Miracle-dz/UniFAR-FTUs huggingface dataset:
ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction

Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples.
Optical Spectropolarimetry of Asymptotic Giant Branch and Post-Asymptotic Giant Branch Stars

Spectropolarimetric observations are presented for 21 AGB stars, 13 proto-planetary nebulae (PPNs), and two R CrB-type stars. The spectra cover the wavelength range from ~4200 to 8400 Å with 16 Å resolution. Among the AGB stars, 8 of 14 M giants, five of six carbon stars, and zero of one S star showed intrinsic polarization. At least 9 of 13 PPNs exhibited intrinsic polarization, while the R CrB-type stars show intrinsic polarization during fading episodes. There is a statistical correlation between mean polarization, ⟨P⟩, and IR color, K - [12], among the AGB stars such that redder stars tend to be more polarized. The PPN sample is significantly redder and more polarized, on average, than the AGB stars. This increase in ⟨P⟩ with increased reddening is consistent with an evolutionary sequence in which AGB stars undergo increasing mass loss, with growing asymmetries in the dust distribution as they evolve up and then off the AGB into the short-lived PPN phase. A related trend is found between polarization and mass-loss rate in gas, gas. The detectability of polarization increases with mass-loss rate, and probably all AGB stars losing mass at >10-6 M☉ yr-1 have detectable polarization. Multiple observations of three polarized AGB stars show that in some cases ⟨P⟩ increases with mV, and in others it decreases. If polarization arises from scattering of starlight off an aysmmetric distribution of grains, then the distribution varies with time. Polarized features are detected in the TiO bands of three M-type Mira variables, in the CN bands of the carbon stars R Lep and V384 Per, and in the Swan bands of C2 in R CrB and two PPNs. Polarization effects in the molecular bands appear to be more common and the effects are larger in O-rich than C-rich objects.
Swept-source optical coherence tomography angiography automatic analysis of microvascular changes secondary to systemic hypertension

Introduction The aim of our study is to report swept-source optical coherence tomography angiography (SS-OCTA) quantitative parameters of retinal and choroidal microvasculature in patients with systemic hypertension (HTN) using a built-in software of SS-OCTA. Methods We performed a retrospective study. This study enrolled 93 eyes of 51 subjects with HTN and 71 eyes of 38 healthy subjects. OCTA quantitative parameters (vessel density (VD) and foveal avascular zone (FAZ) area of superficial capillary plexus (SCP), middle capillary plexus (MCP), deep capillary plexus (DCP), total capillary plexus (TCP) and choriocapillaris (CC)) of the OCTA cube of 4,5 mm × 4,5 mm were recorded. Results A decrease of parafoveal VD in CC, DCP and TCP were demonstrated between HTN group and control group (p < 0,05). Conversely, no differences were demonstrated in parafoveal VD of SCP and MCP (p > 0,05). Subgroup analysis revealed a diminution of central VD at SCP, DCP and TCP in patients taking one antihypertensive drug compared to patients treated with two medications (p < 0,05). Correlation analysis showed a significant, albeit weak, negative correlation between HTN duration, and parafoveal VD in the SCP and FAZ area at SCP, DCP and TCP (p < 0,05 and r < 0,300). Conclusion When normative data are available, OCTA might be used as a potential tool in the prevention and follow-up of end-organ damage secondary to HTN. Nonetheless, further studies are needed to confirm this hypothesis.
Time-Dependent Green Location-Routing Problem under Carbon Cap-and-Trade Policy

Considering carbon emissions in location-routing decisions can contribute to the promotion of sustainable development in the field of transportation. This paper investigates the time-dependent green location-routing problem (TDGLRP) incorporating carbon emissions. The TDGLRP model is formulated as an optimization problem with the goal of minimizing the total cost under the carbon cap-and-trade emission policy. The total cost considered consists of that caused by the construction of distribution centers, the fuel consumption of vehicles, carbon emissions under the carbon cap-and-trade policy, vehicle use, labor, and dispatch of vehicles. A two-stage hybrid heuristic algorithm that integrates the customized greedy algorithm and the ant colony algorithm is proposed to solve this problem. The simulation results illustrate that the proposed model together with the intelligent optimization algorithm could calculate the location of distribution centers and vehicle routing efficiently by alleviating traffic congestion and reducing the total logistics cost and carbon emissions.
Operation of ohmic Ti/Al/Pt/Au multilayer contacts to GaN at 600 °C in air

The high-temperature characteristics (at 600 °C) of Ti/Al/Pt/Au multilayer contacts to gallium nitride (GaN) in air are reported. Microfabricated circular-transfer-line-method test structures were subject to 10 h of thermal storage at 600 °C. Intermittent electrical characterization during thermal storage showed minimal variation in the contact resistance after 2 h and that the specific contact resistivity remained on the order of 10−5 Ω-cm2. In addition, the thermally stored multilayer contacts to GaN showed ohmic I-V characteristics when electrically probed at 600 °C. The microstructural analysis with atomic force microscopy showed minimal changes in surface roughness after thermal storage. Observations of the thermochemical reactions after thermal storage using Auger electron spectroscopy chemical depth profiling showed diffusion of Pt and minimal additional Al oxidation. The results support the use of Ti/Al/Pt/Au multilayer metallization for GaN-based sensors and electronic devices that will operate w.
Epidemiology and Management of Proximal Femoral Fractures in Italy between 2001 and 2016 in Older Adults: Analysis of the National Discharge Registry

This study aims to determine the annual incidence of proximal femoral fractures in Italy in the period between 2001 and 2016 among older adults, and to describe the trends in the clinical management of these cases. Data were retrieved from the National Hospital Discharge records issued by the Italian Ministry of Health and from the Italian Institute for Statistics. The number of hospitalizations increased between 2001 and 2016, while the age-adjusted yearly incidence decreased from 832.2 per 100,000 individuals to 706.2. The median age was 83 years (IQR 78–88) with a large majority of females (76.6%). The type of fracture varied with age in female subjects, with older women more frequently reporting pertrochanteric fractures. Therapeutic strategies for the different types of fracture depended on patients’ age. During the study years, improvements in fracture classification and management strategies were observed, with a clear decreasing trend for non-operative solutions. In conclusion, the number of proximal femur fractures in older adults is growing, even if at a lower rate compared to population aging. The Italian surgical practice changed during the study period towards the implementation of the most recent guidelines.
Extracellular Vesicles as Biomarkers in Liver Disease

Extracellular vesicles (EVs) are membrane-derived vesicles released by a variety of cell types, including hepatocytes, hepatic stellate cells, and immune cells in normal and pathological conditions. Depending on their biogenesis, there is a complex repertoire of EVs that differ in size and origin. EVs can carry lipids, proteins, coding and non-coding RNAs, and mitochondrial DNA causing alterations to the recipient cells, functioning as intercellular mediators of cell–cell communication (auto-, para-, juxta-, or even endocrine). Nevertheless, many questions remain unanswered in relation to the function of EVs under physiological and pathological conditions. The development and optimization of methods for EV isolation are crucial for characterizing their biological functions, as well as their potential as a treatment option in the clinic. In this manuscript, we will comprehensively review the results from different studies that investigated the role of hepatic EVs during liver diseases, including non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, alcoholic liver disease, fibrosis, and hepatocellular carcinoma. In general, the identification of patients with early-stage liver disease leads to better therapeutic interventions and optimal management. Although more light needs to be shed on the mechanisms of EVs, their use for early diagnosis, follow-up, and prognosis has come into the focus of research as a high-potential source of ‘liquid biopsies’, since they can be found in almost all biological fluids. The use of EVs as new targets or nanovectors in drug delivery systems for liver disease therapy is also summarized.
Multiqubit W states lead to stronger nonclassicality than Greenberger-Horne-Zeilinger states

The N-qubit states of the W class, for N>10, lead to more robust (against noise admixture) violations of local realism, than the Greenberger-Horne-Zeilinger (GHZ) states. These violations are most pronounced for correlations for a pair of qubits, conditioned on specific measurement results for the remaining N-2 qubits. The considerations provide us with a qualitative difference between the W state and GHZ state in the situation when they are separately sent via depolarizing channels. For sufficiently high amount of noise in the depolarizing channel, the GHZ states cannot produce a distillable state between two qubits, whereas the W states can still produce a distillable state in a similar situation.
Hexagonal Array Factor in Closed Form

A closed-form expression is produced for the array factor of the electronically scanned, uniform-amplitude, finite-size hexagonal array. The underlying arguments depend upon a rotational symmetry cleavage of the hexagon into three congruent parallelograms and, for each such parallelogram, the adoption of a reciprocal lattice in {u,v} observation space. In particular, the reciprocal lattice machinery succeeds in splitting the basic two-dimensional parallelogram array factor into a linear array sine function ratio (LASFR) product pair, which latter form makes contact with an earlier treatment of fairly general array configurations under the unifying viewpoint of affine transformations. Of course, as the individual parallelogram array factor contributions are summed, a need arises to acknowledge an element overcount at array center and along the three lines of parallelogram contiguity, and, when this is done, the composite array factor is found to reduce along its scanned boresight to the proper value 1 + 3N(N + 1) for its element population size, with N ≥ 0 being the number of hexagon rings. Two numerical implementations of the master array factor formula confirm a priori analytical anticipations as to the symmetric deployment in {u, v} space of satellite beam prominences, of both close-in and, when admitted into visible space u 2 + v 2 ≤ 1, genuine grating lobe character.
Bimorph Dual-Electrode ScAlN PMUT with Two Terminal Connections

This paper presents a novel bimorph Piezoelectric Micromachined Ultrasonic Transducer (PMUT) fabricated with 8-inch standard CMOS-compatible processes. The bimorph structure consists of two layers of 20% scandium-doped aluminum nitride (Sc0.2Al0.8N) thin films, which are sandwiched among three molybdenum (Mo) layers. All three Mo layers are segmented to form the outer ring and inner plate electrodes. Both top and bottom electrodes on the outer ring are electrically linked to the center inner plate electrodes. Likewise, the top and bottom center plate electrodes are electrically connected to the outer ring in the same fashion. This electrical configuration maximizes the effective area of the given PMUT design and improves efficiency during the electromechanical coupling process. In addition, the proposed bimorph structure further simplifies the device’s electrical layout with only two-terminal connections as reported in many conventional unimorph PMUTs. The mechanical and acoustic measurements are conducted to verify the device’s performance improvement. The dynamic mechanical displacement and acoustic output under a low driving voltage (1 Vpp) are more than twice that reported from conventional unimorph devices with a similar resonant frequency. Moreover, the pulse-echo experiments indicate an improved receiving voltage of 10 mV in comparison with the unimorph counterpart (4.8 mV). The validation of device advancement in the electromechanical coupling effect by using highly doped ScAlN thin film, the realization of the proposed bimorph PMUT on an 8-inch wafer paves the path to production of next generation, high-performance piezoelectric MEMS.
Engineered Bacteriorhodopsin Film with Oriented Patterns for the Improvement of the Photoelectric Response

The use of photosensitive proteins has become a competitive solar energy solution, owing to its pollution-free nature, high conversion efficiency, and good biocompatibility. Bacteriorhodopsin (bR) is an important light-sensitive protein that is widely used in the fabrication of photoelectronic devices. However, research on the optimization and comparison of the immobilization techniques is lacking. In this study, in order to obtain bR films with a high energy conversion efficiency, three immobilization techniques, namely dropcasting, electrophoretic sedimentation, and Langmuir–Blodgett deposition, were used to fabricate films, and their topographical and photoelectrical characteristics were compared. All three immobilization techniques can transfer bR molecules to substrates, forming functional photosensitive bR films. The absorption of the bR films at 568 nm reached the highest value of 0.3 under the EPS technique. The peak photocurrent for the EPS technique reached 5.03 nA. In addition, the EPS technique has the highest efficiency factor of 13.46, indicating that it can generate the highest value of photocurrent under the same light conditions, owing to the improved orientation, and no significant decrease in the peak photocurrent was observed after three weeks, which indicates the stability of the photoelectric response. These results indicate that the EPS technique has a great potential for the photoelectrical device fabrication and solar-energy conversion.
Adaptation to high rates of chromosomal instability and aneuploidy through multiple pathways in budding yeast

Both an increased frequency of chromosome missegregation (chromosomal instability, CIN) and the presence of an abnormal complement of chromosomes (aneuploidy) are hallmarks of cancer. To better understand how cells are able to adapt to high levels of chromosomal instability, we previously examined yeast cells that were deleted of the gene BIR1, a member of the chromosomal passenger complex (CPC). We found bir1Δ cells quickly adapted by acquiring specific combinations of beneficial aneuploidies. In this study, we monitored these yeast strains for longer periods of time to determine how cells adapt to high levels of both CIN and aneuploidy in the long term. We identify suppressor mutations that mitigate the chromosome missegregation phenotype. The mutated proteins fall into four main categories: outer kinetochore subunits, the SCFCdc4 ubiquitin ligase complex, the mitotic kinase Mps1, and the CPC itself. The identified suppressor mutations functioned by reducing chromosomal instability rather than alleviating the negative effects of aneuploidy. Following the accumulation of suppressor point mutations, the number of beneficial aneuploidies decreased. These experiments demonstrate a time line of adaptation to high rates of CIN.
Modular Multi-Sensor Fusion for Underwater Localization for Autonomous ROV Operations

Localization filters for underwater vehicles are mostly tailored for specific sensor suites, environments, or missions. It is also well known that the underwater environment can evolve over time and throughout the mission, affecting the vehicle’s sensors, e.g., tide, currents, and vehicle proximity to structures, especially in harbor areas. In this paper, the Modular and Robust Sensor-Fusion Framework (MaRS) is extended to work with underwater vehicles and their environment. It enables efficient use of asynchronous sensors and handles measurement outliers and outages. Sensor-frame initialization and online extrinsic calibration methods are also explored. Tests are performed in real harbor-like environments using a small remotely operated vehicle (ROV) and show improved handling of sensors and state estimation results.
Macroalgae Specialized Metabolites: Evidence for Their Anti-Inflammatory Health Benefits

Inflammation is an organism’s response to chemical or physical injury. It is split into acute and chronic inflammation and is the last, most significant cause of death worldwide. Nowadays, according to the World Health Organization (WHO), the greatest threat to human health is chronic disease. Worldwide, three out of five people die from chronic inflammatory diseases such as stroke, chronic respiratory diseases, heart disorders, and cancer. Nowadays, anti-inflammatory drugs (steroidal and non-steroidal, enzyme inhibitors that are essential in the inflammatory process, and receptor antagonists, among others) have been considered as promising treatments to be explored. However, there remains a significant proportion of patients who show poor or incomplete responses to these treatments or experience associated severe side effects. Seaweeds represent a valuable resource of bioactive compounds associated with anti-inflammatory effects and offer great potential for the development of new anti-inflammatory drugs. This review presents an overview of specialized metabolites isolated from seaweeds with in situ and in vivo anti-inflammatory properties. Phlorotannins, carotenoids, sterols, alkaloids, and polyunsaturated fatty acids present significant anti-inflammatory effects given that some of them are involved directly or indirectly in several inflammatory pathways. The majority of the isolated compounds inhibit the pro-inflammatory mediators/cytokines. Studies have suggested an excellent selectivity of chromene nucleus towards inducible pro-inflammatory COX-2 than its constitutive isoform COX-1. Additional research is needed to understand the mechanisms of action of seaweed’s compounds in inflammation, given the production of sustainable and healthier anti-inflammatory agents.
Real-world outcomes from use of CDK4/6 inhibitors in the management of advanced/metastatic breast cancer in Asia

Background: Oestrogen receptor positive, human epidermal growth factor receptor-2 (HER2) negative breast cancer (BC) is the most frequently diagnosed BC subtype. Combinations of cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) with anti-oestrogen therapy have led to improved survival compared with anti-oestrogen therapy alone for advanced/metastatic BC. The evaluation of CDK4/6i in the real-world facilitates treatment planning, insights into the incidence of drug toxicities, dose modifications including dose delays (DDs) and dose reductions (DRs) and improves prognostic accuracy in subgroups, for example geriatric patients, who are under-represented in clinical trials. Methods: This multi-centre study analysed retrospective and prospective data from 456 patients treated with CDK4/6i between January 2015 and December 2020. We examined patient characteristics, variation in prescribing practices, efficacy and toxicity outcomes. Results: In all, 456 patients were included in this study. The median age was 59 (range: 24–92). In total, 85 (19%) were ⩾70 years old. In all, 122 (27%) and 119 (26%) of patients were treated in the first-line and second-line settings, respectively. In total, 25 (5%), 31 (7%) and 145 (32%) of patients had brain, peritoneum and liver metastasis, respectively, at the time of CDK4/6i initiation. On univariate analysis, heavily pre-treated patients and those with distant metastases, involving the liver, brain or peritoneum, had significantly shorter progression-free survival (PFS) and 24-month overall survival (OS). Elderly patients (⩾70) had a shorter PFS; OS results were not mature. Majority of patients (n = 362, 80%) initiated treatment with the United States FDA-approved starting dose of CDK4/6i. In all, 330 (72%) had at least one DD and 217 (48%) patients required at least one DR, but these dose modifications were not associated with poorer survival outcomes. Patients age ⩾70 were more likely to require dose modifications leading to a lower treatment dose. The most common reason for DD/DR was neutropenia (60%) and the incidence of febrile neutropenia was only 2%. Conclusions: Our study indicates CDK4/6i is effective and safe. Age ⩾ 70, distant metastases to liver, peritoneal or brain were negative prognostic factors. Age ⩾ 70 was associated with significantly increased requirement for dose modification; however, this did not impact survival outcomes. These findings provide reassurance that survival outcomes are not adversely affected in elderly patients when DD/DR is indicated.
Inference for Events with Dependent Risks in Multiple Endpoint Studies

Abstract Kaplan–Meier and cumulative incidence functions are not sufficient descriptive devices for studies that have multiple time-to-event endpoints. For example, in cancer treatment research the probability of tumor recurrence conditional on not having died from treatment-related toxicities and the prevalence of graft-versus-host disease among leukemia-free patients surviving a bone marrow transplant are of interest. These quantities can be estimated nonparametrically using simple functions of several Kaplan–Meier and cumulative incidence estimates for events with possibly dependent risks. We derive asymptotic distribution theory for such functions by representing Kaplan–Meier, cumulative incidence, and cumulative hazard estimators as sums of iid random variables. Variance estimation also follows directly from this representation. Two-sample test statistics with asymptotic null distribution theory are presented. Several examples illustrate the utility of these results.