Miracle-dz/UniFAR-FTUs huggingface dataset:
Plastome Phylogenomics Provide Insight into the Evolution of Taxus

The taxonomy of an ancient gymnosperm genus Taxus, with high value in horticulture and medicine, is perplexing because of few reliable morphological characters for diagnosing species. Here, we performed a comprehensive investigation of the evolutionary dynamics of Taxus chloroplast genomes and estimated phylogenetic relationships, divergence times, and ancestral distributions of Taxus species by comparing 18 complete chloroplast genomes. The variations across the chloroplast genome of different Taxus species indicated that remarkably varied genome variations across lineages have reshaped the genome architecture. Our well-resolved phylogeny supported that T. brevifolia Nutt. was basal lineages followed by the other North America lineages. Divergence time estimation and ancestral range reconstruction suggested that the Taxus species originated in North America in the Late Cretaceous and revealed that extant Taxus species shared a common ancestor whose ancestral distribution area was probably in North America and afterwards the earliest members expanded to Southeast Asia from where Chinese Taxus species originated. The predominant European species have more closer relationship with the Eastern Asian species and the speciation of Eurasia species arose from several dispersal and vicariance events in the Miocene. Genome-wide scanning revealed 18 positively selected genes that were involved in translation and photosynthesis system in Taxus, which might be related to the adaptive evolution of Taxus species. The availability of these complete chloroplast genomes not only enhances our understanding of the elusive phylogenetic relationships and chloroplast genome evolution such as conservation, diversity, and gene selection within Taxus genus but also provides excellent templates and genetic bases for further exploration of evolution of related lineages as well as for plant breeding and improvement.
A Blockchain-Based Self-Sovereign Identity Approach for Inter-Organizational Business Processes

Blockchain presents a promising and revolutionary technology for organizations’ collaboration, particularly for Inter-Organizational Business Processes (IOBP). It addresses the lack-of-trust problem thanks to its transparency and decentralized features. However, while the adoption of Blockchain technology can alleviate some of IOBP’s challenges, it does so at the expense of significant privacy issues. In fact, some process execution data, such as customers’ data or business secrets, cannot be shared across the collaborating organizations owing to regulatory restrictions such as the General Data Protection Regulation (GDPR). To address trust and privacy issues in IOBP, this paper presents a Blockchain-based Self-Sovereign Identity (SSI) approach. The SSI concept is combined with a registry proof smart contract to provide an efficient privacy-preserving solution. The proposed approach is applied to the pharmaceutical supply chain case study and implemented on the Ethereum Blockchain.
Time evolution of Two-qubit Entanglement

We show that the entanglement dynamics for a closed two-qubit system is part of a 10-dimensional complex linear differential equation defined on a supersphere, and the coefficients therein are completely determined by the Hamiltonian. We apply the result to investigate two physical examples of Josephson junction qubits and exchange Hamiltonians, deriving analytic solutions for the time evolution of entanglement. The Hamiltonian coefficients determines whether the entanglement is periodic. These results allow of investigating how to generate and manipulate entanglements efficiently, which are required by both quantum computation and quantum communication.
Process-oriented documentation of user requirements for analytical applications4challenges, state of the art and evaluation of a service-based configuration approach

In recent years, the integration of process design in conjunction with the use of analytical applications to provide information tailored to user requirements to support operational process activities (e.g., Operational BI) has become increasingly widespread. In analytical software development/implementation projects, the insufficient involvement of analytical end users with their process context and the resulting unclear requirements/expected analytical software functions are still one of the main reasons for analytical project failure. Embedded in a Design Science Research Process, this paper shows the shortcomings of existing approaches, tools and models (1. BPMN process model extensions, 2. configurators in analytical applications, 3. models used in analytical implementation projects) for the documentation/conceptual configuration of analytical requirements. As a second part, this paper presents the evaluation results of a new process-oriented and service-based configuration approach for analytical applications, whose practicability, usefulness and acceptance were evaluated in expert reviews and in analytical development projects.
Second order Bonferroni-type, product-type and setwise probability inequalities

This review paper considers a variety of lower bounds to Prob(Xi < c, ? , Xn < c) involving one and two-dimensional marginal probabilities. Some of these bounds, e.g., Bonierroni-type, do not require conditions on the random variables. Others of these inequalities, e.g., product-type, require positive dependence conditions on X\, ? , Xn for the inequalities to hold. Because all of the two-dimensional bounds depend on the labeling order of the random variables, various permutation-optimized versions of the bounds are described. Relationships among the various bounds are also considered.
A Quantum Field Theory Twist to Photon Angular Momentum

Grup de F´isica Te`orica & IFAE, Universitat Aut`onoma de Barcelona, 08193 Bellaterra (Barcelona), Spain(Dated: February 1, 2008)A quantum ﬁeld theory approach is put forward to generalize the concept of classical spatial lightbeams carrying orbital angular momentum to the single-photon level. This quantization frameworkis carried out both in the paraxial and nonparaxial regimes. Upon extension to the optical phasespace, closed-form expressions are found for a photon Wigner representation describing transforma-tions on the orbital Poincar´e sphere of unitarily related families of paraxial spatial modes.
A Novel Sensor System for In Vivo Perception Reconstruction Based on Long Short-Term Memory Networks

Monitoring bodily pressure could provide valuable medical information for both doctors and patients. Long-term implantation of in vivo sensors is highly desirable in situations where perception reconstruction is needed. In particular, for fecal incontinence, artificial anal sphincters without perceptions could not remind patients when to defecate and even cause ischemic tissue necrosis due to uncontrolled clamping pressure. To address these issues, a novel self-packaging strain gauge sensor system is designed for in vivo perception reconstruction. In addition, long short-term memory (LSTM) networks, which show excellent performance in processing time series-related features and fitting properties, are used in this article to improve the prediction accuracy of the perception model. The proposed system has been tested and compared with the traditional linear regression (LR) approach using data from in vitro experiments. The results show that the Root-Mean-Square Error (RMSE) is reduced by more than 69%, which demonstrates that the prediction accuracy of the proposed LSTM model is higher than that of the LR model to reach a more accurate prediction of the amount of intestinal content. Furthermore, outcomes of in vivo experiments show that the robustness of the novel sensor system based on long short-term memory networks is verified through experiments with limited data.
Locating Logic Faculty in the Mental System

Taken from Chomsky’s Knowledge of Language (1986), it is noted that logical form (LF) is not a direct reflection of deep structure (D-structure). It has induced a question, where is then 'logic' located in the human psychology (in the sense of the mind-system) if it is not in the D-structure. To answer this question, we will try to see how different languages (in this paper, English, Malay and Turkish) are structured differently on the surface (S-structure) yet can have the same internal syntax (D-structure). However, when there is a change in semantics (in the sense of intended meaning), a change in LF is noted, although the D-structure might remain the same. Making sense of this, we argue that D-structure is not the innermost faculty of the human innate system (mind) but rather, how S-structure is to D-structure, that is how D-structure is to the human logic faculty. In other words, with D-structure, logic faculty is more profound.
Superior preservation of capillaries, myofibrils and mitochondria after long-term extracorporeal perfusion of free muscle flaps – A descriptive electron microscopy study

BACKGROUND: Extracorporeal perfusion (ECP) is a promising technique for prolonged tissue preservation, but might have side effects. For instance, increased radical oxygen species or capillary endothelial damage. OBJECTIVE: To assess ultra-morphological muscle damage during 36-hour ECP of porcine musculocutaneous flaps, hypothesizing that it would delay the onset of damage compared to static cold storage (SCS). METHODS: Bilateral flaps were retrieved from three Dutch Landrace pigs. Three flaps were preserved for 36 hours by hypothermic storage 4-6°C (control group) and three flaps by ECP with cooled University of Wisconsin solution. Muscle biopsies were taken at 0 h, 12 h and 36 h and assessed with transmission electron microscopy. RESULTS: Muscle architecture was best preserved by ECP, with a delayed onset and decreased severity of muscle damage. After 36 hours, damage was two-fold lower in ECP-flaps compared to SCS-flaps. Myofibril architecture was best preserved. Mitochondria were greatly preserved with swelling being the most prominent feature. Capillaries were moderately but differently damaged during ECP, with focal endothelial thinning as opposed to luminal obstruction in SCS-preserved flaps. CONCLUSIONS: This experiment described favourable cellular preservation of skeletal muscle flaps during ECP compared to SCS. Results showed less severe ultra-morphological damage and a later onset of damage.
Integrating plant wax abundance and isotopes for paleo-vegetation and paleoclimate reconstructions: a multi-source mixing model using a Bayesian framework

Abstract. Plant wax n-alkane chain length distribution and isotopes have been studied in modern ecosystems as proxies to reconstruct vegetation and climate of the past. However, most paleo-proxies focus on either concentrations or isotopes, whereas both carry complementary information on the mixing sources. We propose a multi-source mixing model in a Bayesian framework that evaluates both chain length distributions and isotopes simultaneously. The model consists of priors that include user-defined source groups and their associated parametric distributions of n-alkane concentration and δ13C. The mixing process involves newly defined mixing fractions such as fractional leaf mass contribution (FLMC) that can be used in vegetation reconstruction. Markov Chain Monte Carlo is used to generate samples from the posterior distribution of these parameters conditioned on both data types. We present three case studies from distinct settings. The first involves n-C27, n-C29, and n-C31 alkanes in lake surface sediments of Lake Qinghai, China. The model provides more specific interpretations on the n-alkane input from aquatic sources than the conventional Paq proxy. The second involves n-C29, n-C31, and n-C33 alkanes in lake surface sediments in Cameroon, western Africa. The model produces mixing fractions of forest C3, savanna C3, and C4 plants, offering additional information on the dominant biomes compared to the traditional two-end-member mixing regime. The third couples the vegetation source model to a hydrogen isotope model component, using biome-specific apparent fractionation factors (εa) to estimate the δ2H of mean annual precipitation. By leveraging chain length distribution, δ13C, and δ2H data of four n-alkane chains, the model produces estimated precipitation δ2H with relatively small uncertainty limits. The new framework shows promise for interpretation of paleo-data but could be further improved by including processes associated with n-alkane turnover in plants, transport, and integration into sedimentary archives. Future studies on modern plants and catchment systems will be critical to develop calibration datasets that advance the strength and utility of the framework.
Versatile Germanium Photodiodes with 3dB Bandwidths from 110 GHz to 265 GHz

We demonstrate waveguide coupled germanium fin p-i-n photodiode being on a par with state-of-the-art III-V devices. The intrinsic, undoped germanium regions of the photodiodes are sandwiched in between two complementary in situ-doped silicon regions, circumventing ion-implantation into Ge. By scaling the width of the germanium, different combinations of bandwidths and responsivities can be obtained. Optoelectrical 3-dB bandwidths reaching up to 265 GHz at (1550 nm) 1 mA photocurrent and 2 V reverse bias are shown for a device with ~100 nm narrow germanium fin. Certainly, broader germanium region will yield higher responsivities but on the expense of 3-dB bandwidths. Increase of the germanium width from 100 nm to 450 nm results in a change in internal responsivity from 0.3 A/W to 1 A/W at -2 V bias. The impact of high photocurrent on performance of our new photodiodes will be presented in this paper.
MiniManager: Uma Proposta de Plataforma Web para Emulação de Redes Heterogêneas de Comunicação Móvel

Durante o desenvolvimento de redes de comunicação, a experimentação e a análise de dados auxiliam os pesquisadores e os tomadores de decisão na definição das melhores estratégias de transmissão, recepção e roteamento. Um dos métodos utilizados para reproduzir a realidade das redes de comunicação é a emulação, provendo insumos para avaliar a reação e o desempenho do sistema sob teste. Diante de algumas lacunas identificadas no processo de emulação de redes, este artigo apresenta o MiniManager, uma aplicação baseada no Mininet-WiFi que facilita a gestão e a configuração de experimentos, por meio de uma interface intuitiva e um sistema capaz de capturar a proveniência dos dados resultantes das emulações.
Twisted and coiled polymer muscle actuated soft 3D printed robotic hand with Peltier cooler for drug delivery in medical management

Many robotic hands have been proposed to have unique designs and capabilities, focusing on sensing, actuation, and control. This paper presents experimental studies on a soft 3D-printed robotic hand whose fingers are actuated by twisted and coiled polymer (TCPFL) muscles, driven by resistive heating, and cooled by water and Peltier mechanism (thermoelectric cooling) for increasing the actuation frequency. The hand can be utilized for pick and place applications of drugs in clinical settings, which may be repetitive for humans. A combination of ABS plastic and thermoplastic polyurethane material is used to additively manufacture the robotic hand. The hand along with a housing tank for the muscles and Peltier coolers has a length of 380 mm and weighs 560 gm. The fabrication process of the TCPFL actuators coiled with 160 µm diameter nichrome wires is presented. The actuation frequency in the air for TCPFL is around 0.01 Hz. This study shows the effect of water and Peltier cooling on improving the actuation frequency of the muscles to 0.056 Hz. Experiments have been performed with a flex sensor integrated at the back of each finger to calculate its bend-extent while being actuated by the TCPFL muscles. All these experiments are also used to optimize the TCPFL actuation. Overall, a low-cost and lightweight 3D printed robotic hand is presented in this paper, which significantly increases the actuation performance with the help of cooling methods, that can be used in applications in medical management.
Atopy and Multisensitizations in Specific IgE Microarrays and Their Impact on Severe Asthma

(1) Asthma is a chronic inflammatory airway disease. Around 3–10% of patients experience severe refractory asthma. These patients with high symptom intensity and frequent exacerbations present a challenge for allergologists. Their allergic vs. non-allergic profile might be different from the standard asthmatic group and this difference is vital in qualifying for anti-IgE biologicals. The aim of the study was to analyze multiple sensitizations in patients with severe asthma and assess their impact on the course of the disease. (2) Forty-two patients with severe asthma according to GINA were enrolled. They experienced at least two exacerbations during the past year and had uncontrolled asthma despite high inhaled steroid use. A microarray serum Alex test (allergen-specific IgE to 295 extracts and components) was performed together with Complete Blood Count tests, the Asthma Control Questionnaire (ACQ), the Mini Asthma Quality of Life Questionnaire (MiniAQLQ), and spirometry. (3) There were 29 female and 13 male patients. The patient mean age was 50.4 (22–70). In 25 (60%) patients, inhalant sensitizations were detected. In 9 (21%) cases, a new perennial allergen was discovered that might enable anti-IgE treatment in the future. In the entire studied group, 8 patients (19%) would still not qualify for anti-IgE, anti-IL4, or anti-IL5 treatment. A linear regression analysis revealed that a Canis familiaris allergen (Can f 1) correlated with worse asthma control in ACQ. An Aspergillus allergen (Asp f 6) correlated negatively with Forced Expiratory Volume in one second (FEV1). (4) The study presents the usefulness of the ALEX test in 21% of patients with severe asthma in qualification for anti-IgE treatment. It highlights the impact of canine and Aspergillus sensitizations on worse control in patients with severe asthma.
The hybrid B-type pulsator γ Pegasi: mode identification and complex seismic modelling

We present interpretation of the oscillation spectrum of the early B-type star $\gamma$ Pegasi, in which both low order p/g and high-order g-modes are observed. Using amplitudes and phases of the photometric and radial velocity variations, we identify/constrain the mode degree, $\ell$, for all 14 detected frequencies. Seismic models fitting two pulsational frequencies corresponding to the modes $\ell=0$, p$_1$ and $\ell=1$, g$_1$ were constructed. This set of models contains those which reproduce also the empirical values of the complex nonadiabatic parameter $f$ associated to these two mode frequencies. Unfortunately, there are no models reproducing the values of $f$ for both frequencies simultaneously, regardless of model atmospheres, opacity data, chemical mixture as well as opacity enhancement in the $Z-$ and Deep Opacity Bumps. Most probably, some modifications of the opacities in stellar interiors are still required.
PARP Inhibitors in Advanced Prostate Cancer in Tumors with DNA Damage Signatures

Simple Summary This review paper seeks to summarize the current literature on the role of PARP Inhibitors in Advanced Prostate Cancer in tumors with defects in genes associated with DNA damage repair. It will give particular attention to the role of PARPi in tumors with non-BRCA DNA damage repair genes. The aim of this review is to summarize the literature on PARPi and their activity treating BRCA and non BRCA tumors with DNA damage signatures. Abstract Since 2010, significant progress has been made in the treatment of metastatic castrate resistant prostate cancer (mCRPC). While these advancements have improved survival, mCRPC remains a lethal disease, with a precision medicine framework that is lagging behind compared to other cancers. Poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) studies in prostate cancer (PCa) have focused primarily on the homologous recombination repair (HRR) genes, specifically BRCA1 and BRCA2. While homologous recombination deficiency (HRD) can be prompted by germline or somatic BRCA1/2 genetic mutations, it can also exist in tumors with intact BRCA1/BRCA2 genes. While the sensitivity of PARPi in tumors with non-BRCA DNA damage signatures is not as well established, it has been suggested that genomic alterations in DNA damage repair (DDR) genes other than BRCA may confer synthetic lethality with PARPI in mCRPC. The aim of this review is to summarize the literature on PARPi and their activity treating BRCA and non BRCA tumors with DNA damage signatures.
Seeing things or seeing scenes: Investigating the capabilities of V&L models to align scene descriptions to images

Images can be described in terms of the objects 001 they contain, or in terms of the types of scene 002 or place that they instantiate. In this paper we 003 address to what extent pretrained Vision and 004 Language models can learn to align descrip-005 tions of both types with images. We com-006 pare 3 state-of-the-art models, VisualBERT, 007 LXMERT and CLIP. We ﬁnd that (i) V&L 008 models are susceptible to stylistic biases ac-009 quired during pretraining; (ii) only CLIP per-010 forms consistently well on both object-and 011 scene-level descriptions. A follow-up ablation 012 study shows that CLIP uses object-level infor-013 mation in the visual modality to align with 014 scene-level textual descriptions
EVOLUTION IN THE DUST LANE FRACTION OF EDGE-ON L*V SPIRAL GALAXIES SINCE z = 0.8

The presence of a well-defined and narrow dust lane in an edge-on spiral galaxy is the observational signature of a thin and dense molecular disk, in which gravitational collapse has overcome turbulence. Using a sample of galaxies out to z ∼ 1 extracted from the COSMOS survey, we identify the fraction of massive (L*V) disks that display a dust lane. Our goal is to explore the evolution in the stability of the molecular interstellar medium (ISM) disks in spiral galaxies over a cosmic timescale. We check the reliability of our morphological classifications against changes in rest-frame wavelength, resolution, and cosmic dimming with (artificially redshifted) images of local galaxies from the Sloan Digital Sky Survey. We find that the fraction of L*V disks with dust lanes in COSMOS is consistent with the local fraction (≈80%) out to z ∼ 0.7. At z = 0.8, the dust lane fraction is only slightly lower. A somewhat lower dust lane fraction in starbursting galaxies tentatively supports the notion that a high specific star formation rate can efficiently destroy or inhibit a dense molecular disk. A small subsample of higher redshift COSMOS galaxies display low internal reddening (E[B − V]), as well as a low incidence of dust lanes. These may be disks in which the growth of the dusty ISM disk lags behind that of the stellar disk. We note that at z = 0.8, the most massive galaxies display a lower dust lane fraction than lower mass galaxies. A small contribution of recent mergers or starbursts to this most massive population may be responsible. The fact that the fraction of galaxies with dust lanes in COSMOS is consistent with little or no evolution implies that models to explain the spectral energy distribution or the host galaxy dust extinction of supernovae based on local galaxies are still applicable to higher redshift spirals. It also suggests that dust lanes are long-lived phenomena or can be reformed over very short timescales.