julilili42/papers huggingface dataset:
Towards the discovery of novel molecular clocks in Prokaryotes
2023-06-18

Diel cycle is of enormous biological importance as it imposes daily oscillation in environmental conditions, which temporally structures most ecosystems. Organisms developed biological time-keeping mechanisms - circadian clocks - that provide a significant fitness advantage over competitors by optimising the synchronisation of their biological activities. While circadian clocks are ubiquitous in Eukaryotes, they are so far only characterised in <i>Cyanobacteria</i> within Prokaryotes. However, growing evidence suggests that circadian clocks are widespread in the bacterial and archaeal domains. As Prokaryotes are at the heart of crucial environmental processes and are essential to human health, unravelling their time-keeping systems provides numerous applications in medical research, environmental sciences, and biotechnology. In this review, we elaborate on how novel circadian clocks in Prokaryotes offer research and development perspectives. We compare and contrast the different circadian systems in <i>Cyanobacteria</i> and discuss about their evolution and taxonomic distribution. We necessarily provide an updated phylogenetic analysis of bacterial and archaeal species that harbour homologs of the main cyanobacterial clock components. Finally, we elaborate on new potential clock-controlled microorganisms that represent opportunities of ecological and industrial relevance in prokaryotic groups such as anoxygenic photosynthetic bacteria, methanogenic archaea, methanotrophs or sulphate-reducing bacteria.
LeanStereo: A Leaner Backbone based Stereo Network
2023-06-18

Recently, end-to-end deep networks based stereo matching methods, mainly because of their performance, have gained popularity. However, this improvement in performance comes at the cost of increased computational and memory bandwidth requirements, thus necessitating specialized hardware (GPUs); even then, these methods have large inference times compared to classical methods. This limits their applicability in real-world applications. Although we desire high accuracy stereo methods albeit with reasonable inference time. To this end, we propose a fast end-to-end stereo matching method. Majority of this speedup comes from integrating a leaner backbone. To recover the performance lost because of a leaner backbone, we propose to use learned attention weights based cost volume combined with LogL1 loss for stereo matching. Using LogL1 loss not only improves the overall performance of the proposed network but also leads to faster convergence. We do a detailed empirical evaluation of different design choices and show that our method requires 4x less operations and is also about 9 to 14x faster compared to the state of the art methods like ACVNet [1], LEAStereo [2] and CFNet [3] while giving comparable performance.
Reconfigurable dipole receive array for dynamic parallel imaging at ultra‐high magnetic field
2023-06-18

Purpose To extend the concept of 3D dynamic parallel imaging, we developed a prototype of an electronically reconfigurable dipole array that provides sensitivity alteration along the dipole length. Methods We developed a radiofrequency array coil consisting of eight reconfigurable elevated‐end dipole antennas. The receive sensitivity profile of each dipole can be electronically shifted toward one or the other end by electrical shortening or lengthening the dipole arms using positive‐intrinsic‐negative‐diode lump‐element switching units. Based on the results of electromagnetic simulations, we built the prototype and tested it at 9.4 T on phantom and healthy volunteer. A modified 3D SENSE reconstruction was used, and geometry factor (g‐factor) calculations were performed to assess the new array coil. Results Electromagnetic simulations showed that the new array coil was capable of alteration of its receive sensitivity profile along the dipole length. Electromagnetic and g‐factor simulations showed closely agreeing predictions when compared to the measurements. The new dynamically reconfigurable dipole array provided significant improvement in geometry factor compared to static dipoles. We obtained up to 220% improvement for 3 × 2 ( R y × R z ) acceleration compared to the static configuration case in terms of maximum g‐factor and up to 54% in terms of mean g‐factor for the same acceleration. Conclusion We presented an 8‐element prototype of a novel electronically reconfigurable dipole receive array that permits rapid sensitivity modulations along the dipole axes. Applying dynamic sensitivity modulation during image acquisition emulates two virtual rows of receive elements along the z‐direction, and therefore improves parallel imaging performance for 3D acquisitions.
Distilling Stereo Networks for Performant and Efficient Leaner Networks
2023-06-18

Knowledge distillation has been quite popular in vision for tasks like classification and segmentation however not much work has been done for distilling state-of-the-art stereo matching methods despite their range of applications. One of the reasons for its lack of use in stereo matching networks is due to the inherent complexity of these networks, where a typical network is composed of multiple two- and three-dimensional modules. In this work, we systematically combine the insights from state-of-the-art stereo methods with general knowledge-distillation techniques to develop a joint framework for stereo networks distillation with competitive results and faster inference. Moreover, we show, via a detailed empirical analysis, that distilling knowledge from the stereo network requires careful design of the complete distillation pipeline starting from backbone to the right selection of distillation points and corresponding loss functions. This results in the student networks that are not only leaner and faster but give excellent performance . For instance, our student network while performing better than the performance oriented methods like PSMNet [1], CFNet [2], and LEAStereo [3]) on benchmark SceneFlow dataset, is 8x, 5x, and 8x faster respectively. Furthermore, compared to speed oriented methods having inference time less than 100ms, our student networks perform better than all the tested methods. In addition, our student network also shows better generalization capabilities when tested on unseen datasets like ETH3D and Middlebury.
Antimicrobial Transformation Products in the Aquatic Environment: Global Occurrence, Ecotoxicological Risks, and Potential of Antibiotic Resistance
2023-06-19

The global spread of antimicrobial resistance (AMR) is concerning for the health of humans, animals, and the environment in a One Health perspective. Assessments of AMR and associated environmental hazards mostly focus on antimicrobial parent compounds, while largely overlooking their transformation products (TPs). This review lists antimicrobial TPs identified in surface water environments and examines their potential for AMR promotion, ecological risk, as well as human health and environmental hazards using <i>in silico</i> models. Our review also summarizes the key transformation compartments of TPs, related pathways for TPs reaching surface waters and methodologies for studying the fate of TPs. The 56 antimicrobial TPs covered by the review were prioritized via scoring and ranking of various risk and hazard parameters. Most data on occurrences to date have been reported in Europe, while little is known about antibiotic TPs in Africa, Central and South America, Asia, and Oceania. Occurrence data on antiviral TPs and other antibacterial TPs are even scarcer. We propose evaluation of structural similarity between parent compounds and TPs for TP risk assessment. We predicted a risk of AMR for 13 TPs, especially TPs of tetracyclines and macrolides. We estimated the ecotoxicological effect concentrations of TPs from the experimental effect data of the parent chemical for bacteria, algae and water fleas, scaled by potency differences predicted by quantitative structure-activity relationships (QSARs) for baseline toxicity and a scaling factor for structural similarity. Inclusion of TPs in mixtures with their parent increased the ecological risk quotient over the threshold of one for 7 of the 24 antimicrobials included in this analysis, while only one parent had a risk quotient above one. Thirteen TPs, from which 6 were macrolide TPs, posed a risk to at least one of the three tested species. There were 12/21 TPs identified that are likely to exhibit a similar or higher level of mutagenicity/carcinogenicity, respectively, than their parent compound, with tetracycline TPs often showing increased mutagenicity. Most TPs with increased carcinogenicity belonged to sulfonamides. Most of the TPs were predicted to be mobile but not bioaccumulative, and 14 were predicted to be persistent. The six highest-priority TPs originated from the tetracycline antibiotic family and antivirals. This review, and in particular our ranking of antimicrobial TPs of concern, can support authorities in planning related intervention strategies and source mitigation of antimicrobials toward a sustainable future.
Intraoperative MRI-Guided Resection Is Not Superior to 5-Aminolevulinic Acid Guidance in Newly Diagnosed Glioblastoma: A Prospective Controlled Multicenter Clinical Trial
2023-06-19

PURPOSE Prospective data suggested a superiority of intraoperative MRI (iMRI) over 5-aminolevulinic acid (5-ALA) for achieving complete resections of contrast enhancement in glioblastoma surgery. We investigated this hypothesis in a prospective clinical trial and correlated residual disease volumes with clinical outcome in newly diagnosed glioblastoma. METHODS This is a prospective controlled multicenter parallel-group trial with two center-specific treatment arms (5-ALA and iMRI) and blinded evaluation. The primary end point was complete resection of contrast enhancement on early postoperative MRI. We assessed resectability and extent of resection by an independent blinded centralized review of preoperative and postoperative MRI with 1-mm slices. Secondary end points included progression-free survival (PFS) and overall survival (OS), patient-reported quality of life, and clinical parameters. RESULTS We recruited 314 patients with newly diagnosed glioblastomas at 11 German centers. A total of 127 patients in the 5-ALA and 150 in the iMRI arm were analyzed in the as-treated analysis. Complete resections, defined as a residual tumor ≤0.175 cm3, were achieved in 90 patients (78%) in the 5-ALA and 115 (81%) in the iMRI arm ( P = .79). Incision-suture times ( P &lt; .001) were significantly longer in the iMRI arm (316 v 215 [5-ALA] minutes). Median PFS and OS were comparable in both arms. The lack of any residual contrast enhancing tumor (0 cm3) was a significant favorable prognostic factor for PFS ( P &lt; .001) and OS ( P = .048), especially in methylguanine-DNA-methyltransferase unmethylated tumors ( P = .006). CONCLUSION We could not confirm superiority of iMRI over 5-ALA for achieving complete resections. Neurosurgical interventions in newly diagnosed glioblastoma shall aim for safe complete resections with 0 cm3 contrast-enhancing residual disease, as any other residual tumor volume is a negative predictor for PFS and OS.
XRBcats: Galactic low-mass X-ray binary catalogue
2023-06-19

We present a new catalogue of low-mass X-ray binaries (LMXBs) in the Galaxy. The catalogue contains source names, coordinates, source types, fluxes, distances, system parameters, and other characteristic properties of 349 LMXBs, including systems that have been newly discovered or reclassified since the most recently reported LMXB catalogues. The aim of this catalogue is to provide a list of all currently known Galactic objects identified as LMXBs with some basic information on each system (including X-ray and optical/IR properties where possible). Literature published before May 2023 has been taken into account where possible when compiling this information. References for all reported properties as well as object-finding charts in several energy bands are provided as part of the catalogue. We plan to update the catalogue regularly, in particular to reflect new objects discovered in the ongoing large-scale surveys such as Gaia and eROSITA.
The good and the bad of T cell cross-reactivity: challenges and opportunities for novel therapeutics in autoimmunity and cancer
2023-06-19

T cells are main actors of the immune system with an essential role in protection against pathogens and cancer. The molecular key event involved in this absolutely central task is the interaction of membrane-bound specific T cell receptors with peptide-MHC complexes which initiates T cell priming, activation and recall, and thus controls a range of downstream functions. While textbooks teach us that the repertoire of mature T cells is highly diverse, it is clear that this diversity cannot possibly cover all potential foreign peptides that might be encountered during life. TCR cross-reactivity, i.e. the ability of a single TCR to recognise different peptides, offers the best solution to this biological challenge. Reports have shown that indeed, TCR cross-reactivity is surprisingly high. Hence, the T cell dilemma is the following: be as specific as possible to target foreign danger and spare self, while being able to react to a large spectrum of body-threatening situations. This has major consequences for both autoimmune diseases and cancer, and significant implications for the development of T cell-based therapies. In this review, we will present essential experimental evidence of T cell cross-reactivity, implications for two opposite immune conditions, i.e. autoimmunity vs cancer, and how this can be differently exploited for immunotherapy approaches. Finally, we will discuss the tools available for predicting cross-reactivity and how improvements in this field might boost translational approaches.
Exploring the relationship between epigenetic DNA methylation and cardiac fibrosis through Raman microspectroscopy
2023-06-19

Cardiomyopathies are associated with severe fibrotic remodeling of the heart, which is characterized by the excessive accumulation of collagen type I (COL I). In this study, we used marker-independent Raman microspectroscopy (RMS) to gain a deeper understanding of the disease’s underlying molecular and cellular mechanisms.
Turbinal bones are still one of the last frontiers of the tetrapod skull: hypotheses, challenges and perspectives
2023-06-19

Turbinals are bony or cartilaginous structures that are present in the nasal cavity of most tetrapods. They are involved in key functions such as olfaction, heat, and moisture conservation, as well as protection of the respiratory tract. Despite recent studies that challenged long-standing hypotheses about their physiological and genomic correlation, turbinals remain largely unexplored, particularly for non-mammalian species. Herein, we review and synthesise the current knowledge of turbinals using an integrative approach that includes comparative anatomy, physiology, histology and genomics. In addition, we provide synonyms and correspondences of tetrapod turbinals from about 80 publications. This work represents a first step towards drawing hypotheses of homology for the whole clade, and provides a strong basis to develop new research avenues.
Perpendicular Alignment of 2D Nanoplatelet Emitters in Electrospun Fibers: A Result of the Barus Effect?
2023-06-19

Abstract Stable jet electrospinning (SJES) is a special form of optical fiber generation that prevents chaotic fiber whipping typical for conventional electrospinning procedures. Incorporation of highly emissive semiconductor nanoplatelets (NPLs) in such fibers has very high potential in optical data transmission, optological circuits, fiber lasers, solar light concentrators and many other fields because NPLs exhibit strongly directed emission from their surface plane due to various in‐plane transition dipole moments. However, potential orientation control of 2D‐NPLs in SJES is entirely unknown as electric fields and various mechanical forces contribute in a complex manner simultaneously. Here, the observation of counter‐intuitive yet very beneficial orientation of rectangular CdSe/CdS 2D‐NLP in SJES perpendicular to the fiber drawing axis is reported. Scanning electron microscopy, 3D‐single particle excitation polarization microscopy, 3D‐photogoniometry, polarized emission spectroscopy and small angle X‐ray scattering (SAXS) demonstrate aggregation free perpendicular alignment of the NPLs in poly(methyl methacrylate) (PMMA) fibers, resulting in dominant emission in directions parallel to the fiber. It is suggested that the observed vertical alignment is due to normal forces resulting from viscoelastic expansion when the polymer solution leaves the cannula (Barus effect) and that using such perpendicular nano‐emitter alignment forces allows for the generation of novel materials also beyond fibers.
P4-LISP: A P4-Based High-Performance Router for the Locator/Identifier Separation Protocol
2023-06-19

The networking paradigm locator/identifier split decouples locating and identifying functionality of addresses. Thereby it improves multi-homing, fail-over, mobility, traffic engineering over the Internet, and routing scalability.The Locator/Identifier Separation Protocol (LISP) is a prominent incarnation of that paradigm which recently became an Internet standard. However, existing LISP implementations are either proprietary or have limited performance, which makes their deployment difficult in high-speed networks. Programming Protocol-independent Packet Processors (P4) is a programming language that facilitates the implementation of custom data plane processing on high-performance switches with line rates of up to 400 Gbit/s.In this work, we present P4-LISP, an open-source P4-based proof of concept implementation of a high-performance LISP router. It supports all relevant features such as ITR, ETR, RTR, P-ITR, P-ETR, NAT-traversal, LISP-NAT, and mobile nodes. As control plane, the open-source implementation lispers.net has been integrated on the switch. Security features are added to protect the control plane from being overloaded by the high-performance data plane. The paper describes the architecture of P4-LISP in detail and extensively evaluates performance, functionality, controller performance, and overload protection.
CBM Silicon Tracking System integration: from module production to ladder assembly
2023-06-19

The Silicon Tracking System (STS) is the core detector of the Compressed Baryonic Matter (CBM) experiment at the future FAIR facility. It is located inside of a 1 Tm dipole magnet to achieve a momentum resolution of 2% for charged particles. The functional building block of STS is a module consisting of double-sided silicon micro-strip sensor connected via microcables to front-end electronics located outside of the detector’s physics acceptance of 25°[1]. Self-triggering read-out electronics based on the STS-XYTER ASIC is used, which is capable of acquiring data at collision rates of upto 10 MHz. The system comprises of low-mass detector modules, distributed on 8 tracking stations with a material budget of 1-2% X 0 per station. The stations are made from mechanical half-units onto which ultra-light carbon fiber support structures, or ladders, are mounted which hold the sensors. The positioning of modules after mounting them on the ladder is expected to be in the order of 100 μm. This contribution aims to provide an overview on the module assembly procedure and how modules are integrated on to the ladders along with the challenges faced during the integration. These techniques have been successfully demonstrated in the ongoing FAIR Phase-0 Programme of mini-CBM, where 11 such modules were successfully installed. Additional assemblies have also been made for various test setups.
Unnatural endo type-B PPAPs as novel compounds with activity against Mycobacterium tuberculosis.
2023-06-19

Before the emergence of SARS-CoV-2, tuberculosis (TB) was the leading cause of infectious disease mortality worldwide. Like all antibiotic-exposed bacteria Mycobacterium tuberculosis (Mtb) developed multidrug-resistant (MDR) and exten-sively drug-resistant (XDR) strains which require new antibiotics with novel mechanism of actions. Hyperforin, a natural type-A polyprenylated polycyclic acylphloroglucinol (PPAP) isolated from St. John’s wort, is known for its antibacterial, antidepressant and antimycobacterial activity. However, hyperforin is not stable and easily degradable in light, heat it and oxidizes. Here we report photo- and benchstable type-B PPAPs with structural similarity to hyperforin and enhanced an-timycobacterial activity. We tested a panel of PPAPs and identified our previously reported molecule PPAP22 as lead compound. Converting PPAP22 into the corresponding sodium salt, PPAP53, enhanced the solubility dramatically. We show that PPAP53 inhibits the growth of virulent, extracellular Mtb. Strikingly, the activity is more pronounced intracel-lular Mtb residing in human primary macrophages without damaging the host cell or lung cells. Importantly PPAP53 was also highly active against drug-resistant Mtb. Additionally, we analysed the in vitro properties of PPAP53 in terms of CYP-induction and PXR interaction. Taken together we introduce type-B PPAPs are a new class of antimycobacterial com-pounds, with remarkable activity and favorouble physical properties.
Solutions for humidity and temperature monitoring in the Silicon Tracking System of Compressed Baryonic Matter Experiment: Sensors, Testing and DCS integration
2023-06-19

The Compressed Baryonic Matter (CBM) is one of the leading scientific programs of the future Facility for Anti-proton and Ion Research (FAIR), Darmstadt, Germany. The Silicon Tracking System (STS) will be the core detector system of CBM for charged-particle reconstruction and momentum measurement. It will be placed inside a 1Tm magnet and kept at an ambient temperature of about −10degC to mitigate radiation-induced bulk current in the silicon sensors. Due to the conditions inside the STS reliable monitoring and control of humidity and temperature is required to avoid icing or water condensation on the electronics or silicon sensors. Fiber Optic Sensors (FOS) based on Fiber Bragg Grating (FBG) have proven to be suitable environmental monitoring sensors due to their resilience to the magnetic field, ionizing radiation, and miniature size. In this contribution, we introduce two different approaches to implement relative humidity (RH) and temperature FBG FOS. The first approach is based on inscribing both RH and temperature FBG into one fiber and the second one features two separate FBGs arrays. In both cases, the RH-sensitive FBGs are coated with polyimide.
Application of the Three-fluid Hydrodynamics-based Generator THESEUS to CBM. Proton rapidity- transverse mass spectra reconstruction and correction
2023-06-19

The Compressed Baryonic Matter experiment (CBM) aims at studying the area of the QCD phase diagram at high net baryon densities and moderate temperatures. It is predicted by the Three-Fluid Hydrodynamics-based Event Simulator (THESEUS) that one of the signatures of the phase transition is a change in shape of the mid-rapidity curvature and yield. In this contribution we present the CBM performance for proton (y) and transverse mass (m T ) spectra. The results are obtained for Au+Au collisions at 3.5-12A GeV/c produced by THESEUS model. The CBM detector response is simulated with the GEANT3 engine and reconstruction is done using the CbmRoot framework. Protons are identified with Time-of-Flight technique using 2 different approaches. The obtained spectra are corrected for detector biases using the UrQMD event generator. Results are compared with simulated values. Sources of systematic biases are discussed. The CBM detector is sensitive to the difference between 1st order EoS and hadron gas and crossover in the framework of the THESEUS model.