bluuebunny/crossref_metadata_2025_split huggingface dataset:
Management of Five Hundred Patients With Gut Failure at a Single Center
Authors: Abu-Elmagd Kareem M. , Armanyous Sherif R. , Fujiki Masato , Parekh Neha R. , Osman Mohammed , Scalish Marissa , Newhouse Elizabeth , Fouda Yasser , Lennon Elizabeth , Shatnawei Abdullah , Kirby Donald , Steiger Ezra , Khanna Ajai , Radhakrishnan Kadakkal , Quintini Cristiano , Hashimoto Koji , Barnes Julie , Costa Guilherme 
Published: August 2019

Objective(s):
To define the evolving role of integrative surgical management including transplantation for patients gut failure (GF).

Methods:
A total of 500 patients with total parenteral nutrition-dependent catastrophic and chronic GF were referred for surgical intervention particularly transplantation and comprised the study population. With a mean age of 45 ± 17 years, 477 (95%) were adults and 23 (5%) were children. Management strategy was guided by clinical status, splanchnic organ functions, anatomy of residual gut, and cause of GF. Surgery was performed in 462 (92%) patients and 38 (8%) continued medical treatment. Definitive autologous gut reconstruction (AGR) was achievable in 378 (82%), primary transplant in 42 (9%), and AGR followed by transplant in 42 (9%). The 84 transplant recipients received 94 allografts; 67 (71%) liver-free and 27 (29%) liver-contained. The 420 AGR patients received a total of 790 reconstructive and remodeling procedures including primary reconstruction, interposition alimentary-conduits, intestinal/colonic lengthening, and reductive/decompressive surgery. Glucagon-like peptide-2 was used in 17 patients.

Results:
Overall patient survival was 86% at 1-year and 68% at 5-years with restored nutritional autonomy (RNA) in 63% and 78%, respectively. Surgery achieved a 5-year survival of 70% with 82% RNA. AGR achieved better long-term survival and transplantation better (P = 0.03) re-established nutritional autonomy. Both AGR and transplant were cost effective and quality of life better improved after AGR. A model to predict RNA after AGR was developed computing anatomy of reconstructed gut, total parenteral nutrition requirements, cause of GF, and serum bilirubin.

Conclusions:
Surgical integration is an effective management strategy for GF. Further progress is foreseen with the herein-described novel techniques and established RNA predictive model.
Laparoscopic Paraesophageal Hernia Repair and Pulmonary Embolism
Authors: Davila Daniel G. , Stetler Jamil L. , Lin Edward , Davis Steven Scott , Yheulon Christopher G. 
Published: August 2019

Objective:
Pulmonary embolism (PE) following laparoscopic paraesophageal hernia repair (PEHR) is rare but occurs at a higher frequency than other laparoscopic procedures. We describe a series of patients who developed PEs after PEHR in hopes of capturing potential risk factors for further study.

Materials and Methods:
Five cases of PE after PEHR were observed between 2017 and 2018. Individual and perioperative risk factors, and postoperative courses were reviewed.

Results:
Patients had a mean age of 73 years (range, 59 to 86). All were female. Two patients presented acutely. Three patients underwent revisional surgery. The average procedure duration was 248 minutes (range, 162 to 324). All patients had gastrostomy tubes placed. The diagnosis of PE occurred within 3 to 19 days postoperatively. Four were treated with 3 months of oral anticoagulation; 1 was managed expectantly.

Conclusions:
Highly complex cases, marked by revisional status, need for mesh, large hernia size, and percutaneous endoscopic gastrostomy placement are likely at increased risk for PEs. Preoperative venous thromboembolism chemoprophylaxis should be considered in the majority of laparoscopic PEHR patients.
Efficacy and Safety of Multiband Mucosectomy Versus Cap-assisted Endoscopic Resection For Early Esophageal Cancer and Precancerous Lesions: A Systematic Review and Meta-Analysis
Authors: Dan Xiang , Lv Xiu-He , San Zhi-Jie , Geng Sang , Wang Yan-Qiang , Li Shao-Hua , Xie Hua-Hong 
Published: August 2019

Background:
The effectiveness of multiband mucosectomy (MBM) for early esophageal cancer and precancerous lesions is still in uncertainty. We aimed to evaluate the efficacy and safety of this procedure and to compare it with cap-assisted endoscopic resection (EMR-cap).

Methods:
A systematic search of both English and Chinese databases was performed from inception to April 30, 2019. Complete resection rate, local recurrence rate, and procedure time were considered the primary outcome measures. Prevalence of complications was considered the secondary outcome measure. All data analyses were performed using Review Manager Software.

Results:
Two randomized controlled trials (RCTs) and 3 non-RCTs were included in the final meta-analysis. When compared with the EMR-cap technique, MBM had a similar complete resection rate [odds ratio (OR)=2.09, 95% confidence interval (CI): 0.78-5.60, P=0.14], a similar local recurrence rate (OR=0.50, 95% CI: 0.09-2.67, P=0.42), a shorter resection time (mean difference: −9.08, 95% CI: −13.86 to −4.30, P=0.0002), a shorter procedure time (mean difference: −13.36, 95% CI: −17.85 to −8.86, P<0.00001), a lower bleeding rate (OR=0.45, 95% CI: 0.24-0.83, P=0.01), a similar perforation rate (OR=0.55, 95% CI: 0.15-2.06, P=0.37), and a similar stricture rate (OR=0.77, 95% CI: 0.10-5.84, P=0.80). The results of non-RCTs were consistent with those of RCTs.

Conclusions:
MBM is similar to EMR-cap in terms of efficacy and safety for endoscopic resection of early cancer and precancerous lesions of the esophagus. However, MBM is less time-consuming.
Systemic Commitments of the Context-Dependency; Basics of Elementary Coordination in Circadian Cycles
Authors: Park Chulwook 
Published: August 2019

AbstractThe present study was attempted to measure whether the dynamics of elementary coordination is influenced by an overarching temporal structure that is embedded in circadian rhythms (part 1) as well as the systemic proof associated with the intelligent capabilities (part 2). For part 1, evidence of entrainment or any influence of the embedding rhythm were examined on the stability or attractor location. The estimations from the dynamics of the relative phase between the two oscillations show that while (i) circadian effects under the artificially perturbed manipulation were not straightforward along the day-night temperature cycle, (ii) the circadian effect divided by the ordinary circadian seems to be constant along the day-night cycle. Corresponding to this evidence related to performance consequences depending on the organism and environmental interaction, the part 2 determined the impact of circadian (mis)alignment on biological functions and raised the possibility that the disruption of circadian systems may contribute to physical complications. The observations entail rules that self-attunement of current performance may develop not at a single component but across many nested, inter-connected scales. These inter-dependencies from different object phase may allow a potential context-dependent explanation for goal-oriented movements and the emergent assumption of a principle of organisms embedded into their environmental contexts.
Frequency specific network effective connectivity: ERP analysis of recognition memory process by directed connectivity estimators
Authors: Bayazi Mohammad Javad Darvishi , Nasrabadi Ali Motie , Curran Tim 
Published: August 2019

AbstractVarious processes occur in memory retrieval in recognition memory and it is necessary to investigate memory brain function. Most of the research in past decades have focused on particular brain region function, but the interaction between these has a major role in human cognition. In this study, we used the memory retrieval task to investigate the underlying mechanism of recognition memory. The connectivity between brain regions is estimated from scalp electroencephalography signals that were recorded from twenty-three healthy subject participated in recognition memory task to correctly classify old/new words. Multivariate autoregressive models (MVAR) are used for the determination of Granger causality to estimate the effective connectivity in the time-frequency domain. We use GPDC and dDTF methods because they have almost resolved the previous problems in estimations. Results show that brain regions in the old condition have greater global connectivity in the theta and gamma band compared to the new words retrieval. Connectivity within and between the brain’s hemisphere may be related to correct rejection. The left frontal has a crucial role in recollection. theta and gamma specific connectivity pattern between temporal, parietal and frontal cortex may disclose the retrieval mechanism. old/new comparison resulted in the different patterns of network connection. These results and other evidence emphasize the role of frequency of causal network interactions in the memory process.
A Targeted Mass Spectrometry Approach to detect and quantify Oxidised Phospholipids in plasma samples of Diabetic patients
Authors: Thakker Alpesh , Spickett Corinne M , Pitt Andrew 
Published: August 2019

AbstractPhospholipid oxidation by adventitious damage generates a wide variety of products with potentially novel biological activities that can modulate inflammatory processes associated with various diseases such as atherosclerosis, acute Pancreatitis and Type 2 diabetes. To understand the biological importance of oxidised phospholipids (OxPL) and their potential role as disease biomarkers requires precise information about the abundance of these compounds in cells and tissues. There are many chemiluminescence and spectroscopic assays available for detecting oxidised phospholipids, but they all have some limitations. Mass spectrometry coupled with liquid chromatography is a powerful and sensitive approach but its application to complex biological samples remains challenging.The aim of this work was to develop improved methods for detection of OxPLs, specifically by using targeted mass spectrometry approaches (precursor ion [PIS] and neutral loss [NL] scanning), high resolution mass spectrometry and alternative chromatographic approaches. Initial experiments were carried out using oxidation products generated in vitro from a commercially available phosphatidylcholine (PC) and phosphatidylethanolamine (PE) mixture in order to optimise the chromatography separation parameters and mass spectrometry parameters. The chromatographic separation of oxidised phosphatidylcholines (OxPCs) and oxidised phosphatidylethanolamines (OXPEs) was evaluated using C8, C18 and C30 reverse phase, polystyrene – divinylbenzene based monolithic and mixed – mode hydrophilic interaction (HILIC) columns, interfaced with mass spectrometry. Our results suggest that the divinylbenzene based reverse phase monolithic column gave best separation of short chain OxPCs and OxPEs from long chain oxidised and native PCs and PEs.Targeted mass spectrometric approaches for the selective identification of short chain OxPCs using PIS for m/z 184 Da and NL for m/z 34 Da for identification of hydroperoxides were tested on OxPC mixture, it enabled identification of low abundant oxidation products such as: γ-hydroxy alkenals and alkenoates and saturated aldehydes collectively termed as “short - chain oxidation products” such as PONPC, POVPC and HOOA-PC. The combination of these chromatographic and MS methods allowed identification of several oxidised molecular species in plasma of diabetic patients. Quantitative differences in oxidised products were observed in diabetic samples and the trend showed high abundance of oxidised phosphatidylcholine species in diabetic samples, compared to healthy plasma samples. However, the difference in abundance was statistically not significant when the samples were analysed using Progenesis QI software, performing global normalisation and ANOVA analysis because of inherent biological variability observed for OxPC species in samples.
Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation
Authors: Flores-Tinoco Carlos Eduardo , Christen Matthias , Christen Beat 
Published: August 2019

Biological nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds a significant promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of nitrogen-fixing organisms is to identify the metabolic blueprint for symbiotic nitrogen fixation. Here, we report on the CATCH-N cycle, a novel metabolic network based on co-catabolism of plant-provided arginine and succinate to drive the energy-demanding process of symbiotic nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle shares aspects with plant mitochondrial arginine degradation path-way. However, it uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of nitrogen than classical arginine catabolism — two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a specific mechanism to sustain bacterial metabolism in the microoxic and acid environment of symbiosomes. In sum, our systems-level findings provide the theoretical framework and enzymatic blueprint for the rational design of plants and plant-associated organisms with new properties for improved nitrogen fixation.Significance StatementSymbiotic bacteria assimilate nitrogen from the air and fix it into a form that can be used by plants in a process known as biological nitrogen fixation. In agricultural systems, this process is restricted mainly to legumes, yet there is considerable interest in exploring whether similar symbioses can be developed in non-legumes including cereals and other important crop plants. Here we present systems-level findings on the minimal metabolic function set for biological nitrogen fixation that provides the theoretical framework for rational engineering of novel organisms with improved nitrogen-fixing capabilities.
Phosphoinositide-binding proteins mark, shape and functionally modulate highly-diverged endocytic compartments in the parasitic protistGiardia lamblia
Authors: Cernikova Lenka , Faso Carmen , Hehl Adrian B. 
Published: August 2019

AbstractPhosphorylated derivatives of phosphatidylinositol (PIPs), are key membrane lipid residues involved in clathrin-mediated endocytosis (CME). CME relies on PI(4,5)P2 to mark endocytic sites at the plasma membrane (PM) associated to clathrin-coated vesicle (CCV) formation. The highly diverged parasitic protistGiardia lambliapresents disordered and static clathrin assemblies at PM invaginations, contacting specialized endocytic organelles called peripheral vacuoles (PVs). The role for clathrin assemblies in fluid phase uptake and their link to internal membranes via PIP-binding adaptors is unknown.Here we provide evidence for a robust link between clathrin assemblies and fluid-phase uptake inG. lambliamediated by proteins carrying predicted PX, FYVE and NECAP1 PIP-binding modules. We show that chemical and genetic perturbation of PIP-residue binding and turnover elicits novel uptake and organelle-morphology phenotypes. A combination of co-immunoprecipitation andin silicoannotation techniques expands the initial PIP-binding network with addition of new members. Our data indicate that, despite the partial conservation of lipid markers and protein cohorts known to play important roles in dynamic endocytic events in well-characterized model systems, theGiardialineage presents a strikingly divergent clathrin-centered network. This includes several PIP-binding modules, often associated to domains of currently unknown function that shape and modulate fluid-phase uptake at PVs.
fMRI detects bilateral brain network activation following unilateral chemogenetic activation of direct striatal projection neurons
Authors: Nakamura Yuki , Nakamura Yukari , Pelosi Assunta , Djemai Boucif , Debacker Clément , Hervé Denis , Girault Jean-Antoine , Tsurugizawa Tomokazu 
Published: August 2019

AbstractAlthough abnormal structural and functional connectivity in the striatum during neurological disorders has been reported using functional magnetic resonance imaging (fMRI), the effects of cell-type specific neuronal stimulation on fMRI and related behavioral alterations are not well understood. In this study, we successfully combined DREADD-technology with fMRI (chemo-fMRI) to investigate the alterations of spontaneous neuronal activity induced by the unilateral activation of dopamine D1 receptor-expressing neurons (D1-neurons) in the mouse dorsal striatum (DS). We compared the effects of two different DREADD ligands, clozapine (CLZ) and clozapine-N-oxide (CNO), on behavior and fMRI. We found that the effects of CLZ on behavior were more rapid than those of CNO. In fMRI, both systemic CLZ and CNO administrations, which evoked unilateral activations of D1-neurons in DS, increased the fractional amplitude of low frequency fluctuations (fALFF) in the thalamus and bilateral cortex. In addition, we found the increased gamma-band of local field potentials in DS and bilateral cortex after CLZ-evoked unilateral activation of D1-neuron in the striatum. These results provide bases for better interpretation of cell type-specific activity changes in fMRI.
Leveraging shared connectivity to aggregate heterogeneous datasets into a common response space
Authors: Nastase Samuel A. , Liu Yun-Fei , Hillman Hanna , Norman Kenneth A. , Hasson Uri 
Published: August 2019

AbstractConnectivity hyperalignment can be used to estimate a single shared response space across disjoint datasets. We develop a connectivity-based shared response model that factorizes aggregated fMRI datasets into a single reduced-dimension shared connectivity space and subject-specific topographic transformations. These transformations resolve idiosyncratic functional topographies and can be used to project response time series into shared space. We evaluate this algorithm on a large collection of heterogeneous, naturalistic fMRI datasets acquired while subjects listened to spoken stories. Projecting subject data into shared space dramatically improves between-subject story time-segment classification and increases the dimensionality of shared information across subjects. This improvement generalizes to subjects and stories excluded when estimating the shared space. We demonstrate that estimating a simple semantic encoding model in shared space improves between-subject forward encoding and inverted encoding model performance. The shared space estimated across all datasets is distinct from the shared space derived from any particular constituent dataset; the algorithm leverages shared connectivity to yield a consensus shared space conjoining diverse story stimuli.HighlightsConnectivity SRM estimates a single shared space across subjects and stimuliTopographic transformations resolve idiosyncrasies across individualsShared connectivity space enhances spatiotemporal intersubject correlationsSemantic model-based encoding and decoding improves across subjectsTransformations project into a consensus space conjoining diverse stimuli
Evoked and spontaneous pain assessment during tooth pulp injury
Authors: Rossi Heather Lynn , See Lily Pachanin , Foster William , Pitake Saumitra , Gibbs Jennifer , Schmidt Brian , Mitchell Claire H. , Abdus-Saboor Ishmail 
Published: August 2019

AbstractInjury of the tooth pulp is excruciatingly painful and yet the receptors and neural circuit mechanisms that transmit this form of pain remain poorly defined in both the clinic and preclinical rodent models. Easily quantifiable behavioral assessment in the rodent orofacial area remains a major bottleneck in uncovering molecular mechanisms that govern inflammatory pain in the tooth. Here we use a dental pulp injury model in the mouse and expose the tooth pulp to the outside environment, a procedure we have previously shown produces pulpal inflammation. We demonstrate here with RNAscope technology in the trigeminal ganglion of injured mice, an upregulation of genes that contribute to the inflammatory pain state. Using both evoked and spontaneous measures of pain in the orofacial area, including application of von Frey Hair filaments and pain feature detection with the mouse grimace scale, we reveal a differential timeline of induction of spontaneous pain versus mechanical allodynia following pulpal injury. This work demonstrates that tooth pain can be easily assessed in freely behaving mice using approaches common for other types of pain assessment. Harnessing these assays in the orofacial area during gene manipulation should assist in uncovering mechanisms for tooth pulp inflammation and other forms of trigeminal pain.
Copy-number variation contributes 9% of pathogenicity in the inherited retinal degenerations
Authors: Zampaglione Erin , Kinde Benyam , Place Emily M. , Navarro-Gomez Daniel , Maher Matthew , Jamshidi Farzad , Nassiri Sherwin , Mazzone J. Alex , Finn Caitlin , Schlegel Dana , Comander Jason , Pierce Eric A. , Bujakowska Kinga M. 
Published: August 2019

ABSTRACTPurposeCurrent sequencing strategies can genetically solve 55-60% of inherited retinal degeneration (IRD) cases, despite recent progress in sequencing. This can partially be attributed to elusive pathogenic variants (PVs) in known IRD genes, including copy number variations (CNVs), which we believe are a major contributor to unsolved IRD cases.MethodsFive hundred IRD patients were analyzed with targeted next generation sequencing (NGS). The NGS data was used to detect CNVs with ExomeDepth and gCNV and the results were compared to CNV detection with a SNP-Array. Likely causal CNV predictions were validated by quantitative (q)PCR.ResultsLikely disease-causing single nucleotide variants (SNVs) and small indels were found in 55.8% of subjects. PVs in USH2A (11.6%), RPGR (4%) and EYS (4%) were the most common. Likely causal CNVs were found in an additional 8.8% of patients. Of the three CNV detection methods, gCNV showed the highest accuracy. Approximately 30% of unsolved subjects had a single likely PV in a recessive IRD gene.ConclusionsCNV detection using NGS-based algorithms is a reliable method that greatly increases the genetic diagnostic rate of IRDs. Experimentally validating CNVs helps estimate the rate at which IRDs might be solved by a CNV plus a more elusive variant.