MS1Connect: a mass spectrometry run similarity measure

Interpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repos- itory, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires comput- ing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols. We propose a method, MS1Connect, that calculates the simi- larity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though this data is not used by MS1Connect.

Accelerated Aging Characterizes the Early Stage of Alzheimer’s Disease

For Alzheimer’s disease (AD), aging is the main risk factor, but whether cognitive impairments due to aging resemble early AD deficits is not yet defined. When working with mouse models of AD, the situation is just as complicated, because only a few studies track the progression of the disease at different ages, and most ignore how the aging process affects control mice. In this work, we addressed this problem by comparing the aging process of PS2APP (AD) and wild-type (WT) mice at the level of spontaneous brain electrical activity under anesthesia. Using local field potential recordings, obtained with a linear probe that traverses the posterior parietal cortex and the entire hippocampus, we analyzed how multiple electrical parameters are modified by aging in AD and WT mice. With this approach, we highlighted AD specific features that appear in young AD mice prior to plaque deposition or that are delayed at 12 and 16 months of age. Furthermore, we identified aging characteristics present in WT mice but also occurring prematurely in young AD mice. In short, we found that reduction in the relative power of slow oscillations (SO) and Low/High power imbalance are linked to an AD phenotype at its onset. The loss of SO connectivity and cortico-hippocampal coupling between SO and higher frequencies as well as the increase in UP-state and burst durations are found in young AD and old WT mice. We show evidence that the aging process is accelerated by the mutant PS2 itself and discuss such changes in relation to amyloidosis and gliosis.

Myeloid Sarcoma of the Bladder in a Patient with Chronic myelomonocytic Leukaemia

BackgroundMyeloid sarcoma is a rare extramedullary tumour of immature granulocytes, most commonly involving the skin, bone, lymph nodes, and soft tissue. It is usually associated with a diagnosis of relapsed or de novo acute myeloid leukaemia, acute lymphoblastic transformation of a myelodysplastic/myeloproliferative neoplasm, or can occur as isolated myeloid sarcoma.Case reportA 66-year-old female with a 7-year history of stable chronic myelomonocytic leukaemia presents with urgency, frequency, dysuria symptoms, and without new constitutional symptoms. She is found to have atypical, multifocal lesions on the right posterolateral wall of the bladder with associated hydronephrosis. Pathology reveals the diagnosis as myeloid sarcoma; surprisingly, bone marrow evaluation does not show evidence of acute leukaemic transformation.ConclusionsMyeloid sarcoma occurring in patients with chronic myelomonocytic leukaemia is extremely rare, and there are no cases reported in the English literature of these patients developing lesions in the bladder. The urological manifestations of an underlying haematological malignancy are best managed with a combination of systemic chemotherapy and allogeneic stem cell transplant, and in this case, the only surgical intervention required was ureteric stenting and tissue biopsy. Although rare, it is essential to consider alternative diagnoses when confronted with an atypical bladder tumour; failure to do so may result in patient harm by exposure to unnecessary intervention and delay to potentially curative treatment.

PEMBANGUNAN PEMERINTAHAN MADINAH MELALUI PEMIKIRAN DAN USAHA INTELEKTUAL PERSPEKTIF PERADABAN ISLAM MASA NABI MUHAMMAD SAW

Civilization can only be built through a strong and mature leadership process. The Prophet Muhammad SAW as a leader was able to show evidence that he was able to build a pluralistic, heterogeneous and pluralistic social order of society, especially in the city of Medina where basically the people of the city highly uphold these values. Driven by the spirit of Islam, Prophet Muhammad SAW moved and fought as a revolutionary who succeeded in bringing Islam into a perfect religion to be accepted by the people of Medina. This can be seen from a major event which became known as the Medina Charter. The Hijrah agenda is a benchmark for the existence of Islam in conveying messages of peace starting from the city of Medina. This research was conducted with a Library Research approach and searches from journals and scientific articles with the aim of producing accurate and scientifically accountable research.

Reduced synaptic activity and dysregulated extracellular matrix pathways are common phenotypes in midbrain neurons derived from sporadic and mutation-associated Parkinson's disease patients

Several mutations that cause Parkinson's disease (PD) have been identified over the past decade. These account for 15-25% of PD cases; the rest of the cases are considered sporadic. Currently, it is accepted that PD is not a single monolithic disease but rather a constellation of diseases with some common phenotypes. While rodent models exist for some of the PD-causing mutations, research on the sporadic forms of PD is lagging due to a lack of cellular models. In our study, we differentiated PD patient-derived dopaminergic (DA) neurons from induced pluripotent stem cells (iPSCs) of several PD-causing mutations as well as from sporadic PD patients. Strikingly, we observed a common neurophysiological phenotype: Neurons derived from PD patients had a severe reduction in the rate of synaptic currents compared to those derived from healthy controls. While the relationship between mutations in genes such as the SNCA and LRRK2 and a reduction in synaptic transmission has been investigated before, here we show evidence that the pathogenesis of the synapses in neurons is a general phenotype in PD. Analysis of RNA sequencing results displayed changes in gene expression in different synaptic mechanisms as well as other affected pathways such as extracellular matrix-related pathways. Some of these dysregulated pathways are common to all PD patients (monogenic or idiopathic). Our data, therefore, shows pathways and mechanisms that are central and convergent to PD and suggests a strong involvement of the tetra-partite synapse in PD pathology.

Effect of Diet Supplementation with the Mycotoxin Binder Montmorillonite on the Bioavailability of Vitamins in Dairy Cows

The objective of this study was to determine the effect of the mycotoxin binder montmorillonite (MMT) supplemented in the diet of dairy cows on the bioavailability of vitamins A, D, E, B1 and B6. Six multiparous Holstein-Friesian cows were used in a crossover design with two periods. Treatments were a control diet with or without MMT. Vitamins were infused individually into the abomasum through the ruminal cannula. Blood samples were collected from the jugular vein at 0, 1, 2, 3, 4, 6, 9, 12, 24 and 48 h after the administration of each vitamin. Results showed that vitamin A reached maximal concentration (Tmax) at 5.3 h after dosing, the maximal concentration (Cmax) was 1.2 times higher than the basal concentration (Cbasal), and the area under the curve (AUC) was 739 arbitrary units. Vitamin B6 reached the Tmax at 13 h after dosing, the Cmax was 1.4 times higher than the Cbasal, and the AUC was 222 arbitrary units. No differences were observed in Cbasal, Tmax, Cmax and AUC of vitamin A and B6 between control vs. MMT-supplemented cows. Plasma concentrations of vitamins D, E and B1 had no concentration peaks, and were not affected by MMT addition. The lack of a response suggests that their plasma concentration may be tightly regulated. Results of this study do not show evidence that MMT affects the bioavailability of vitamins A and B6 in vivo.

Expanding the Time Domain of Multiple Populations: Evidence of Nitrogen Variations in the ∼1.5 Gyr Old Star Cluster NGC 1783

We present the result of a detailed analysis of Hubble Space Telescope UV and optical deep images of the massive and young (∼1.5 Gyr) stellar cluster NGC 1783 in the Large Magellanic Cloud. This system does not show evidence of multiple populations (MPs) along the red giant branch (RGB) stars. However, we find that the cluster main sequence (MS) shows evidence of a significant broadening (50% larger than what is expected from photometric errors) along with hints of possible bimodality in the MP sensitive (m F343N − m F438W, m F438W) color–magnitude diagram (CMD). Such an effect is observed in all color combinations including the m F343N filter, while it is not found in the optical CMDs. This observational evidence suggests we might have found light-element chemical abundance variations along the MS of NGC 1783, which represents the first detection of MPs in a system younger than 2 Gyr. A comparison with isochrones including MP-like abundances shows that the observed broadening is compatible with a N abundance enhancement of Δ([N/Fe]) ∼ 0.3. Our analysis also confirms previous results about the lack of MPs along the cluster RGB. However, we find that the apparent disagreement between the results found on the MS and the RGB is compatible with the mixing effects linked to the first dredge up. This study provides new key information about the MP phenomenon and suggests that star clusters form in a similar way at any cosmic age.

A Taxonomy of Property Measures to Unify Active Learning and Human-centered Approaches to Data Labeling

Strategies for selecting the next data instance to label, in service of generating labeled data for machine learning, have been considered separately in the machine learning literature on active learning and in the visual analytics literature on human-centered approaches. We propose a unified design space for instance selection strategies to support detailed and fine-grained analysis covering both of these perspectives. We identify a concise set of 15 properties, namely measureable characteristics of datasets or of machine learning models applied to them, that cover most of the strategies in these literatures. To quantify these properties, we introduce Property Measures (PM) as fine-grained building blocks that can be used to formalize instance selection strategies. In addition, we present a taxonomy of PMs to support the description, evaluation, and generation of PMs across four dimensions: machine learning (ML) Model Output , Instance Relations , Measure Functionality , and Measure Valence . We also create computational infrastructure to support qualitative visual data analysis: a visual analytics explainer for PMs built around an implementation of PMs using cascades of eight atomic functions. It supports eight analysis tasks, covering the analysis of datasets and ML models using visual comparison within and between PMs and groups of PMs, and over time during the interactive labeling process. We iteratively refined the PM taxonomy, the explainer, and the task abstraction in parallel with each other during a two-year formative process, and show evidence of their utility through a summative evaluation with the same infrastructure. This research builds a formal baseline for the better understanding of the commonalities and differences of instance selection strategies, which can serve as the stepping stone for the synthesis of novel strategies in future work.

Petrology of Mafic Dykes from the Njimom Area (West-Cameroon): A Contribution to the Characterization of Late Paleozoic and Mesozoic Magmatism in the Southern Continental Part of the Cameroon Volcanic Line

In the western Cameroon, crop out several dyke swarms of Paleozoic–Mesozoic age. These dykes intrude the Precambrian basement in the southern continental part of the Cretaceous Cameroon Volcanic Line. In the Njimom area, two groups of mafic dykes that crosscut the Neoproterozoic basement rocks have been observed. A first group intrudes the mylonites whereas the second group intrudes the granites. The dykes are alkaline basalts and hawaiites. The mineralogical assemblage of both groups of dykes consists of plagioclase, clinopyroxene, altered olivine, and opaque oxides. The dykes that cross-cut the Precambrian mylonitic gneisses show moderate TiO2 (1.7–2.0 wt.%), low MgO (4.4–7.1 wt.%), and compatible trace element concentrations (e.g., Cr = 70–180 ppm; Ni = 30–110 ppm). The dykes that intrude the granites have TiO2 contents between 2.3 and 2.5 wt.% and moderate compatible trace element concentrations (e.g., Cr = 260–280 ppm; Ni = 170–230 ppm). MgO varies from 5.9 to 9.2 wt.%. All mafic dykes are enriched in light lanthanide element and show moderate Zr/Nb and high Zr/Y, Nb/Yb, and Ti/V ratios similar to those of average ocean island basalt (OIB)-type magmas. Some dykes that intrude the mylonites show evidence of contamination by continental crust. The composition of the clinopyroxenes of the dykes that intrude the mylonites clearly indicate different and unrelated parental magmas from dykes that intrude the granites. Contents and fractionation of the least and the most incompatible elements suggest low degrees of partial melting (3–5%) of heterogeneous source slightly enriched in incompatible elements in the spinel stability field. The geochemical features of Njimom dykes (in particular the dykes that intrude the granites) are similar to those of Paleozoic and Mesozoic dykes recorded in the southern continental part of the Cameroon Volcanic Line, suggesting multiple reactivations of pre-existing fractures that resulted in the fragmentation of western Gondwana and the opening of the South Atlantic Ocean.

Cultural and geological heritage in time elapsed during historical Kingdoms in Yogyakarta Special Region, Indonesia

Yogyakarta, Indonesia is known for its kingdom government system for all its living history; since 8-10th century Mataram Hindu-Buddhist temples to the present Muslim Ngayogyokarto Hadiningrat. Those stretch of history resulted in many artefacts and chronicles. A cultural imaginary line that linking Merapi Volcano in the north and the Indian Ocean in the south through the Yogyakarta Palace in the middle has a sacral geo-cultural heritage, explaining a prosperity gentle volcanic town, a beautiful scheme of the open panoramic features with several temples standing on the plain and mountainous landscapes in between the rest of earthquakes and the volcanic eruptions. Many temples were partly buried under volcanic materials, and some others show evidence of being shaken several times by earthquakes. Boulders of volcanic materials varying in size and shapes are present in the plain of Yogyakarta, near Cangkiringan, Ngemplak and Ngaglik. Landslides exposed many geological features, such as faults, rock formation and stratigraphy, and some unstable slopes. Cultural and geological heritages at Yogyakarta Region were created over the time.