Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.

Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair resolution. However, the peak calling step hinders ChIP-exo application since the published algorithms tend to generate false-positive and false-negative predictions. Here, we report the development of DEOCSU (DEep-learning Optimized ChIP-exo peak calling SUite), a novel machine learning-based ChIP-exo peak calling suite. DEOCSU entails the deep convolutional neural network model which was trained with curated ChIP-exo peak data to distinguish the visualized data of bona fide peaks from false ones. Performance validation of the trained deep-learning model indicated its high accuracy, high precision and high recall of over 95%. Applying the new suite to both in-house and publicly available ChIP-exo datasets obtained from bacteria, eukaryotes and archaea revealed an accurate prediction of peaks containing canonical motifs, highlighting the versatility and efficiency of DEOCSU. Furthermore, DEOCSU can be executed on a cloud computing platform or the local environment. With visualization software included in the suite, adjustable options such as the threshold of peak probability, and iterable updating of the pre-trained model, DEOCSU can be optimized for users' specific needs.

Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis.

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts. In the present study, host-pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. These observations suggest that the utilization of metabolites such as arginine by intracellular MAP might affect host NO production. Our dual RNA-seq data can provide novel insights by capturing the global transcriptome with higher resolution, especially in MAP, thus enabling a more systematic understanding of host-pathogen interactions.

FPCB as an Acoustic Matching Layer for 1D Linear Ultrasound Transducer Arrays.

An acoustic matching layer is an essential component of an ultrasound transducer to achieve maximum ultrasound transmission efficiency. Here, we develop a flexible printed circuit board (FPCB) with a composite structure consisting of multiple polyimide and copper layers and demonstrate it as a novel acoustic matching layer. With a flexible substrate and robust ACF bonding, the FPCB not only serves as an acoustic matching layer between piezoelectric elements and the surrounding medium but also as a ground for the electrical connection between the transducer array elements and the folded substrate. A 1D linear ultrasound transducer array with the FPCB matching layer exhibits larger output pressure, wider -3dB bandwidth, and higher ultrasound beam intensity compared to that of an ultrasound transducer array with the alumina/epoxy matching layer, which is one of the most commonly applied composite matching layers. The enhanced transmission performance verifies that the proposed FPCB is an excellent matching layer for 1D linear ultrasound transducer arrays.

Neurokinin-1 Receptor Antagonism Ameliorates Dry Eye Disease by Inhibiting Antigen-Presenting Cell Maturation and T Helper 17 Cell Activation.

Neuroinflammation plays an important role in the pathogenesis of ocular surface disease, including dry eye disease (DED), but little is known about the contribution of substance P (SP) to DED. In this study, we investigated the expression of SP at the ocular surface and evaluated its effect on maturation of antigen-presenting cells (APCs), the key cell component involved in the induction of type 17 helper T-cell (Th17) response in DED. The effect of topical blockade of SP signaling was further investigated using neurokinin-1 receptor (NK1R) inhibitors on APC maturation, Th17 cell activation, and disease severity in a mouse model of DED. The results demonstrate that SP is constitutively expressed at the ocular surface, and trigeminal ganglion neurons are the major source of SP in DED. SP derived from trigeminal ganglion enhanced the expression of major histocompatibility complex class II maturation marker by bone marrow-derived dendritic cells, an effect that is abrogated by blockade of SP signaling using NK1R antagonist spantide. Finally, using a well-established murine model of DED, topical treatment of DED mice with NK1R antagonists CP-99,994 and L-733,060 suppressed APC acquisition of major histocompatibility complex class II, reduced Th17 cell activity, and ameliorated DED severity. These findings are of translational value, as they suggest that antagonizing NK1R-mediated SP signaling may be an effective strategy in suppressing Th17-mediated ocular surface disease.

Corneal Lymphangiogenesis: Current Pathophysiological Understandings and Its Functional Role in Ocular Surface Disease.

The cornea is a transparent and avascular tissue that plays a central role in light refraction and provides a physical barrier to the external environment. Corneal avascularity is a unique histological feature that distinguishes it from the other parts of the body. Functionally, corneal immune privilege critically relies on corneal avascularity. Corneal lymphangiogenesis is now recognized as a general pathological feature in many pathologies, including dry eye disease (DED), corneal allograft rejection, ocular allergy, bacterial and viral keratitis, and transient corneal edema. Currently, sizable data from clinical and basic research have accumulated on the pathogenesis and functional role of ocular lymphangiogenesis. However, because of the invisibility of lymphatic vessels, ocular lymphangiogenesis has not been studied as much as hemangiogenesis. We reviewed the basic mechanisms of lymphangiogenesis and summarized recent advances in the pathogenesis of ocular lymphangiogenesis, focusing on corneal allograft rejection and DED. In addition, we discuss future directions for lymphangiogenesis research.

Surgical Strategy for T2 Gallbladder Cancer: Nationwide Multicenter Survey in Korea.

BACKGROUND: Although all guidelines suggest that T2 gallbladder (GB) cancer should be treated by extended cholecystectomy (ECx), high-level scientific evidence is lacking because there has been no randomized controlled trial on GB cancer. METHODS: A nationwide multicenter study between 2000 and 2009 from 14 university hospitals enrolled a total of 410 patients with T2 GB cancer. The clinicopathologic findings and long-term follow-up results were analyzed after consensus meeting of Korean Pancreas Surgery Club. RESULTS: The 5-year cumulative survival rate (5YSR) for the patients who underwent curative resection was 61.2%. ECx group showed significantly better 5YSR than simple cholecystectomy (SCx) group (65.4% vs. 54.0%, P = 0.016). For N0 patients, there was no significant difference in 5YSR between SCx and ECx groups (68.7% vs. 73.6%, P = 0.173). Systemic recurrence was more common than locoregional recurrence (78.5% vs. 21.5%). Elevation of cancer antigen 19-9 level preoperatively and lymph node (LN) metastasis were significantly poor prognostic factors in a multivariate analysis. CONCLUSION: ECx including wedge resection of GB bed should be recommended for T2 GB cancer. Because systemic recurrence was more common and recurrence occurred more frequently in patients with LN metastasis, postoperative adjuvant therapy should be considered especially for the patients with LN metastasis.

Estimation of axial curvature of anterior sclera: correlation between axial length and anterior scleral curvature as affected by angle kappa.

BACKGROUND: Though the development and fitting of scleral contact lenses are expanding steadily, there is no simple method to provide scleral metrics for scleral contact lens fitting yet. The aim of this study was to establish formulae for estimation of the axial radius of curvature (ARC) of the anterior sclera using ocular biometric parameters that can be easily obtained with conventional devices. METHODS: A semi-automated stitching method and a computational analysis tool for calculating ARC were developed by using the ImageJ and MATLAB software. The ARC of all the ocular surface points were analyzed from the composite horizontal cross-sectional images of the right eyes of 24 volunteers; these measurements were obtained using anterior segment optical coherence tomography for a previous study (AS-OCT; Visante). Ocular biometric parameters were obtained from the same volunteers with slit-scanning topography and partial coherence interferometry. Correlation analysis was performed between the ARC at 8 mm to the axis line (ARC[8]) and other ocular parameters (including age). With ARC obtained on several nasal and temporal points (7.0, 7.5, 8.0, 8.5, and 9.0 mm from the axis line), univariate and multivariate linear regression analyses were performed to develop a model for estimating ARC with the help of ocular biometric parameters. RESULTS: Axial length, spherical equivalent, and angle kappa showed correlations with temporal ARC[8] (tARC[8]; Pearson's r = 0.653, -0.579, and -0.341; P = 0.001, 0.015, and 0.015, respectively). White-to-white corneal diameter (WTW) and anterior chamber depth (ACD) showed correlation with nasal ARC[8] (nARC[8]; Pearson's r = -0.492 and -0.461; P = 0.015 and 0.023, respectively). The formulae for estimating scleral curvatures (tARC, nARC, and average ARC) were developed as a function of axial length, ACD, WTW, and distance from the axis line, with good determinant power (72 - 80 %; SPSS ver. 22.0). Angle kappa showed strong correlation with axial length (Pearson's r = -0.813, P <0.001), and the different correlation patterns of nasal and temporal ARC with axial length can be explained by the ocular surface deviation represented by angle kappa. CONCLUSIONS: Axial length, ACD, and WTW are useful parameters for estimating the ARC of the anterior sclera, which is important for the haptic design of scleral contact lenses. Angle kappa affects the discrepancies between the nasal and temporal scleral curvature.

Surgical strategy for T1 gallbladder cancer: a nationwide multicenter survey in South Korea.

BACKGROUND: The aim of this study was to investigate the clinical features and clinical outcomes of T1 gallbladder (GB) cancer and to determine an appropriate surgical strategy for T1 GB cancer. METHODS: A nationwide multicenter study, in which 16 University Hospitals in Korea participated, was performed from 1995 to 2004. A total of 258 patients, 117 patients with T1a and 141 patients with T1b disease were enrolled. Clinicopathologic findings and long-term follow-up results were analyzed after a consensus meeting of the Korean Pancreas Surgery Club was held. RESULTS: Simple cholecystectomy was performed in 95 patients (81.2 %) with T1a tumor and in 89 patients (63.1 %) with T1b tumor (p < 0.01). Lymph node metastasis was observed in 2.9 % of T1a patients and in 9.9 % of T1b patients (p = 0.391). A significant difference in 5-year disease-specific survival (DSS) rates was observed between T1a and T1b patients (96.4 vs 84.8 %, respectively, p = 0.03). However, no significant 5-year DSS rate difference was observed between those who underwent simple cholecystectomy or extended cholecystectomy, regardless of whether lymph node dissection was performed or whether lymph node metastasis was present. There was no significant difference in recurrence-free survival between simple cholecystectomy and extended cholecystectomy. CONCLUSIONS: There was no superiority of extended cholecystectomy over simple cholecystectomy in the aspect of survival and recurrence especially in T1b gallbladder cancer. Furthermore, the effectiveness of regional lymphadenectomy for treatment purpose remains questionable. Therefore, simple cholecystectomy could be recommended as a surgical strategy of T1 gallbladder cancer.

Measurement of anterior scleral curvature using anterior segment OCT.

PURPOSE: To investigate and validate methods for measuring the radius of anterior scleral curvature using anterior segment optical coherence tomography images. METHODS: Twenty-four volunteers were enrolled in this study. Anterior segment optical coherence tomography images, centered on horizontal/vertical limbus, including adjacent anterior sclera, were obtained in addition to conventional images centered on the optical axis. Central horizontal, nasal, and temporal optical coherence tomography images were consolidated to a new image for subsequent analyses. The reference points of limbal surface and three scleral points were marked nasally and temporally. The radius of a best-fit circle to the six scleral points was derived (the BFC [best-fit circle] method) and the radii of two circles, the centers of which are on the optical axis and pass through the points of the scleral surface at 2 mm from the limbus nasally and temporally, were calculated (the axial method). To assess the reliability and accuracy of each method, intraobserver and interobserver agreements were analyzed and the radii of contact lenses with known curvatures were measured. RESULTS: The mean (±SD) radius of a BFC was 13.12 (±0.80) mm. The mean (±SD) radius of nasal anterior scleral curvature (13.33 ± 1.12 mm) was significantly greater than that of temporal anterior scleral curvature (12.32 ± 0.77 mm) (paired samples t test, p < 0.001). The BFC and axial methods showed excellent intraobserver and interobserver agreements for measurements (intraclass correlation coefficient > 0.75, p < 0.001), whereas both methods showed a tendency to slightly underestimate the actual curvature of a rigid contact lens of known dimensions (-0.07 ± 0.13 mm [the BFC method] and -0.19 ± 0.07 mm [the axial method], Wilcoxon signed rank test, p = 0.173 and p = 0.028, respectively). CONCLUSIONS: Anterior segment optical coherence tomography is a valuable tool for measuring the radii of anterior scleral curvatures by image processing and mathematical calculation and can provide useful information in specific clinical situations such as designing scleral lenses.

Effects of Taraxaci Herba (Dandelion) on Testosterone Propionate-Induced Benign Prostatic Hyperplasia in Rats.

Benign prostatic hyperplasia (BPH) is the non-malignant enlargement of the prostate, associated with lower urinary tract symptoms (LUTSs). Taraxaci Herba (TH), commonly known as dandelion, has traditionally been utilized in East Asia to treat symptoms related to LUTSs. Based on this traditional use, our study aimed to explore the inhibitory effects of TH on BPH progression using a testosterone propionate-induced rat model. To induce BPH, male Sprague Dawley rats were castrated and injected subcutaneously with testosterone propionate (3 mg/kg/day) for 28 days. Concurrently, TH extract was administered orally at doses of 100 and 300 mg/kg/day throughout the four-week period of testosterone propionate injections. The TH extract significantly reduced both the absolute and relative weights of the prostate, along with histopathological changes in the gland. Moreover, it lowered serum levels of testosterone and dihydrotestosterone and reduced the expression of the androgen receptor in the prostate. Additionally, the TH extract modulated the protein expressions of Bax and Bcl-2, which are key regulators of apoptosis in prostate cells. Collectively, our findings suggest that TH inhibits BPH development partially by modulating androgen signaling and inducing apoptosis within the prostate.

Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure.

Antimicrobial resistance (AMR) in pathogenic bacteria poses a significant threat to public health, yet there is still a need for development in the tools to deeply understand AMR genes based on genetic or structural information. In this study, we present an interactive web database named Blanket Overarching Antimicrobial-Resistance gene Database with Structural information (BOARDS, sbml.unist.ac.kr), a database that comprehensively includes 3,943 reported AMR gene information for 1,997 extended spectrum beta-lactamase (ESBL) and 1,946 other genes as well as a total of 27,395 predicted protein structures. These structures, which include both wild-type AMR genes and their mutants, were derived from 80,094 publicly available whole-genome sequences. In addition, we developed the rapid analysis and detection tool of antimicrobial-resistance (RADAR), a one-stop analysis pipeline to detect AMR genes across whole-genome sequencing (WGSs). By integrating BOARDS and RADAR, the AMR prevalence landscape for eight multi-drug resistant pathogens was reconstructed, leading to unexpected findings such as the pre-existence of the MCR genes before their official reports. Enzymatic structure prediction-based analysis revealed that the occurrence of mutations found in some ESBL genes was found to be closely related to the binding affinities with their antibiotic substrates. Overall, BOARDS can play a significant role in performing in-depth analysis on AMR.IMPORTANCEWhile the increasing antibiotic resistance (AMR) in pathogen has been a burden on public health, effective tools for deep understanding of AMR based on genetic or structural information remain limited. In this study, a blanket overarching antimicrobial-resistance gene database with structure information (BOARDS)-a web-based database that comprehensively collected AMR gene data with predictive protein structural information was constructed. Additionally, we report the development of a RADAR pipeline that can analyze whole-genome sequences as well. BOARDS, which includes sequence and structural information, has shown the historical landscape and prevalence of the AMR genes and can provide insight into single-nucleotide polymorphism effects on antibiotic degrading enzymes within protein structures.

Effects of ginsenoside Rg3 on α9α10 nicotinic acetylcholine receptor-mediated ion currents.

Ginsenosides is a low molecular weight substance found in ginseng as one of the active ingredients. Ginsenosides, like other herbal medicines, has a wide range of neuropharmacological actions including neuroprotective effects. The α9α10 nicotinic acetylcholine receptor is one of numerous nicotinic acetylcholine receptors that exists as a heteropentameric form in auditory hair cells of the cochlea. In this study, we report the effects of ginsenosides on rat α9α10 nicotinic acetylcholine receptor-mediated ion currents using the two-electrode voltage clamp technique. Treatment with acetylcholine evoked inward currents (IACh) in oocytes heterologously expressing the α9α10 nicotinic acetylcholine receptor. Ginsenosides blocked IACh in order of potency of Rg3> Rb2> CK>Re = Rg2> Rf>Rc> Rb1> Rg1 with reversible manners, and the blocking effect of Rg3 on IACh was same after pre-application than co-application of Rg3. The half maximal inhibitory concentration (IC50) of Rg3 was 39.6 ± 4.9 µm. Rg3-induced IACh inhibition was not affected by acetylcholine concentration and was independent of membrane holding potential. Although the inhibitory effect of Rg3 on IACh was abolished in oocytes expressing α9 subunit alone, indicating that the presence of α10 subunit might be required for Rg3-induced regulations of α9α10 nicotinic acetylcholine receptor channel activity. These results indicate that α10 subunit of α9α10 nicotinic acetylcholine receptor might play an important role in Rg3-induced regulation of the α9α10 nicotinic acetylcholine receptor.

Inhibitory Effects of Ginsenoside Metabolites, Compound K and Protopanaxatriol, on GABAC Receptor-Mediated Ion Currents.

Ginsenosides, one of the active ingredients of Panax ginseng, show various pharmacological and physiological effects, and they are converted into compound K (CK) or protopanaxatriol (M4) by intestinal microorganisms. CK is a metabolite derived from protopanaxadiol (PD) ginsenosides, whereas M4 is a metabolite derived from protopanaxatriol (PT) ginsenosides. The γ-aminobutyric acid receptorC (GABAC) is primarily expressed in retinal bipolar cells and several regions of the brain. However, little is known of the effects of ginsenoside metabolites on GABAC receptor channel activity. In the present study, we examined the effects of CK and M4 on the activity of human recombinant GABAC receptor (ρ1) channels expressed in Xenopus oocytes by using a 2-electrode voltage clamp technique. In oocytes expressing GABAC receptor cRNA, we found that CK or M4 alone had no effect in oocytes. However, co-application of either CK or M4 with GABA inhibited the GABA-induced inward peak current (IGABA ). Interestingly, pre-application of M4 inhibited IGABA more potently than CK in a dose-dependent and reversible manner. The half-inhibitory concentration (IC50) values of CK and M4 were 52.1±2.3 and 45.7±3.9 µM, respectively. Inhibition of IGABA by CK and M4 was voltage-independent and non-competitive. This study implies that ginsenoside metabolites may regulate GABAC receptor channel activity in the brain, including in the eyes.

Activation of lysophosphatidic Acid receptor is coupled to enhancement of ca(2+)-activated potassium channel currents.

The calcium-activated K(+) (BKCa) channel is one of the potassium-selective ion channels that are present in the nervous and vascular systems. Ca(2+) is the main regulator of BKCa channel activation. The BKCa channel contains two high affinity Ca(2+) binding sites, namely, regulators of K(+) conductance, RCK1 and the Ca(2+) bowl. Lysophosphatidic acid (LPA, 1-radyl-2-hydroxy-sn-glycero-3-phosphate) is one of the neurolipids. LPA affects diverse cellular functions on many cell types through G protein-coupled LPA receptor subtypes. The activation of LPA receptors induces transient elevation of intracellular Ca(2+) levels through diverse G proteins such as Gαq/11, Gαi, Gα12/13, and Gαs and the related signal transduction pathway. In the present study, we examined LPA effects on BKCa channel activity expressed in Xenopus oocytes, which are known to endogenously express the LPA receptor. Treatment with LPA induced a large outward current in a reversible and concentration-dependent manner. However, repeated treatment with LPA induced a rapid desensitization, and the LPA receptor antagonist Ki16425 blocked LPA action. LPA-mediated BKCa channel activation was also attenuated by the PLC inhibitor U-73122, IP3 inhibitor 2-APB, Ca(2+) chelator BAPTA, or PKC inhibitor calphostin. In addition, mutations in RCK1 and RCK2 also attenuated LPA-mediated BKCa channel activation. The present study indicates that LPA-mediated activation of the BKCa channel is achieved through the PLC, IP3, Ca(2+), and PKC pathway and that LPA-mediated activation of the BKCa channel could be one of the biological effects of LPA in the nervous and vascular systems.

Severe Adverse Events of Periocular Acupuncture: A Review of Cases.

Acupuncture is recognized as a component of alternative medicine and is increasingly used worldwide. Many studies have shown the various effects of acupuncture around the eyes for ophthalmologic or nonophthalmologic conditions. For ophthalmologic conditions, the effect of acupuncture on dry eye syndrome, glaucoma, myopia, amblyopia, ophthalmoplegia, allergic rhinoconjunctivitis, blepharospasm, and blepharoptosis has been reported. Recently, several studies on dry eye syndrome have been reported and are in the spotlight. However, given the variety of study designs and reported outcomes of periocular acupuncture, research is still inconclusive, and further studies are required. In addition, although a systematic and reliable safety assessment is required, to the best of our knowledge, there have been no reports of a literature review of ocular complications resulting from periocular acupuncture. This review collected cases of ocular injury as severe adverse events from previously published case reports of periocular acupuncture. A total of 14 case reports (15 eyes of 14 patients) of adverse events published between 1982 and 2020 were identified. This review article provides a summary of the reported cases and suggestions for the prevention and management of better visual function prognosis.

A Machine Learning Approach Reveals a Microbiota Signature for Infection with Mycobacterium avium subsp. paratuberculosis in Cattle.

Although Mycobacterium avium subsp. paratuberculosis (MAP) has threatened public health and the livestock industry, the current diagnostic tools (e.g., fecal PCR and enzyme-linked immunosorbent assay [ELISA]) for MAP infection have some limitations, such as inconsistent results due to intermittent bacterial shedding or low sensitivity during the early stage of infection. Therefore, this study aimed to develop a novel biomarker focusing on elucidating the gut microbial signature of MAP-positive ruminants, since the clinical signs of MAP infection are closely related to dysbiosis. 16S rRNA-based gut microbial community analysis revealed both a decrease in microbial diversity and the emergence of several distinct taxa following MAP infection. To determine the discriminant taxa diagnostic of MAP infection, machine learning-based feature selection and predictive model construction were applied to taxon abundance data or their transformed derivatives. The selected taxa, such as Clostridioides (formerly Clostridium) difficile, were used to build models using a support vector machine, linear support vector classification, k-nearest neighbor, and random forest with 10-fold cross-validation. The receiver operating characteristic-area under the curve (ROC-AUC) analysis of the models revealed their high accuracy, up to approximately 96%. Collectively, taxonomic signatures of cattle gut microbiotas according to MAP infection status could be identified by feature selection tools and applied to establish a predictive model for the infection state. IMPORTANCE Due to the limitations, such as intermittent bacterial shedding or poor sensitivity, of the current diagnostic tools for Johne's disease, novel biomarkers are urgently needed to aid control of the disease. Here, we explored the fecal microbiota of Johne's disease-affected cattle and tried to discover distinct microbial characteristics which have the potential to be novel noninvasive biomarkers. Through 16S rRNA sequencing and machine learning approaches, a dozen taxa were selected as taxonomic signatures to discriminate the disease state. In addition, when constructing predictive models using relative abundance data of the corresponding taxa, the models showed high accuracy for classification, even including animals with subclinical infection. Thus, our study suggested novel noninvasive microbiological biomarkers that are robustly expressed regardless of subclinical infection and the applicability of machine learning for diagnosis of Johne's disease.

Multifocal skull-compensated transcranial focused ultrasound system for neuromodulation applications based on acoustic holography.

Transcranial focused ultrasound stimulation is a promising therapeutic modality for human brain disorders because of its noninvasiveness, long penetration depth, and versatile spatial control capability through beamforming and beam steering. However, the skull presents a major hurdle for successful applications of ultrasound stimulation. Specifically, skull-induced focal aberration limits the capability for accurate and versatile targeting of brain subregions. In addition, there lacks a fully functional preclinical neuromodulation system suitable to conduct behavioral studies. Here, we report a miniature ultrasound system for neuromodulation applications that is capable of highly accurate multiregion targeting based on acoustic holography. Our work includes the design and implementation of an acoustic lens for targeting brain regions with compensation for skull aberration through time-reversal recording and a phase conjugation mirror. Moreover, we utilize MEMS and 3D-printing technology to implement a 0.75-g lightweight neuromodulation system and present in vivo characterization of the packaged system in freely moving mice. This preclinical system is capable of accurately targeting the desired individual or multitude of brain regions, which will enable versatile and explorative behavior studies using ultrasound neuromodulation to facilitate widespread clinical adoption.

Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution.

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters.

Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli.

The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in Escherichia coli. We comprehensively predict alternative nitrogen sources, including cytosine and cytidine, which trigger differential activation of Nac using a model-driven workflow. In accordance with the prediction, genome-wide measurements with ChIP-exo and RNA-seq were performed. Integrative data analysis reveals that the Nac and NtrC regulons consist of 97 and 43 genes under alternative nitrogen conditions, respectively. Functional analysis of Nac at the transcriptional level showed that Nac directly down-regulates amino acid biosynthesis and restores expression of tricarboxylic acid (TCA) cycle genes to alleviate nitrogen-limiting stress. We also demonstrate that both TFs coherently modulate α-ketoglutarate accumulation stress due to nitrogen limitation by co-activating amino acid and diamine degradation pathways. A systems-biology approach provided a detailed and quantitative understanding of both TF's roles and how nitrogen and carbon metabolic networks respond complementarily to nitrogen-limiting stress.

Multivariable analysis of cholecystectomy after gastrectomy: laparoscopy is a feasible initial approach even in the presence of common bile duct stones or acute cholecystitis.

BACKGROUND: When performing cholecystectomy after gastrectomy, we often encounter problems, such as adhesions, nutritional insufficiency, and bowel reconstruction. The purpose of this study was to identify the factors related to surgical outcome of these associated procedures, with emphasis on the use of a laparoscopic approach. METHODS: We retrospectively analyzed data from 58 patients who had a history of cholecystectomy after gastrectomy. Differences between subgroups with respect to operation time, length of postoperative hospital stay, and complications were analyzed. To identify the factors related with outcomes of cholecystectomy after gastrectomy, we performed multivariable analysis with the following variables: common bile duct (CBD) exploration, laparoscopic surgery, gender, acute cholecystitis, history of stomach cancer, age, body mass index, period of surgery, and interval between cholecystectomy and gastrectomy. RESULTS: We found one case (2.9%) of open conversion. The CBD exploration was the most significant independent factor (adjusted odds ratio (OR), 45.15; 95% confidence interval (CI), 4.53-450.55) related to longer operation time. Acute cholecystitis also was a significant independent factor (adjusted OR, 14.66; 95% CI, 1.46-147.4). The laparoscopic approach was not related to operation time but was related to a shorter hospital stay (adjusted OR, 0.057; 95% CI, 0.004-0.74). Acute cholecystitis was independently related to the occurrence of complications (adjusted OR, 27.68; 95% CI, 1.15-666.24); however, CBD exploration and laparoscopic surgery were not. A lower BMI also was an independent predictor of the occurrence of complications (adjusted OR, 0.41; 95% CI, 0.2-0.87). CONCLUSIONS: The laparoscopic approach is feasible for cholecystectomy after gastrectomy, even in cases with CBD stones or acute cholecystitis. This approach does not appear to increase operation time or complication rate and was shown to decrease the length of postoperative hospital stay.