Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes.

ZipSeq: barcoding for real-time mapping of single cell transcriptomes.

Spatial transcriptomics seeks to integrate single cell transcriptomic data within the three-dimensional space of multicellular biology. Current methods to correlate a cell's position with its transcriptome in living tissues have various limitations. We developed an approach, called 'ZipSeq', that uses patterned illumination and photocaged oligonucleotides to serially print barcodes ('zipcodes') onto live cells in intact tissues, in real time and with an on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in vitro wound healing, live lymph node sections and a live tumor microenvironment. In all cases, we discovered new gene expression patterns associated with histological structures. In the tumor microenvironment, this demonstrated a trajectory of myeloid and T cell differentiation from the periphery inward. A combinatorial variation of ZipSeq efficiently scales in the number of regions defined, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation.

Homogeneous nucleation of crystalline methane hydrate in molecular dynamics transition paths sampled under realistic conditions.

Methane hydrates are important from a scientific and industrial perspective, and form by nucleation and growth from a supersaturated aqueous solution of methane. Molecular simulation is able to shed light on the process of homogeneous nucleation of hydrates, using straightforward molecular dynamics or rare event enhanced sampling techniques with atomistic and coarse grained force fields. In our previous work [Arjun, T. A. Berendsen, and P. G. Bolhuis, Proc. Natl. Acad. Sci. U. S. A. 116, 19305 (2019)], we performed transition path sampling (TPS) simulations using all atom force fields under moderate driving forces at high pressure, which enabled unbiased atomistic insight into the formation of methane hydrates. The supersaturation in these simulations was influenced by the Laplace pressure induced by the spherical gas reservoir. Here, we investigate the effect of removing this influence. Focusing on the supercooled, supersaturated regime to keep the system size tractable, our TPS simulations indicate that nuclei form amorphous structures below roughly 260 K and crystalline sI structures above 260 K. For these temperatures, the average transition path lengths are significantly longer than in our previous study, pushing the boundaries of what can be achieved with TPS. The temperature to observe a critical nucleus of certain size was roughly 20 K lower compared to a spherical reservoir due to the lower concentration of methane in the solution, yielding a reduced driving force. We analyze the TPS results using a model based on classical nucleation theory. The corresponding free energy barriers are estimated and found to be consistent with previous predictions, thus adding to the overall picture of the hydrate formation process.

Homogenous nucleation rate of CO2 hydrates using transition interface sampling.

Carbon dioxide and water can form solid clathrate structures in which water cages encapsulate the gas molecules. Such hydrates have sparked much interest due to their possible application in CO2 sequestration. How the solid structure forms exactly from the liquid phase via a homogenous nucleation process is still poorly understood. This nucleation event is rare on the molecular timescale even under moderate undercooling or supersaturation conditions because of the large free energy barrier toward crystallization, rendering a brute force simulation of hydrate nucleation unfeasible for moderate undercooling or supersaturation. Here, we perform transition interface sampling simulations to quantify the homogenous nucleation rate for CO2 hydrate formation using accurate atomistic force fields at 500 bars for three different temperatures between 260 and 273 K. Collecting more than 100 000 pathways comprising roughly two milliseconds of simulation time, we computed a nucleation rate in the amorphous phase of ∼1021 nuclei s-1 cm-3 for a temperature of 260 K and a rate of ∼1012 nuclei s-1 cm-3 for a temperature of 265 K. For a temperature of 273 K, we find that the hydrate forms an sI crystalline phase with a rate of order of ∼101 nuclei s-1 cm-3. We compare these rates to classical nucleation theory estimates as well as experiments, and to nucleation rate estimates for methane hydrates and discuss possible causes of the observed differences. Our findings shed light on the kinetics of this important clathrate and should assist in future hydrate formation investigation.

An extended autoencoder model for reaction coordinate discovery in rare event molecular dynamics datasets.

The reaction coordinate (RC) is the principal collective variable or feature that determines the progress along an activated or reactive process. In a molecular simulation using enhanced sampling, a good description of the RC is crucial for generating sufficient statistics. Moreover, the RC provides invaluable atomistic insight into the process under study. The optimal RC is the committor, which represents the likelihood of a system to evolve toward a given state based on the coordinates of all its particles. As the interpretability of such a high dimensional function is low, a more practical approach is to describe the RC by some low-dimensional molecular collective variables or order parameters. While several methods can perform this dimensionality reduction, they usually require a preselection of these low-dimension collective variables (CVs). Here, we propose to automate this dimensionality reduction using an extended autoencoder, which maps the input (many CVs) onto a lower-dimensional latent space, which is subsequently used for the reconstruction of the input as well as the prediction of the committor function. As a consequence, the latent space is optimized for both reconstruction and committor prediction and is likely to yield the best non-linear low-dimensional representation of the committor. We test our extended autoencoder model on simple but nontrivial toy systems, as well as extensive molecular simulation data of methane hydrate nucleation. The extended autoencoder model can effectively extract the underlying mechanism of a reaction, make reliable predictions about the committor of a given configuration, and potentially even generate new paths representative for a reaction.

Comparable glycaemic control and hypoglycaemia in adults with type 2 diabetes after initiating insulin glargine 300 units/mL or insulin degludec: The DELIVER Naïve D real-world study.

AIM: To compare glycaemic control, hypoglycaemia and treatment discontinuation of insulin glargine 300 units/mL (Gla-300) and insulin degludec (IDeg) in a real-world study of insulin-naïve adults with type 2 diabetes (T2D). MATERIALS AND METHODS: DELIVER Naive D was a retrospective observational study that used electronic medical record data from the IBM Watson Health Explorys database. Insulin-naïve adults with T2D who started Gla-300 or IDeg between March 2015 and September 2017 were identified. Patients were active in the system for ≥12 months before and ≥6 months after starting Gla-300 or IDeg and had HbA1c measurements during 6-month baseline and 3- to 6-month follow-up. Outcomes were compared among 1:1 propensity score-matched cohorts. RESULTS: In the matched cohorts (n = 638 each), the mean age was 59 years, approximately 53% were male, and mean HbA1c was 9.67% (82 mmol/mol). Mean (SD) HbA1c decreases were comparable in the Gla-300 and IDeg cohorts (-1.67% [2.22] and -1.58% [2.20]; P = 0.51), as were HbA1c target attainment [<7% (53 mmol/mol): 23.8% and 27.4%; P = 0.20; <8% (64 mmol/mol): 55.0% and 57.1%; P = 0.63] and treatment discontinuation (29.2% and 32.6%; P = 0.14). Overall and inpatient/emergency department-associated hypoglycaemia incidences and event rates were similar in both cohorts using fixed 6-month or variable on-treatment follow-up. CONCLUSIONS: Among real-world insulin-naïve adults with T2D, initiation of Gla-300 or IDeg resulted in comparable improvements in glycaemic control and similar rates of hypoglycaemia. These real-world data complement and confirm a randomized trial and other real-world studies.

Switching to insulin glargine 300 units/mL in real-world older patients with type 2 diabetes (DELIVER 3).

AIM: To compare the second-generation basal insulin glargine 300 units/mL (Gla-300) and first-generation basal insulins on glycaemic control and hypoglycaemia risk in older adults with type 2 diabetes (T2D). MATERIALS AND METHODS: DELIVER 3 was a retrospective observational cohort study of electronic medical records. A total of 1176 older adults (aged ≥ 65 years) with T2D and ≥1 HbA1c value during 6 month baseline and 3 to 6 month follow-up who switched from basal insulin to Gla-300 were propensity score-matched to 1176 older adults who switched to a first-generation basal insulin [insulin detemir (IDet) or insulin glargine 100 units/mL (Gla-100)]. Outcomes were follow-up HbA1c, achievement of HbA1c <7% and <8%, hypoglycaemia incidence and event rates, and healthcare resource utilization. RESULTS: Following basal insulin switching, HbA1c reductions were greater/similar with Gla-300 versus IDet/Gla-100 (variable follow-up: -0.45% ± 1.40% vs. -0.29% ± 1.57%; P = .021; fixed follow-up: -0.48% ± 1.49% vs. -0.38% ± 1.59%; P = .114), while HbA1c goal attainment was similar in both cohorts. Gla-300 was associated with less hypoglycaemia [event rate: adjusted rate ratio (aRR): 0.63, 95% CI: 0.53-0.75; P < .001] and inpatient/emergency department-associated hypoglycaemia (adjusted hazard ratio: 0.58, 95% CI: 0.37-0.90; P = .016; aRR: 0.43, 95% CI: 0.31-0.60; P < .001) by variable follow-up. By fixed follow-up, hypoglycaemia results significantly or numerically favoured Gla-300. CONCLUSION: Among older adults with T2D, switching to Gla-300 versus Gla-100/IDet was associated with greater/similar improvements in glycaemic control, and generally less hypoglycaemia.

Video-Assisted Thoracoscopic Surgery for Pediatric Empyema by Two-Port Technique: A Single-Center Experience with 167 Consecutive Cases.

BACKGROUND/PURPOSE: The aim of our study is to determine efficacy, safety, and feasibility of video-assisted thoracoscopic surgery (VATS) in childhood empyema with a technique of only two ports and open instruments at a tertiary care center in India. METHODS: This is a retrospective study of patients below 18 years, with empyema presenting to the Department of Pediatric Surgery of a Tertiary Care Referral Hospital in India, over a period of 9 years who underwent VATS decortication. Only two ports with open surgical instruments were used. The patients were assessed on the basis of mean duration of preoperative symptoms, duration of surgery, average blood loss, postoperative pain relief, complications, and need for redo surgery. RESULTS: A total of 97 patients underwent primary VATS decortications without inserting an intercostal drainage (ICD) tube and 70 patients as a secondary procedure after ICD tube was inserted. Mean duration of symptoms was 11 days. The average blood loss during surgery was estimated to be 170 cc. The mean duration of surgery was 90 min. The most common postoperative complication was air leak seen in 19.16% of patients. Minor leaks usually settled by 24 h. In eight patients, a negative suction had to be applied to the ICD tube for persistent air leak. The average length of postoperative stay was 4 days. Two patients required a repeat open decortication procedure due to nonresolution of symptoms and poor lung expansion after VATS. Patients had minimal pain and excellent cosmetic outcome after VATS. CONCLUSION: Two-port VATS decortication procedure is as feasible and effective as three-port procedure for decortication with better cosmetic result and pain relief.

Cholinergic systems are essential for late-stage maturation and refinement of motor cortical circuits.

Previous studies reported that early postnatal cholinergic lesions severely perturb early cortical development, impairing neuronal cortical migration and the formation of cortical dendrites and synapses. These severe effects of early postnatal cholinergic lesions preclude our ability to understand the contribution of cholinergic systems to the later-stage maturation of topographic cortical representations. To study cholinergic mechanisms contributing to the later maturation of motor cortical circuits, we first characterized the temporal course of cortical motor map development and maturation in rats. In this study, we focused our attention on the maturation of cortical motor representations after postnatal day 25 (PND 25), a time after neuronal migration has been accomplished and cortical volume has reached adult size. We found significant maturation of cortical motor representations after this time, including both an expansion of forelimb representations in motor cortex and a shift from proximal to distal forelimb representations to an extent unexplainable by simple volume enlargement of the neocortex. Specific cholinergic lesions placed at PND 24 impaired enlargement of distal forelimb representations in particular and markedly reduced the ability to learn skilled motor tasks as adults. These results identify a novel and essential role for cholinergic systems in the late refinement and maturation of cortical circuits. Dysfunctions in this system may constitute a mechanism of late-onset neurodevelopmental disorders such as Rett syndrome and schizophrenia.

TGF-ß1-induced phospholamban expression alters esophageal smooth muscle cell contraction in patients with eosinophilic esophagitis.

BACKGROUND: Eosinophilic esophagitis (EoE) is a chronic antigen-mediated disease characterized by esophageal eosinophilia, remodeling, and fibrosis. TGF-ß1 is a central regulator of EoE remodeling and increases esophageal smooth muscle (ESM) cell contraction. OBJECTIVE: In this study we aimed to understand the molecular mechanisms by which TGF-ß1 could induce ESM cell contraction. METHODS: We used primary human ESM cells and esophageal myofibroblasts (EMFs) to assess the mechanisms of TGF-ß1-induced contraction. We analyzed the expression, phosphorylation, and function of phospholamban (PLN), a sarcoendoplasmic reticulum regulatory protein induced by TGF-ß1. Expression of PLN, phospho-PLN, and its regulatory pathway was analyzed in the ESM of biopsy specimens from patients with EoE and control subjects. Gene silencing in EMFs from patients with EoE was used to understand the role of PLN in contraction. RESULTS: TGF-ß1 induced and phosphorylated PLN in primary human ESM cells and EMFs from patients with EoE. PLN and phospho-PLN levels were increased in smooth muscle from patients with EoE compared with that seen in smooth muscle from control subjects in vivo. PLN inhibition significantly diminished TGF-ß1-induced EMF contraction in patients with EoE. PLN expression and ESM/EMF contraction depended on TGF-ß receptor I signals. CONCLUSION: We describe a previously unrecognized mechanism for ESM cell contraction that depends on TGF-ß1, its receptors, and PLN. Because PLN levels are increased in smooth muscle from patients with EoE and PLN silencing diminishes contraction, we provide a novel potential mechanistic framework and therapeutic target for ESM dysfunction in patients with EoE.

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

BACKGROUND: The rapid advancements in the field of genome sequencing are aiding our understanding on many biological systems. In the last five years, computational biologists and bioinformatics specialists have come up with newer, better and more efficient tools towards the discovery, analysis and interpretation of different genomic variants from high-throughput sequencing data. Availability of reliable simulated dataset is essential and is the first step towards testing any newly developed analytical tools for variant discovery. Although there are tools currently available that can simulate variants, none present the possibility of simulating all the three major types of variations (Single Nucleotide Polymorphisms, Insertions and Deletions and Copy Number Variations) and can generate reads taking a realistic error-model into consideration. Therefore, an efficient simulator and read generator is needed that can simulate variants taking the error rates of true biological samples into consideration. RESULTS: We report SInC (Snp, Indel and Cnv) an open-source variant simulator and read generator capable of simulating all the three common types of biological variants taking into account a distribution of base quality score from a most commonly used next-generation sequencing instrument from Illumina. SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes. CONCLUSIONS: We have come up with a user-friendly multi-variant simulator and read-generator tools called SInC. SInC can be downloaded from http://sourceforge.net/projects/sincsimulator.

Anti-IL-5 therapy reduces mast cell and IL-9 cell numbers in pediatric patients with eosinophilic esophagitis.

BACKGROUND: Eosinophilic esophagitis (EoE) is a clinicopathologic entity of increasing worldwide prevalence. IL-5 is essential for eosinophil trafficking, and anti-IL-5 therapy decreases esophageal eosinophilia. EoE is associated with prominent mast cell infiltration. OBJECTIVE: We investigated whether anti-IL-5 (mepolizumab) treatment reduced esophageal mast cell accumulation in biopsy specimens from pediatric patients with EoE from a previous randomized anti-IL-5 trial. METHODS: A subanalysis was completed for children treated with 0.55, 2.5, or 10 mg/kg mepolizumab monthly for 12 weeks followed by no treatment until week 24. Quantitative immunochemistry was used to assess the numbers of eosinophils, tryptase-positive mast cells, IL-9(+) cells, and mast cell-eosinophil couplets before and after treatment. RESULTS: Forty-three biopsy specimens had adequate tissue for paired analysis. Forty percent of subjects responded to anti-IL-5 (defined as <15 eosinophils per high-power field [hpf] after mepolizumab therapy), and 77% of all subjects had decreased numbers of mast cells after anti-IL-5. In responders epithelial mast cell numbers decreased from 62 to 19 per hpf (P < .001), were significantly lower than in nonresponders after therapy (P < .05), and correlated with eosinophil numbers (r = 0.75, P < .0001). Mast cells and eosinophils were found in couplets before therapy, and these were significantly decreased only in responders after anti-IL-5 (P < .001). Esophageal eosinophils comprised the majority of cells that made the mast cell growth factor IL-9. IL-9(+) cell numbers decreased from 102 to 71 per hpf (P < .001) after anti-IL-5. CONCLUSIONS: Pediatric patients with EoE had significantly fewer mast cells, IL-9(+) cells, and mast cell-eosinophil couplets in the esophageal epithelium after anti-IL-5 therapy. Because eosinophils were one source of IL-9, they might support esophageal mastocytosis.

Dysregulation of CD4+ and CD8+ resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis.

BACKGROUND: Colitis caused by checkpoint inhibitors (CPI) is frequent and is treated with empiric steroids, but CPI colitis mechanisms in steroid-experienced or refractory disease are unclear. METHODS: Using colon biopsies and blood from predominantly steroid-experienced CPI colitis patients, we performed multiplexed single-cell transcriptomics and proteomics to nominate contributing populations. RESULTS: CPI colitis biopsies showed enrichment of CD4+resident memory (RM) T cells in addition to CD8+ RM and cytotoxic CD8+ T cells. Matching T cell receptor (TCR) clonotypes suggested that both RMs are progenitors that yield cytotoxic effectors. Activated, CD38+ HLA-DR+ CD4+ RM and cytotoxic CD8+ T cells were enriched in steroid-experienced and a validation data set of steroid-naïve CPI colitis, underscoring their pathogenic potential across steroid exposure. Distinct from ulcerative colitis, CPI colitis exhibited perturbed stromal metabolism (NAD+, tryptophan) impacting epithelial survival and inflammation. Endothelial cells in CPI colitis after anti-TNF and anti-cytotoxic T-lymphocyte-associated antigen 4 (anti-CTLA-4) upregulated the integrin α4ß7 ligand molecular vascular addressin cell adhesion molecule 1 (MAdCAM-1), which may preferentially respond to vedolizumab (anti-α4ß7). CONCLUSIONS: These findings nominate CD4+ RM and MAdCAM-1+ endothelial cells for targeting in specific subsets of CPI colitis patients.

Citation classics in pediatric orthopaedics.

BACKGROUND: The purpose of this study was to identify the clinical pediatric orthopaedic articles with at least 100 citations published in all orthopaedic journals and to examine their characteristics. METHODS: All journals dedicated to orthopaedics and its subspecialties were selected from the Journal Citation Report 2001 under the subject category "orthopedics." Articles cited 100 times or more were identified using the database of the Science Citation Index Expanded (SCI-EXPANDED, 1900 to present). The articles were ranked in a comprehensive list. Two authors independently reviewed the full text of each article and applied the inclusion and exclusion criteria to the list of articles. The 2 lists were then compared. All disagreements were resolved by consensus with input from the senior author. The final list of pediatric orthopaedic articles was then compiled. RESULTS: There were a total of 49 journals under the search category "orthopedics." Five journals were excluded as they were non-English journals. The remaining 44 journals were screened for articles with at least 100 citations. A total of 135 clinical pediatric orthopaedic articles cited at least 100 times were included. The most cited article was cited 692 times. The mean number of citations per article was 159 (95% confidence interval, 145-173). All the articles were published between 1949 and 2001, with 1980 and 1989 producing the most citation classics (34). The majority (90) originated from the United States, followed by the United Kingdom (12) and Canada (11). Scoliosis/kyphosis was the most common topic with 26 papers. The second most common subject was hip disorders (24). Therapeutic studies were the most common study type (71). Ninety-seven papers were assigned a 4 for level of evidence. CONCLUSIONS: The list of citation classics in pediatric orthopaedic articles is useful for several reasons. It identifies important contributions to the field of pediatric orthopaedics and their originators; it facilitates the understanding and discourse of modern pediatric orthopaedic history and reveals trends in pediatric orthopaedics.

Casting for infantile scoliosis: the pitfall of increased peak inspiratory pressure.

BACKGROUND: Serial cast correction is a popular treatment option for progressive infantile scoliosis. Body casting can lead to chest and abdominal expansion restriction and result in decreased chest wall compliance. There are no studies evaluating the effects of casting on ventilation in infantile scoliosis. This study examines changes in peak inspiratory pressure (PIP) during serial casting for infantile scoliosis. METHODS: We retrospectively reviewed data obtained from 37 serial Cotrel elongation, derotation, and flexion cast corrections in patients with infantile scoliosis. Patient demographics, radiographic measurements, and anesthesia data were recorded. Anesthesia technique was standardized: children were intubated with rigid endotracheal tubes (ETTs); tidal volume was held constant at 8 to 10 cm(3)/kg using volume control ventilation; and PIP was recorded at baseline, after cast application before window cutout, and after window cutout before extubation. Any complications were documented. We assessed the PIP changes with a repeated measures analysis of variance (ANOVA). RESULTS: The mean age at first casting was 21.8 months (range, 12 to 42 mo) and mean follow-up since first casting was 22.4 months (range, 13 to 40 mo) with mean major Cobb angle of 53±15 degrees. The mean PIP was 15.5±4.9 cm H(2)O before casting, 31.9±7.9 cm H(2)O after cast application, and 20.4±5.6 cm H2O after making windows. There was a 106% increase after casting and 32% increase after window cutout from the baseline PIP levels. There was a significant difference in PIP on repeated measures ANOVA (P<0.0001). Intraoperatively, there was difficulty in maintaining ventilation during 2 procedures and 1 hypotensive episode. One patient developed hypoxemia after casting and another had delayed difficulty in breathing. CONCLUSIONS: Casting resulted in an increased PIP due to transient restrictive pulmonary process; after windows were cut out, the PIP reduced but not to baseline. In patients with underlying pulmonary disease, the casting process may induce respiratory complications, and a proper period of observation after casting is necessary. LEVEL OF EVIDENCE: Case series, level 4.

Flexion-extension cervical spine MRI in children with skeletal dysplasia: is it safe and effective?

BACKGROUND: Skeletal dysplasias may be associated with cervical spinal instability or stenosis. Cervical spine flexion-extension plain radiographs in children with skeletal dysplasia are difficult to interpret. The purpose of this study was to review the indications, efficacy, and safety of performing flexion-extension magnetic resonance imaging (MRI) under sedation/anesthesia in these children. METHODS: Retrospective, Institutional Review Board-approved review of 31 children with skeletal dysplasia who underwent 38 cervical spine flexion-extension MRI studies under sedation/anesthesia. Indications included abnormal neurological examination, suspected instability, stenosis, or inconclusive findings on flexion-extension radiographs. Studies were performed by the radiology technologist as directed by the radiologist with an anesthesiologist present. MRI was evaluated for odontoid hypoplasia, os odontoideum, cerebrospinal fluid effacement, cord compression, spinal cord changes, cervical canal narrowing in the neutral, flexion, and extension positions. Neurological examinations were recorded before and after MRI to assess safety. RESULTS: The average age at MRI was 3 years, 2 months. In 6 patients whose plain radiographs showed C1-C2 or subaxial instability, flexion-extension MRI showed no cord compression. Nine patients with inconclusive plain radiographs had abnormal MRI findings. An os odontoideum not seen on plain radiographs was diagnosed in 3 patients on flexion-extension MRI. On the basis of the MRI findings, 14 patients underwent surgery, 9/14 had increased cord compression in flexion or extension compared with neutral, and observation was continued in 17 others. Patients who underwent surgery had significant cord compression on MRI. There were no significant changes in the neurological examinations after MRI. CONCLUSIONS: Cervical spine flexion-extension MRI under sedation/anesthesia in children with skeletal dysplasia is safe under adequate supervision and is necessary to guide accurate medical and surgical decision making. Flexion-extension MRI is useful for identifying dynamic changes in canal diameter resulting in cord compression not seen on plain radiographs, and it is also useful for identifying patients with suspected plain film instability who may not have stenosis or cord compression on MRI. STUDY DESIGN: Level IV-retrospective case series.

Machine-guided path sampling to discover mechanisms of molecular self-organization.

Molecular self-organization driven by concerted many-body interactions produces the ordered structures that define both inanimate and living matter. Here we present an autonomous path sampling algorithm that integrates deep learning and transition path theory to discover the mechanism of molecular self-organization phenomena. The algorithm uses the outcome of newly initiated trajectories to construct, validate and-if needed-update quantitative mechanistic models. Closing the learning cycle, the models guide the sampling to enhance the sampling of rare assembly events. Symbolic regression condenses the learned mechanism into a human-interpretable form in terms of relevant physical observables. Applied to ion association in solution, gas-hydrate crystal formation, polymer folding and membrane-protein assembly, we capture the many-body solvent motions governing the assembly process, identify the variables of classical nucleation theory, uncover the folding mechanism at different levels of resolution and reveal competing assembly pathways. The mechanistic descriptions are transferable across thermodynamic states and chemical space.

Endogenous noise of neocortical neurons correlates with atypical sensory response variability in the Fmr1-/y mouse model of autism.

Excessive neural variability of sensory responses is a hallmark of atypical sensory processing in autistic individuals with cascading effects on other core autism symptoms but unknown neurobiological substrate. Here, by recording neocortical single neuron activity in a well-established mouse model of Fragile X syndrome and autism, we characterized atypical sensory processing and probed the role of endogenous noise sources in exaggerated response variability in males. The analysis of sensory stimulus evoked activity and spontaneous dynamics, as well as neuronal features, reveals a complex cellular and network phenotype. Neocortical sensory information processing is more variable and temporally imprecise. Increased trial-by-trial and inter-neuronal response variability is strongly related to key endogenous noise features, and may give rise to behavioural sensory responsiveness variability in autism. We provide a novel preclinical framework for understanding the sources of endogenous noise and its contribution to core autism symptoms, and for testing the functional consequences for mechanism-based manipulation of noise.

Effectiveness and Safety of Immune Checkpoint Inhibitors in Cancer Patients With Autoimmune Disease: A Retrospective Cohort Study.

Although immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, patients with pre-existing autoimmune diseases (PADs) have largely been excluded from clinical trials evaluating this drug class. This study evaluates the effectiveness and safety of ICI therapy in individuals with PAD in a real-world setting. A retrospective study of patients exposed to ICI therapy between 2012 and 2019 was conducted. Patients with PAD were identified and matched to an ICI-exposed group without PAD based on age, sex, and cancer type. Primary outcomes included toxicity, time to treatment failure, overall survival, and objective response rate. The association between PAD status and outcomes was determined using Cox and logistic regression modeling. A total of 813 patients exposed to ICI therapy were identified, of which 8.2% (N=67) had a PAD. When compared with a matched cohort without PAD (N=132), there was no significant difference in the rates of new immune-related adverse events (irAEs, 42.4% in the non-PAD group vs. 47.8% in the PAD group, P=0.474). After controlling for the type of ICI, there was no significant association between PAD status and irAE (odds ratio 1.67, 95% CI: 0.9-3.21 P=0.1). There was no significant association between overall survival and PAD status (hazard ratio 1.12, 95% CI: 0.76-1.66. P=0.56) or between time to treatment failure and PAD status (hazard ratio 0.82, 95% CI: 0.6-1.12, P=0.22). There was an association between PAD status and objective response rate (odds ratio 3.28, 95% CI: 1.28-8.38, P=0.013). In summary, PAD status was not associated with enhanced toxicity when compared with patients without PAD, with similar oncologic effectiveness between these 2 groups.

Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data.

In the past decade, high-dimensional single cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation which are computationally intense and difficult to evaluate and optimize. Here we present Cyclone, an analysis pipeline integrating dimensionality reduction, clustering, evaluation and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification, but also enables the unsupervised identification of lymphocytes and mononuclear phagocytes subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on variety of cytometry datasets which will further power immunology research and provide a scaffold for biological discovery.