A protein identification method for proteomics using amino acid composition analysis with IoT-based remote control.

In the present study, we developed a protein identification method using low-cost and easy-to-operate amino acid composition analysis. The identification program automatically compares the quantitative result for each amino acid concentration obtained from the amino acid analysis to the amino acid composition data retrieved from the UniProt protein database. We found that the accuracy of protein identification using amino acid composition analysis was comparable to that of mass spectrometry analysis. The method was able to distinguish and identify differences in amino acid substitutions of several residues between proteins with high sequence homology. The identification accuracy of proteins was also improved by correcting the concentrations in the program for Cys, Trp, and Ile residues, which cannot be quantified by general sample preparation for amino acid analysis. Moreover, the amino acid analyzer was remotely controlled in accordance with the growing demand for remote work. The measured amino acid data were automatically uploaded to the IoT portal within a few minutes of each measurement, allowing researchers to download data and analyze them using the identification program anywhere and at any time by connecting to a network. The results indicated that the present method is useful for protein identification.

Machine learning prediction of hematoma expansion in acute intracerebral hemorrhage.

To examine whether machine learning (ML) approach can be used to predict hematoma expansion in acute intracerebral hemorrhage (ICH) with accuracy and widespread applicability, we applied ML algorithms to multicenter clinical data and CT findings on admission. Patients with acute ICH from three hospitals (n = 351) and those from another hospital (n = 71) were retrospectively assigned to the development and validation cohorts, respectively. To develop ML predictive models, the k-nearest neighbors (k-NN) algorithm, logistic regression, support vector machines (SVMs), random forests, and XGBoost were applied to the patient data in the development cohort. The models were evaluated for their performance on the patient data in the validation cohort, which was compared with previous scoring methods, the BAT, BRAIN, and 9-point scores. The k-NN algorithm achieved the highest area under the receiver operating characteristic curve (AUC) of 0.790 among all ML models, and the sensitivity, specificity, and accuracy were 0.846, 0.733, and 0.775, respectively. The BRAIN score achieved the highest AUC of 0.676 among all previous scoring methods, which was lower than the k-NN algorithm (p = 0.016). We developed and validated ML predictive models of hematoma expansion in acute ICH. The models demonstrated good predictive ability, showing better performance than the previous scoring methods.

Relationship of brain edema after deep brain stimulation surgery with motor and cognitive function.

Background: Some patients with Parkinson's disease (PD) develop peri-lead brain edema after deep brain stimulation (DBS) surgery. The influence of edema on neurological function is not well characterized. We investigated the relationship of brain edema after DBS surgery with motor and cognitive function. Methods: Thirteen patients with PD (6 males and 7 females; mean age: 61.2 years) who underwent bilateral subthalamic nucleus (STN) DBS surgery were included. All patients underwent magnetic resonance imaging (MRI) examination on day 6 post-DBS surgery. The volume of edema was measured either in the frontal white matter or STN on fluid attenuated inversion recovery (FLAIR) images. We examined the relationship between these volumes and changes in cognitive and motor function. Results: Patients were divided into those with frontal subcortical edema (FE) ≥3,000 mm3 (FE + group; n = 7) and <3,000 mm3 (FE-group; n = 6). In the FE + group, the postoperative Mini-Mental State Examination score worsened by 2.4 points after one week compared with that immediately before surgery, while that in the FE-group worsened only by 0.2 points (p = 0.038). On comparing patients with peri-STN edema (SE) ≥1,000 mm3 (SE + group; n = 3) and those with SE < 1,000 mm3 (SE-group; n = 10) showed that frequency of DBS tuning in the early postoperative period of the SE + group was lesser than that in the SE-group. Conclusions: Development of FE after DBS surgery was related to transient cognitive decline. On the other hand, SE seemed associated with altered motor function and reduces the requirement for tuning in the initial period after DBS implantation.

Deep Brain Stimulation in a Patient with Parkinson's Disease and Cortical Superficial Siderosis.

Cortical superficial siderosis (cSS) is a rare condition that is regarded as a potential magnetic resonance marker of cerebral amyloid angiopathy (CAA). We describe the case of a 68-year-old man with cSS and Parkinson's disease (PD) who subsequently exhibited incidental microhemorrhages, which were only detected on magnetic resonance imaging (MRI), at one week after deep brain stimulation (DBS) surgery. cSS is now considered to be a significant risk factor for CAA and future bleeding. Therefore, because DBS surgery is invasive and may increase the risk of intracerebral hemorrhage, the procedure should be performed carefully when managing patients with PD and CAA.

Dissipative Kerr soliton microcombs for FEC-free optical communications over 100 channels.

The demand for high-speed and highly efficient optical communication techniques has been rapidly growing due to the ever-increasing volume of data traffic. As well as the digital coherent communication used for core and metro networks, intensity modulation and direct detection (IM-DD) are still promising schemes in intra/inter data centers thanks to their low latency, high reliability, and good cost performance. In this work, we study a microresonator-based frequency comb as a potential light source for future IM-DD optical systems where applications may include replacing individual stabilized lasers with a continuous laser driven microresonator. Regarding comb line powers and spectral intervals, we compare a modulation instability comb and a soliton microcomb and provide a quantitative analysis with regard to telecom applications. Our experimental demonstration achieved a forward error correction (FEC) free operation of bit-error rate (BER) <10-9 with a 1.45 Tbps capacity using a total of 145 lines over the entire C-band and revealed the possibility of soliton microcomb-based ultra-dense wavelength division multiplexing (WDM) with a simple, cost-effective IM-DD scheme, with a view to future practical use in data centers.

Novel Transdural Epiarachnoid Approach for Large Central Disk Herniation in Upper Lumbar Spine.

BACKGROUND AND IMPORTANCE: The treatment for large central disk herniation (LCDH) at upper lumbar spine is often challenging. Previous reports showed various surgical strategies, such as microdiscectomy with posterior fixation, endoscopic surgery, and microdiscectomy through transdural approach. However, there is no consensus regarding which surgical option is better for LCDH at upper lumbar spine. In this report, we describe the novel transdural epiarachnoid approach (TDEA), which uses the corridor of epiarachnoid space for microdiscectomy. Compared with classical transdural approaches, this novel approach may reduce risks of postoperative cerebrospinal fluid leakage and the development of arachnoiditis. CLINICAL PRESENTATION: A 69-yr-old man presented with progressive bilateral radiating leg pain, intermittent claudication, and low back pain. Magnetic resonance images and computed tomography scans revealed LCDH at L2/3 level. We performed microdiscectomy using the TDEA. Postoperative course was uneventful, and his symptoms were relieved after surgery. CONCLUSION: The novel TDEA for LCDH at upper lumbar spine is illustrated with a video. This novel approach has an advantage of the preservation of subarachnoid components compared with classical transdural approaches.

Stereospecificity of hydride transfer and molecular docking in FMN-dependent NADH-indigo reductase of Bacillus smithii.

In this study, we investigated the stereospecificity of hydride transfer from NADH to flavin mononucleotide (FMN) in reactions catalyzed by the FMN-dependent NADH-indigo reductase expressed by thermophilic Bacillus smithii. We performed 1 H-NMR spectroscopy using deuterium-labeled NADH (4R-2 H-NADH) and molecular docking simulations to reveal that the pro-S hydrogen at the C4 position of the nicotinamide moiety in NADH was specifically transferred to the flavin-N5 atom of FNM. Altogether, our findings may aid in the improvement of the indigo dyeing (Aizome) process.

On-chip photon-pair generation in a silica microtoroidal cavity.

Microcavities with high Q factor and small mode volume have the potential to be efficient and compact sources of photon pairs. Here, we demonstrate on-chip photon-pair generation by spontaneous four-wave mixing in a silica microtoroidal cavity and obtain a coincidence-to-accidental ratio of 7.4 ± 0.1 with a pump power of 46 µW. The heralded photons also exhibit antibunching characterized by autocorrelation function values of gc(2)(0)=0.57±0.03<1. Comparing with a scaling model, the main noise source is found to be spontaneous Raman scattering in the cavity. This work opens a new possible means for realizing integrated nonclassical photon sources based on silica photonic circuits toward scalable quantum technologies.

Catalytic properties and crystal structure of UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase from Phytophthora infestans.

We report, for the first time, the three-dimensional structure and biochemical properties of a UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase (GalE-like L-ThrDH) from Phytophthora infestans, a plant disease-causing fungus. We identified GalE-like L-ThrDH using Kyoto Encyclopedia of Genes and Genomes (KEGG) database as a candidate target for the development of a new fungicide. The GalE-like L-ThrDH gene was expressed in Escherichia coli, and its product was purified and characterized. N-Acetylglycine was found to act as a competitive inhibitor of the enzyme (Ki =0.18 mM). The crystal structure of the unique hexameric GalE-like L-ThrDH was determined using the molecular replacement method at a resolution of 2.3 Å, in the presence of NAD+ and citrate, an analogue of the substrate. Based on the molecular docking simulation, N-acetylglycine molecule was modeled into the active site and the binding mode and inhibition mechanism of N-acetylglycine were elucidated.

Structural and biochemical characterization of an extremely thermostable FMN-dependent NADH-indigo reductase from Bacillus smithii.

The FMN-dependent NADH-indigo reductase gene from the thermophilic bacterium Bacillus smithii was overexpressed in Escherichia coli. The expressed enzyme functioned as a highly thermostable indigo reductase that retained complete activity even after incubation at 100 °C for 10 min. Furthermore, B. smithii indigo reductase exhibited high stability over a wider pH range and longer storage periods compared with indigo reductases previously identified from other sources. The enzyme catalyzed the reduction of various azo compounds and indigo carmine. The crystal structures of the wild-type enzyme in complex with FMN/N-cyclohexyl-2-aminoethanesulfonate (CHES) and the Y151F mutant enzyme in complex with FMN were determined by the molecular replacement method and refined at resolutions of 1.97 and 1.95 Å, respectively. Then, indigo carmine molecule was modeled into the active site using the molecular docking simulation and the binding mode of indigo carmine was elucidated. In addition, the structure of B. cohnii indigo reductase, which is relatively less stable than B. smithii indigo reductase, was constructed by homology modeling. The factor contributing to the considerably higher thermostability of B. smithii indigo reductase was analyzed by comparing its structure with that of B. cohnii indigo reductase, which revealed that intersubunit aromatic interactions (F105-F172' and F172-F105') may be responsible for the high thermostability of B. smithii indigo reductase. Notably, site-directed mutagenesis results showed that F105 plays a major role in the intersubunit aromatic interaction.

Systematic identification of genes regulating synaptic remodeling in the Drosophila visual system.

In many animals, neural activity contributes to the adaptive refinement of synaptic properties, such as firing frequency and the number of synapses, for learning, memorizing and adapting for survival. However, the molecular mechanisms underlying such activity-dependent synaptic remodeling remain largely unknown. In the synapses of Drosophila melanogaster, the presynaptic active zone (AZ) forms a T-shaped presynaptic density comprising AZ proteins, including Bruchpilot (Brp). In a previous study, we found that the signal from a fusion protein molecular marker consisting of Brp and mCherry becomes diffuse under continuous light over three days (LL), reflecting disassembly of the AZ, while remaining punctate under continuous darkness. To identify the molecular players controlling this synaptic remodeling, we used the fusion protein molecular marker and performed RNAi screening against 208 neuron-related transmembrane genes that are highly expressed in the Drosophila visual system. Second analyses using the STaR (synaptic tagging with recombination) technique, which showed a decrease in synapse number under the LL condition, and subsequent mutant and overexpression analysis confirmed that five genes are involved in the activity-dependent AZ disassembly. This work demonstrates the feasibility of identifying genes involved in activity-dependent synaptic remodeling in Drosophila, and also provides unexpected insight into the molecular mechanisms involved in cholesterol metabolism and biosynthesis of the insect molting hormone ecdysone.

Role of Computational Fluid Dynamics for Predicting Delayed Cerebral Ischemia After Aneurysmal Subarachnoid Hemorrhage: Study Protocol for a Multicenter Prospective Study.

BACKGROUND: Delayed cerebral ischemia (DCI) is a significant cause of morbidity and mortality after aneurysmal subarachnoid hemorrhage (SAH). Recently, we reported the possibility that computational fluid dynamics (CFD) could predict DCI in terms of the cross-sectional area and flow velocity of the ipsilateral extracranial internal carotid and distal parent arteries in a single-center retrospective study. METHODS: This is a multicenter, prospective, cohort study. Patients with aneurysmal SAH will undergo CFD analyses using preoperative three-dimensional computed tomography angiography, and we will investigate hemodynamic features of cerebral arteries in an acute stage of SAH. Primary outcome measures will be CFD features in patients with subsequent occurrence of DCI. Secondary outcome measures will be CFD features in patients with subsequent occurrence of cerebral vasospasm and cerebral infarction and the relationships with eventual modified Rankin scale score at 3 months. CONCLUSIONS: The present protocol for a multicenter prospective study is expected to provide a novel diagnostic method to predict DCI before aneurysmal obliteration in an acute stage of SAH.

Low Pulvinar Intensity in Susceptibility-Weighted Imaging May Suggest Cognitive Worsening After Deep Brain Stimulation Therapy in Patients With Parkinson's Disease.

Purpose: Deep brain stimulation (DBS) is an established therapy for Parkinson's disease (PD). However, deteriorating cognitive function after DBS is a considerable problem for affected patients. This study was undertaken to assess whether pulvinar findings in susceptibility-weighted imaging (SWI) can suggest cognitive worsening. Methods: We examined 21 patients with PD who underwent DBS along with SWI and neuromelanin-sensitive MR imaging (NMI). We further assessed pulvinar hypointensity based on the SWI findings and also the area of the substantia nigra (SN) pars compacta in NMI. We then examined associations among cognitive changes, pulvinar hypointensity, and SN area. The cognitive function of the patient immediately before surgery was compared with function at 1 year postoperatively. Results: Pulvinar hypointensity in SWI was found in 11 of 21 patients with PD at baseline. One year postoperatively, six of the 21 patients demonstrated a Mini-Mental State Examination score that was ≥3 points lower than the baseline score. We observed pulvinar hypointensity in SWI before DBS surgery in five of these six patients (p = 0.072). During the first postoperative year, six of 21 patients reported both transient or permanent hallucinations; we observed pulvinar hypointensity in these six patients, while 10 patients without pulvinar hypointensity had no hallucinations. Conclusion: Pulvinar hypointensity in SWI in patients with PD may provide information that is useful for suggesting cognitive deterioration after DBS treatment.

Cell surface molecule, Klingon, mediates the refinement of synaptic specificity in the Drosophila visual system.

In the Drosophila brain, neurons form genetically specified synaptic connections with defined neuronal targets. It is proposed that each central nervous system neuron expresses specific cell surface proteins, which act as identification tags. Through an RNAi screen of cell surface molecules in the Drosophila visual system, we found that the cell adhesion molecule Klingon (Klg) plays an important role in repressing the ectopic formation of extended axons, preventing the formation of excessive synapses. Cell-specific manipulation of klg showed that Klg is required in both photoreceptors and the glia, suggesting that the balanced homophilic interaction between photoreceptor axons and the glia is required for normal synapse formation. Previous studies suggested that Klg binds to cDIP and our genetic analyses indicate that cDIP is required in glia for ectopic synaptic repression. These data suggest that Klg play a critical role together with cDIP in refining synaptic specificity and preventing unnecessary connections in the brain.

One-stage Stent-assisted Coil Embolization for Rupture-side-unknown Bilateral Vertebral Artery Dissecting Aneurysms in an Acute Stage: A Case Report.

Bilateral vertebral artery dissecting aneurysms (VADAs) with subarachnoid hemorrhage (SAH) are rare and their management is still challenging. In this report, we successfully performed one-stage stent-assisted coil embolization (SAC) for bilateral VADAs with SAH in an acute stage, because the ruptured side could not be diagnosed. A 47-year-old woman presented with a sudden onset of headache without laterality, and left-side dominant SAH with bilateral VADAs was noted on computed tomography (CT) scans. The size of aneurysmal dome and neck was similar between the two VADAs, and a bleb was observed only on the right VADA. In computational fluid dynamics (CFD) simulations, findings of wall shear stress (WSS), normalized WSS, and WSS gradient suggested that the left VADA was ruptured, while the oscillatory shear index and aneurysm formation indicator suggested the opposite-side one to be ruptured. Thus, we could not determine which VADA was ruptured by clinical data and CFD analyses. Therefore, we performed simultaneous treatment for the bilateral VADAs by using SAC technique 8 h after the onset under dual antiplatelet and anticoagulation therapies. There was no evidence of rebleeding and stent thrombosis. Stent thrombosis was monitored by duplex color-coded ultrasonography after the intervention. She was discharged without neurological deficits, and 6-month follow-up cerebral angiography demonstrated no recanalization of VADAs. This is the first report showing bilateral VADAs with SAH treated by one-stage SAC within 24 h of SAH, and the potential risks are discussed.

Crystal structure of the NADP+ and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.

A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa L-SerDH. The overexpressed enzyme appears to be the most thermostable L-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 °C. The enzyme showed substantial reactivity towards D-serine, in addition to L-serine. Two different crystal structures of P. calidifontis L-SerDH were determined using the Se-MAD and MR method: the structure in complex with NADP+/sulfate ion at 1.18 Å and the structure in complex with NADP+/L-tartrate (substrate analog) at 1.57 Å. The fold of the catalytic domain showed similarity with that of Ps. aeruginosa L-SerDH. However, the active site structure significantly differed between the two enzymes. Based on the structure of the tartrate, L- and D-serine and 3-hydroxypropionate molecules were modeled into the active site and the substrate binding modes were estimated. A structural comparison suggests that the wide cavity at the substrate binding site is likely responsible for the high reactivity of the enzyme toward both L- and D-serine enantiomers. This is the first description of the structure of the novel type of L-SerDH with bound NADP+ and substrate analog, and it provides new insight into the substrate binding mechanism of L-SerDH. The results obtained here may be very informative for the creation of L- or D-serine-specific SerDH by protein engineering.

[Pontine Hemorrhage Suspected due to Dural Arteriovenous Fistula at the Craniocervical Junction:A Case Report].

Dural arteriovenous fistulas occurring at the craniocervical junction(CCJd-AVF)are uncommon; however, they demonstrate a wide range of clinical presentations. We describe the case of a patient with pontine hemorrhage suspected due to CCJd-AVF. A 68-year-old man presented to our hospital with a sudden onset of left hemiparesis. Cranial computed tomography(CT)revealed pontine and subarachnoid hemorrhage. Magnetic resonance imaging, as well as MR, CT, and left vertebral angiograms were performed and showed a CCJd-AVF in addition to a varix coincident with the hematoma cavities. The patient was successfully treated using surgical drainer clipping. A CCJd-AVF presenting concomitantly with a pontine hemorrhage is extremely rare. Careful assessment of the anatomical relationship between the skull base and the surrounding vascular structures is important to plan neurosurgical procedures for direct interruption of the draining vein. Three-dimensional CT angiography is a useful modality that facilitates visualization of complex and anomalous anatomical structures.

Antimicrobial effects of novel peptides cOT2 and sOT2 derived from Crocodylus siamensis and Pelodiscus sinensis ovotransferrins.

In light of the increasing threat of bacterial drug resistance to human health on a global scale, research and development of antimicrobial peptides as a novel class of potent antibiotics has gained considerable attention. The present study focuses on the structural evaluation and membrane interaction of two new cationic antimicrobial peptides, cOT2 and sOT2, derived from Siamese crocodile (Crocodylus siamensis) and Chinese softshell turtle (Pelodiscus sinensis) ovotransferrins. Here, cOT1 (+3) and sOT1 (+3) were derived from reptile ovotransferrins by chromatographic purification and characterized by mass spectrometry and N-terminal sequencing analysis. In order to increase the antimicrobial efficacy, two novel peptides, cOT2 (+6) and sOT2 (+5), were designed and synthesized as "naturally-engineered" by primary amino acid sequence extension of cOT1 and sOT1, respectively. These rational designs of modified peptides were assayed in term of antimicrobial activity. These peptides display strong antimicrobial activity against several bacterial strains, e.g. Vibrio cholerae, Bacillus megaterium, and Bacillus pumilus TISTR 905, with MICs of 7-16.1µM. In terms of structural conformation in mimic environments, CD spectroscopic analysis of the secondary peptides structure features revealed fairly the similarity on α-helical content with magainin II. Hence, the modes of actions have been speculated as toroidal and carpet model. Furthermore, the disruption of intact bacterial cells induced by cOT2 and sOT2 was investigated by SEM and AFM. The results provided evidence that cOT2 and sOT2 have the potential to cause different morphological changes of bacterial cells and that these effects can be enhanced by increasing the peptide concentration.

Complete Amino Acid Sequence of a Copper/Zinc-Superoxide Dismutase from Ginger Rhizome.

Superoxide dismutase (SOD) is an antioxidant enzyme protecting cells from oxidative stress. Ginger (Zingiber officinale) is known for its antioxidant properties, however, there are no data on SODs from ginger rhizomes. In this study, we purified SOD from the rhizome of Z. officinale (Zo-SOD) and determined its complete amino acid sequence using N terminal sequencing, amino acid analysis, and de novo sequencing by tandem mass spectrometry. Zo-SOD consists of 151 amino acids with two signature Cu/Zn-SOD motifs and has high similarity to other plant Cu/Zn-SODs. Multiple sequence alignment showed that Cu/Zn-binding residues and cysteines forming a disulfide bond, which are highly conserved in Cu/Zn-SODs, are also present in Zo-SOD. Phylogenetic analysis revealed that plant Cu/Zn-SODs clustered into distinct chloroplastic, cytoplasmic, and intermediate groups. Among them, only chloroplastic enzymes carried amino acid substitutions in the region functionally important for enzymatic activity, suggesting that chloroplastic SODs may have a function distinct from those of SODs localized in other subcellular compartments. The nucleotide sequence of the Zo-SOD coding region was obtained by reverse-translation, and the gene was synthesized, cloned, and expressed. The recombinant Zo-SOD demonstrated pH stability in the range of 5-10, which is similar to other reported Cu/Zn-SODs, and thermal stability in the range of 10-60 °C, which is higher than that for most plant Cu/Zn-SODs but lower compared to the enzyme from a Z. officinale relative Curcuma aromatica.

Mechanical Recanalization for Acute Embolic Occlusion at the Origin of the Superior Mesenteric Artery.

PURPOSE: We report a combined technique consisting of thrombectomy and thromboaspiration for the treatment of acute embolic occlusion of the superior mesenteric artery (SMA) at the origin. CASE: A 90-year-old female with chronic atrial fibrillation had a sudden onset of abdominal pain and hematochezia due to acute embolic occlusion at the origin of the SMA. Computed tomographic findings showed reversible bowel wall ischemia. We performed mechanical thrombectomy using the Solitaire FR revascularization device, a self-expanding and fully retrievable stent-based thrombectomy system for acute intracranial large artery occlusion, combined with manual aspiration through a 6F guiding sheath placed at the SMA origin via a right brachial approach. Prompt and complete recanalization of the SMA was obtained without distal embolism, and intestinal necrosis was avoided. CONCLUSION: Combined endovascular procedures of mechanical thrombectomy using the Solitaire FR with thromboaspiration may allow prompt recanalization, clot removal, and prevention of distal embolism and therefore would be a new therapy for acute embolic occlusion at the origin of the SMA.