues we generated a neural mass model that complies better with synaptic mediated dynamics, intrinsic alpha behavior, and produces realistic responses. The model is robust to many changes in parameter values but critically depends on the ratio of excitation to inhibition, producing response transients whose features are dependent on this ratio and alpha phase and power. The model is sufficiently flexible so as to be able to easily replicate the range of low frequency oscillations observed in different studies. Consistent with experimental observations, we find phase-dependent response dynamics to both visual and electrical stimulation using this model. The model suggests that stimulation facilitates alpha at particular phases and suppresses it in others due to a phase dependent lag in inhibitory responses. Hence, the model generates insight into the physiological parameters responsible for intrinsic oscillations and testable hypotheses regarding the interactions between visual and electrical stimulation on those oscillations.

Author summary

While there is increasing evidence of the fundamental role brain states play in shaping information processing in the cerebral cortex, a mechanistic understanding of how those brain states are manifested and alter the signals underlying sensory processing and decision making has proved challenging. To address this issue we have modeled a well established signature of inattention in visual cortex: synchronized low frequency (8 - 12 Hz) oscillations. To allow for inferences regarding the local generation of these rhythms within a cortical microcircuit we used a neural mass model approach that incorporates physiologically realistic interactions between 3 populations of neurons. Our model is able to explain a variety of experimental observations that previous neural mass models have not, including spontaneous rhythms in the absence of input, the faithful transmission of strong input transients, a range of oscillation frequencies, and phase dependent visual responses. The model is robust to a range of parameters, but critically depends on the balance between local excitation and inhibition.
A Graph Neural Network Approach to Molecule Carcinogenicity Prediction
Authors: Fradkin Philip , Young Adamo , Atanackovic Lazar , Frey Brendan , Lee Leo J. , Wang Bo
Published: November 2021

Molecular carcinogenicity is a preventable cause of cancer, however, most experimental testing of molecular compounds is an expensive and time consuming process, making high throughput experimental approaches infeasible. In recent years, there has been substantial progress in machine learning techniques for molecular property prediction. In this work, we propose a model for carcinogenicity prediction, CONCERTO, which uses a graph transformer in conjunction with a molecular fingerprint representation, trained on multi-round muta-genicity and carcinogenicity objectives. To train and validate CONCERTO, we augment the training dataset with more informative labels and utilize a larger external validation dataset. Extensive experiments demonstrate that our model yields results superior to alternate approaches for molecular carcinogenicity prediction.
IFN-γ stimulated murine and human neurons mount anti-parasitic defenses against the intracellular parasiteToxoplasma gondii
Authors: Chandrasekaran Sambamurthy , Kochanowsky Joshua A. , Merritt Emily F. , Lagas Joseph S. , Swannigan Ayesha , Koshy Anita A.
Published: November 2021

Dogma holds thatToxoplasma gondiipersists in neurons because neurons cannot clear intracellular parasites, even with IFN-γ stimulation. As several recent studies questioned this idea, we used primary murine neuronal cultures from wild-type and transgenic mice in combination with IFN-γ stimulation and parental and transgenic parasites to reassess IFN-γ dependent neuronal clearance of intracellular parasites. We found that neurons respond to IFN-γ and that a subset of neurons clear intracellular parasites via immunity regulated GTPases. Whole neuron reconstructions from mice infected with parasites that trigger neuron GFP expression only after full invasion revealed that ∼40% of theseT. gondii-invaded neurons no longer harbor parasites. Finally, IFN-γ stimulated human stem cell derived neurons showed a ∼ 50% decrease in parasite infection rate when compared to unstimulated cultures. This work highlights the capability of human and murine neurons to mount cytokine-dependent anti-T. gondiidefense mechanismsin vitroandin vivo.
Biophysical and Architectural Mechanisms of Subthalamic Theta under Response Conflict
Authors: Moolchand Prannath , Jones Stephanie R. , Frank Michael J.
Published: November 2021

The cortico-basal ganglia circuit is needed to suppress prepotent actions and to facilitate controlled behavior. Under conditions of response conflict, the frontal cortex and subthalamic nucleus [STN] exhibit increased spiking and theta band power, which are linked to adaptive regulation of behavioral output. The electrophysiological mechanisms underlying these neural signatures of impulse control remain poorly understood. To address this lacuna, we constructed a novel large-scale, biophysically principled model of the subthalamopallidal [STN-Globus Pallidus externus (GPe)] network, and examined the mechanisms that modulate theta power and spiking in response to cortical input. Simulations confirmed that theta power does not emerge from intrinsic network dynamics but is robustly elicited in response to cortical input as burst events representing action selection dynamics. Rhythmic burst events of multiple cortical populations, representing a state of conflict where cortical motor plans vacillate in the theta range, led to prolonged STN theta and increased spiking, consistent with empirical literature. Notably, theta band signaling required NMDA, but not AMPA, currents, which were in turn related to a triphasic STN response characterized by spiking, silence and bursting periods. Finally, theta band resonance was also strongly modulated by architectural connectivity, with maximal theta arising when multiple cortical populations project to individual STN “conflict detector” units, due to an NMDA-dependent supralinear response. Our results provide insights into the biophysical principles and architectural constraints that give rise to STN dynamics during response conflict, and how their disruption can lead to impulsivity and compulsivity.