Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis.

Mass-Suite (MSS) is a Python-based, open-source software package designed to analyze high-resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) data, particularly for water quality assessment and other environmental applications. MSS provides flexible, user-defined workflows for HRMS data processing and analysis, including both basic functions (e.g., feature extraction, data reduction, feature annotation, data visualization, and statistical analyses) and advanced exploratory data mining and predictive modeling capabilities that are not provided by currently available open-source software (e.g., unsupervised clustering analyses, a machine learning-based source tracking and apportionment tool). As a key advance, most core MSS functions are supported by machine learning algorithms (e.g., clustering algorithms and predictive modeling algorithms) to facilitate function accuracy and/or efficiency. MSS reliability was validated with mixed chemical standards of known composition, with 99.5% feature extraction accuracy and ~ 52% overlap of extracted features relative to other open-source software tools. Example user cases of laboratory data evaluation are provided to illustrate MSS functionalities and demonstrate reliability. MSS expands available HRMS data analysis workflows for water quality evaluation and environmental forensics, and is readily integrated with existing capabilities. As an open-source package, we anticipate further development of improved data analysis capabilities in collaboration with interested users.

Anticoagulation Protocol for Secondary Prevention of Acute Ischemic Stroke Associated with Nonvalvular Atrial Fibrillation.

OBJECTIVES: There is no clear evidence regarding when to initiate oral anticoagulants (OACs) for secondary prevention of recurrent stroke in patients with atrial fibrillation (AF). Therefore, this study aimed to evaluate the safety and efficacy of a novel OAC initiation protocol for secondary prevention of acute ischemic stroke associated with AF. MATERIALS AND METHODS: In this multicenter prospective study 597 consecutive Japanese patients with acute ischemic stroke associated with nonvalvular AF received post-stroke OACs according to a protocol based on severity (clinical (NIHSS) and radiological (ASPECTS + W)), rt-PA use, reperfusion, and hemorrhagic transformation (HT). Primary outcomes of safety and efficacy, including symptomatic hemorrhage, cerebral stroke, and disability were evaluated at 14 and 90 days. RESULTS: Mean OAC initiation time was 2.60±2.14 days from onset. The shortest and longest mean initiation times were 0.47±0.50 and 6.16±0.72 days, respectively. Following OAC administration, no ICH was observed within 90 days. A significantly higher incidence of acute recurrent ischemic events occurred 14 days prior to OAC (4.7%) compared with chronic recurrence within 90 days (0.8%) (P = 0.00013, McNemar's test) . Recurrence prior to OAC use was significantly correlated with days to treatment (P = 0.00224), severity (NIHSS, ASPECTS+W: P = 0.0223, P = 0.0393, respectively), and HAS-BLED (P = 0.0395) and there were no correlations with CHADS2 (P = 0.277) or CHA2DS2-VASc (P = 0.246) (Wilcoxon rank sum-test). CONCLUSIONS: This comprehensive OAC initiation protocol was relatively safe and effective for secondary prevention of stroke in patients with AF. Risk of acute recurrence was high, indicating that OACs should be started as early as possible. (clinical trial registration number: 15B 128).

Isotopic evidence for acidity-driven enhancement of sulfate formation after SO2 emission control.

After the 1980s, atmospheric sulfate reduction is slower than the dramatic reductions in sulfur dioxide (SO2) emissions. However, a lack of observational evidence has hindered the identification of causal feedback mechanisms. Here, we report an increase in the oxygen isotopic composition of sulfate ([Formula: see text]) in a Greenland ice core, implying an enhanced role of acidity-dependent in-cloud oxidation by ozone (up to 17 to 27%) in sulfate production since the 1960s. A global chemical transport model reproduces the magnitude of the increase in observed [Formula: see text] with a 10 to 15% enhancement in the conversion efficiency from SO2 to sulfate in Eastern North America and Western Europe. With an expected continued decrease in atmospheric acidity, this feedback will continue in the future and partially hinder air quality improvements.

Ependymoma-like tumor with mesenchymal differentiation harboring C11orf95-NCOA1/2 or -RELA fusion: A hitherto unclassified tumor related to ependymoma.

Recurrent fusion genes involving C11orf95, C11orf95-RELA, have been identified only in supratentorial ependymomas among primary CNS tumors. Here, we report hitherto histopathologically unclassifiable high-grade tumors, under the tentative label of "ependymoma-like tumors with mesenchymal differentiation (ELTMDs)," harboring C11orf95-NCOA1/2 or -RELA fusion. We examined the clinicopathological and molecular features in five cases of ELTMDs. Except for one adult case (50 years old), all cases were in children ranging from 1 to 2.5 years old. All patients presented with a mass lesion in the cerebral hemisphere. Histologically, all cases demonstrated a similar histology with a mixture of components. The major components were embryonal-appearing components forming well-delineated tumor cell nests composed of small uniform cells with high proliferative activity, and spindle-cell mesenchymal components with a low- to high-grade sarcoma-like appearance. The embryonal-appearing components exhibited minimal ependymal differentiation including a characteristic EMA positivity and tubular structures, but histologically did not fit with ependymoma because they lacked perivascular pseudorosettes, a histological hallmark of ependymoma, formed well-delineated nests, and had diffuse and strong staining for CAM5.2. Molecular analysis identified C11orf95-NCOA1, -NCOA2, and -RELA in two, one, and two cases, respectively. t-distributed stochastic neighbor embedding analysis of DNA methylation data from two cases with C11orf95-NCOA1 or -NCOA2 and a reference set of 380 CNS tumors revealed that these two cases were clustered together and were distinct from all subgroups of ependymomas. In conclusion, although ELTMDs exhibited morphological and genetic associations with supratentorial ependymoma with C11orf95-RELA, they cannot be regarded as ependymoma. Further analyses of more cases are needed to clarify their differences and similarities.

Japanese Herbal Medicine Ninjinyoeito Mediates Its Orexigenic Properties Partially by Activating Orexin 1 Receptors.

Cancer cachexia is highly prevalent in patients with progressive cancer and is characterized by decreased food consumption, and body weight. Japanese herbal medicine Ninjinyoeito (NYT), composed of 12 herbal crude drugs, is prescribed in Asian countries to improve several symptoms such as anorexia and fatigue, which are commonly observed in patients with cancer cachexia. However, the action mechanisms of NYT in improving anorexia or fatigue in patients with cancer are not clear. Therefore, in the present study, we examined the effects of NYT on the activities of several G-protein-coupled receptors (GPCRs), which activate hyperphagia signaling in the central nervous system, using an in vitro assay with the CellKey™ system, which detects the activation of GPCRs as a change in intracellular impedance (ΔZ). NYT increased the ΔZ of human embryonic kidney 293 (HEK293) cells expressing orexin 1 receptor (OX1R) and those expressing neuropeptide Y1 receptor (NPY1R) in a dose-dependent manner. On the contrary, NYT did not significantly increase the ΔZ of HEK293A cells expressing growth hormone secretagogue receptor (GHSR) and those expressing NPY5R. The selective OX1R antagonist SB674042 significantly decreased the NYT-induced increase in ΔZ in OX1R-expressing cells. Contrarily, the selective NPY1R antagonist BIBO3340 failed to inhibit the NPY-induced increase in ΔZ in NPY1R-expressing cells. Additionally, we prepared modified NYT excluding each one of the 12 herbal crude drugs in NYT and investigated the effects on the activity of OX1R. Among the 12 modified NYT formulations, the one without citrus unshiu peel failed to activate OX1R. A screening of each of the 12 herbal crude drugs showed that citrus unshiu peel significantly activated OX1R, which was significantly suppressed by SB674042. These finding suggest that NYT and citrus unshiu peel could increase food intake via activation of orexigenic OX1R-expressing neurons in the hypothalamus. This study provides scientific evidence to support the potential of NYT for cancer patients with anorexia.

An inexpensive microscopy system for microfluidic studies in budding yeast.

Recently, microfluidic technologies have been developed to allow higher throughput collection of yeast replicative lifespan data. Adoption of these devices has been limited, in part, due to the high cost of the motorized microscopy instrumentation from mainline manufacturers. Inspired by recent development of open source microscopy hardware and software, we developed minimal-cost hardware attachments to provide long-term focus stabilization for lower-cost microscopes and open source software to manage concurrent time-lapse image acquisition from multiple microscopes. We hope that these tools will help spur the wider adoption of microfluidic technologies for the study of aging in yeast.

Cationic Amphiphilic Tris-Cyclometalated Iridium(III) Complexes Induce Cancer Cell Death via Interaction with Ca2+-Calmodulin Complex.

In our previous paper, we reported on the preparation of some cationic amphiphilic Ir complexes (2c, 2d) containing KKGG peptides that induce and detect cell death of Jurkat cells. Mechanistic studies suggest that 2c interacts with anionic molecules and/or membrane receptors on the cell surface to trigger an intracellular Ca2+ response, resulting in the induction of cell death, accompanied by membrane disruption. We have continued the studies of cell death of Jurkat cells induced by 2c and found that xestospongin C, a selective inhibitor of an inositol 1,4,5-trisphosphate receptor located on the endoplasmic reticulum (ER), reduces the cytotoxicity of 2c, suggesting that 2c triggers the release of Ca2+ from the ER, leading to an increase in the concentration of cytosolic Ca2+, thus inducing cell death. Moreover, we synthesized a series of new amphiphilic cationic Ir complexes 5a-c containing photoreactive 3-trifluoromethyl-3-phenyldiazirine (TFPD) groups, in an attempt to identify the target molecules of 2c. Interestingly, it was discovered that a TFPD group functions as a triplet quencher of Ir complexes. It was also found that 5b is useful as a turn-on phosphorescent probe of acidic proteins such as bovine serum albumin (BSA) (pI = 4.7) and their complexation was confirmed by luminescence titrations and SDS-PAGE of photochemical products between them. These successful results allowed us to carry out photoaffinity labeling of the target biomolecules of 5b (2c and analogues thereof) in Jurkat cells. A proteomic analysis of the products obtained by the photoirradiation of 5b with Jurkat cells suggests that the Ca2+-binding protein "calmodulin (CaM)" is one of target proteins of the Ir complexes. Indeed, 5b was found to interact with the Ca2+-CaM complex, as evidenced by luminescence titrations and the results of photochemical reactions of 5b with CaM in the presence of Ca2+ (SDS-PAGE). A plausible mechanism for cell death induced by a cationic amphiphilic Ir complex is discussed on the basis of our results.

Design and Synthesis of Amphiphilic and Luminescent Tris-Cyclometalated Iridium(III) Complexes Containing Cationic Peptides as Inducers and Detectors of Cell Death via a Calcium-Dependent Pathway.

Cationic amphiphilic peptides have the potential to function as agents for the treatment of microbial infections and cancer therapy. The cationic and hydrophobic parts of these molecules allow them to associate strongly with negatively charged bacterial or cancer cell membranes, thus exerting antimicrobial and anticancer activities through membrane disruption. Meanwhile, cyclometalated iridium(III) complexes such as fac-Ir(ppy)3 (ppy = 2-phenylpyridine) and fac-Ir(tpy)3 (tpy = 2-(4'-tolyl)pyridine) possess C3-symmetric structures and excellent photophysical properties as phosphorescence materials, which make them important candidates for use in biological applications such as chemosensors, biolabeling, living cell staining, in vivo tumor imaging, and anticancer agents. We recently reported on some regioselective substitution reactions of Ir(tpy)3 and Ir(ppy)3 at the 5'-position (p-position with respect to the C-Ir bond) on the 2-phenylpyridine ligands and their subsequent conversions to a variety of functional groups. We report here on the design and synthesis of amphiphilic and luminescent tris-cyclometalated Ir complexes in which cationic peptides are attached through alkyl chain linkers that work as inducers and detectors of cell death. Ir complexes containing cationic peptides such as a KKGG sequence and alkyl chain linkers of adequate length (C6 and C8) exhibit considerable cytotoxicity against cancer cells such as Jurkat, Molt-4, HeLa-S3, and A549 cells, and that dead cells are well stained with these Ir complexes. Furthermore, an Ir complex in which the KKGG peptide is attached through a C6 linker displayed lower cytotoxicity against normal mouse lymphocytes. Mechanistic studies suggest that Ir complexes containing the KKGG peptide interact with anionic molecules on the cell surface and/or membrane receptors to trigger the Ca(2+) dependent pathway and intracellular Ca(2+) response, resulting in necrosis accompanied by membrane disruption.

[A supratentorial primitive neuroectodermal tumor exhibiting pathological characteristics of medulloepithelioma: a case report].

A 50-year-old female presented with headache symptoms and left hemifacial paresis. Brain computed tomography and magnetic resonance images demonstrated a right frontal lobe tumor with hemorrhage and calcification. A gross total resection was carried out. Pathologically, the tumor exhibited three kinds of structures. The first was an astrocytic area which occupied the large part of this tumor. Small, round cells, which were positive for glial fibrillary acidic protein, were randomly distributed. The second was an epithelioid area with the highest MIB-1 labeling index of the three structures. Undifferentiated tumor cells demonstrated a dense proliferation, and short spindle-shaped cells exhibited an epithelial and a partly luminal alignment that resembled the embryonal neural tube. The third was a sarcomatoid area. Long spindle-shaped cells, which were positive for vimentin, were in a bundle-like form. We diagnosed this tumor as a primitive neuroectodermal tumor (PNET) with epithelial differentiation. PNETs are rare brain tumors with a predominance in children. Histologically, undifferentiated tumor cells demonstrate dense proliferations. The tumor arises from germinal matrix cells that differentiate into neuronal, glial, and ependymal cells. Medulloepithelioma, which is classified in the PNET category, is a very rare brain tumor that usually develops in childhood. Pathological studies have demonstrated that papillary, tubular, or trabecular arrangements of neoplastic neuroepithelium mimic the embryonic neural tube predominantly. In our case, the tumor partly demonstrated epithelial differentiation, which is a feature of medulloepithelioma, not only glial and mesenchymal differentiation. This is a rare case of PNET with uncommon histological features.

Synthesis and anti-influenza virus activity of dihydrofuran-fused perhydrophenanthrenes with a benzyloxy-type side-chain.

As one of our ongoing research project concerning development of a novel anti-influenza virus agent, dihydrofuran-fused perhydrophenanthrenes were derivatized by means of Williamson ether synthesis and Suzuki-Miyaura cross coupling reactions. Newly synthesized compounds were subjected to evaluation of anti-influenza virus activity using influenza A/Aichi/2/68 (H3N2 subtype) virus strain by a plaque titration method. These investigations revealed that incorporation of benzyl-type ether substituents was effective for exerting the inhibition activity of influenza virus proliferation.

[Current status and issues of stroke care in the Hokumou Secondary Medical District: the activity of the Okhotsk Stroke Association].

To achieve good care for stroke patients in the Hokumou Secondary Medical District, we reaffirmed the current status of the services, discovered the keypoints and issues, and searched for solutions to the current problems. The population, its age composition and the number of beds occupied by stroke patients--stratified in acute, convalescent and maintenance stages-were surveyed. The number of patients suffering from stroke under the jurisdiction of this district was compiled, by using the "regional alliance path for stroke," and the severity and outcome of each case were evaluated by using the mRS (modified Rankin Scale). We held seminars for citizens' on the prevention and management of stroke and the attendees were asked to fill out questionnaires, and were organized: networks for medical care and nursing in the Okhotsk Sea area and people's voices were heard at the network meetings; and at the town meetings held at Kitami, Abashiri and Bihoro, the challenges and problems in each area were discussed. The findings obtained from these activities were compiled for the current study. The rate of release of the patients to their home environment was high in the acute stage but low in the convalescent stage. To substantiate the regional management of stroke patients, it is essential that one be familiar with the availability of the limited medical recourses for and dynamics of patients. And yet, there is a limit to the efforts that the medical profession alone can make for the acute and convalescent stages. It is necessary that the health services assist in solving the problems, with the cooperation of the citizens and the nursing network that is involved in homes and nursing facilities for the care of patients in the maintenance stage.

Monolayers (Langmuir films) behavior of multi-component systems composed of a bile acid with different sterols and with their 1:1 mixtures.

Different physicochemical properties of Langmuir films (monolayers) composed of 10 mixed systems of a bile acid, deoxycholic acid (DC) with various plant sterols, such as stigmasterol (Stig), beta-sitosterol (Sito) and campesterol (Camp) and a stanol, cholestanol (Chsta) in addition to an animal sterol, cholesterol (Ch) [these sterols and Chsta are abbreviated as St] and DC with 1:1 St mixtures; (Ch+Chsta), (Ch+Stig), (Stig+Chsta), (Ch+Sito) and (Ch+Camp) on the substrate of 5M aqueous NaCl solution (pH 1.2) at 25 degrees C, were investigated in terms of mean surface area per molecule (A(m)), the partial molecular area (PMA), surface excess Gibbs energy (DeltaG((ex))), interaction parameter (I(p)) as well as activity coefficients (f(1) and f(2)) in 2-D phase of each binary (or ternary) component system and elasticity (Cs(-1)) of formed films; these were analyzed on the basis of the respective surface pressure (pi) versus A(m) isotherms as a function of mole fraction of Sts (X(st)) in the DC/St(s) mixtures at discrete surface pressures. Notable findings are: (i) all the binary component systems did form patched film type monolayers consisting of (a) DC-dominant film solubilizing a trace amount of St molecules and (b) St dominant film dissolving a small amount of DC molecules, (ii) DC in 2-D phase exhibited a transition from LE film to LC film at a constant pressure (pi(C)(1)) accompanied by compression and (iii) DeltaG((ex)) as well as I(p) was found to be greatly dependent on (a) the combinations of DC with different St species and (b) to be markedly varied by a difference in mixing ratio of DC to Sts. Compressibility (or elasticity) analyses and fluorescence microscopy images could support the above findings as well as interpretation.