bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phage-plasmids promote recombination and emergence of phages and plasmids
Authors: Pfeifer Eugen , Rocha Eduardo P. C. 
Published: February 2024

AbstractPhages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.
A mutational atlas for Parkin proteostasis
Authors: Clausen Lene , Voutsinos Vasileios , Cagiada Matteo , Johansson Kristoffer E. , Grønbæk-Thygesen Martin , Nariya Snehal , Powell Rachel L. , Have Magnus K. N. , Oestergaard Vibe H. , Stein Amelie , Fowler Douglas M. , Lindorff-Larsen Kresten , Hartmann-Petersen Rasmus 
Published: February 2024

AbstractProteostasis can be disturbed by mutations affecting folding and stability of the encoded protein. An example is the ubiquitin ligase Parkin, where gene variants result in autosomal recessive Parkinsonism. To uncover the pathological mechanism and provide comprehensive genotype-phenotype information, variant abundance by massively parallel sequencing (VAMP-seq) is leveraged to quantify the abundance of Parkin variants in cultured human cells. The resulting mutational map, covering 9219 out of the 9300 possible single-site amino acid substitutions and nonsense Parkin variants, shows that most low abundance variants are proteasome targets and are located within the structured domains of the protein. Half of the known disease-linked variants are found at low abundance. Systematic mapping of degradation signals (degrons) reveals an exposed degron region proximal to the so-called “activation element”. This work provides examples of how missense variants may cause degradation either via destabilization of the native protein, or by introducing local signals for degradation.
General-purpose programmable photonic processor for advanced radiofrequency applications
Authors: Pérez-López Daniel , Gutierrez Ana , Sánchez David , López-Hernández Aitor , Gutierrez Mikel , Sánchez-Gomáriz Erica , Fernández Juan , Cruz Alejandro , Quirós Alberto , Xie Zhenyun , Benitez Jesús , Bekesi Nandor , Santomé Alejandro , Pérez-Galacho Diego , DasMahapatra Prometheus , Macho Andrés , Capmany José 
Published: February 2024

AbstractA general-purpose photonic processor can be built integrating a silicon photonic programmable core in a technology stack comprising an electronic monitoring and controlling layer and a software layer for resource control and programming. This processor can leverage the unique properties of photonics in terms of ultra-high bandwidth, high-speed operation, and low power consumption while operating in a complementary and synergistic way with electronic processors. These features are key in applications such as next-generation 5/6 G wireless systems where reconfigurable filtering, frequency conversion, arbitrary waveform generation, and beamforming are currently provided by microwave photonic subsystems that cannot be scaled down. Here we report the first general-purpose programmable processor with the remarkable capability to implement all the required basic functionalities of a microwave photonic system by suitable programming of its resources. The processor is fabricated in silicon photonics and incorporates the full photonic/electronic and software stack.
Deglaciation-enhanced mantle CO2 fluxes at Yellowstone imply positive climate feedback
Authors: Clerc Fiona , Behn Mark D. , Minchew Brent M. 
Published: February 2024

AbstractMantle melt generation in response to glacial unloading has been linked to enhanced magmatic volatile release in Iceland and global eruptive records. It is unclear whether this process is important in systems lacking evidence of enhanced eruptions. The deglaciation of the Yellowstone ice cap did not observably enhance volcanism, yet Yellowstone emits large volumes of CO2 due to melt crystallization at depth. Here we model mantle melting and CO2 release during the deglaciation of Yellowstone (using Iceland as a benchmark). We find mantle melting is enhanced 19-fold during deglaciation, generating an additional 250–620 km3. These melts segregate an additional 18–79 Gt of CO2 from the mantle, representing a ~3–15% increase in the global volcanic CO2 flux (if degassed immediately). We suggest deglaciation-enhanced mantle melting is important in continental settings with partially molten mantle – including Greenland and West Antarctica – potentially implying positive feedbacks between deglaciation and climate warming.
Plasticity-induced repression of Irf6 underlies acquired resistance to cancer immunotherapy in pancreatic ductal adenocarcinoma
Authors: Kim Il-Kyu , Diamond Mark S. , Yuan Salina , Kemp Samantha B. , Kahn Benjamin M. , Li Qinglan , Lin Jeffrey H. , Li Jinyang , Norgard Robert J. , Thomas Stacy K. , Merolle Maria , Katsuda Takeshi , Tobias John W. , Baslan Timour , Politi Katerina , Vonderheide Robert H. , Stanger Ben Z. 
Published: February 2024

AbstractAcquired resistance to immunotherapy remains a critical yet incompletely understood biological mechanism. Here, using a mouse model of pancreatic ductal adenocarcinoma (PDAC) to study tumor relapse following immunotherapy-induced responses, we find that resistance is reproducibly associated with an epithelial-to-mesenchymal transition (EMT), with EMT-transcription factors ZEB1 and SNAIL functioning as master genetic and epigenetic regulators of this effect. Acquired resistance in this model is not due to immunosuppression in the tumor immune microenvironment, disruptions in the antigen presentation machinery, or altered expression of immune checkpoints. Rather, resistance is due to a tumor cell-intrinsic defect in T-cell killing. Molecularly, EMT leads to the epigenetic and transcriptional silencing of interferon regulatory factor 6 (Irf6), rendering tumor cells less sensitive to the pro-apoptotic effects of TNF-α. These findings indicate that acquired resistance to immunotherapy may be mediated by programs distinct from those governing primary resistance, including plasticity programs that render tumor cells impervious to T-cell killing.
Real space characterization of nonlinear hall effect in confined directions
Authors: Luo Sheng , Hsu Chuang-Han , Chang Guoqing , Bansil Arun , Lin Hsin , Liang Gengchiau 
Published: February 2024

AbstractThe nonlinear Hall effect (NLHE) is a phenomenon which could produce a transverse Hall voltage in a time-reversal-invariant material. Here, we report the real space characterizations of NLHE evaluated through quantum transport in TaIrTe4 nanoribbon without the explicit Berry curvature dipole (BCD) information. We first characterize the NLHE in both transverse confined directions in global-level measurement. The impact of quantum confinement in NLHE is evaluated by adjusting the width of nanoribbons. Then, the probing area is trimmed to the atomic scale to evaluate the local texture, where we discover its patterns differ among the probed neighboring atomic groups. The analysis of charge distribution reveals the connections between NLHE’s local patterns and its non-centrosymmetric nature, rendering nearly an order of Hall voltage enhancement through probe positioning. Our work paves the way to expand the range of NLHE study and unveil its physics in more versatile material systems.
Versatile spaceborne photonics with chalcogenide phase-change materials
Authors: Kim Hyun Jung , Julian Matthew , Williams Calum , Bombara David , Hu Juejun , Gu Tian , Aryana Kiumars , Sauti Godfrey , Humphreys William 
Published: February 2024

AbstractRecent growth in space systems has seen increasing capabilities packed into smaller and lighter Earth observation and deep space mission spacecraft. Phase-change materials (PCMs) are nonvolatile, reconfigurable, fast-switching, and have recently shown a high degree of space radiation tolerance, thereby making them an attractive materials platform for spaceborne photonics applications. They promise robust, lightweight, and energy-efficient reconfigurable optical systems whose functions can be dynamically defined on-demand and on-orbit to deliver enhanced science or mission support in harsh environments on lean power budgets. This comment aims to discuss the recent advances in rapidly growing PCM research and its potential to transition from conventional terrestrial optoelectronics materials platforms to versatile spaceborne photonic materials platforms for current and next-generation space and science missions. Materials International Space Station Experiment-14 (MISSE-14) mission-flown PCMs outside of the International Space Station (ISS) and key results and NASA examples are highlighted to provide strong evidence of the applicability of spaceborne photonics.
Stretchable liquid metal based biomedical devices
Authors: Deng Yifan , Bu Fan , Wang Yujie , Chee Pei Song , Liu Xiangye , Guan Cao 
Published: February 2024

AbstractPursuit of improved living quality has stimulated great demand for high-performance conformal healthcare devices in modern human society. However, manufacturing of efficient, comfortable and stretchable biomedical apparatus faces huge challenges using traditional materials. Liquid metals (LMs) show remarkable potential to solve this problem due to their extraordinary biocompatibility, stretchability, thermal and electrical conductivity. In recent years, tremendous explorations have attempted to make stretchable biomedical devices with LMs. Herein, we review the stretchable LM-based biomedical devices on the topics of disease treatment and human function augmenting. The representative and up-to-date neural interfaces, alloy cement, e-vessels, soft heaters, exoskeletons, and e-skins are summarized. The existing issues of LMs applied for biomedical devices are also discussed. This review can provide guidance for the follow-up research in LM-based biomedical devices.
Better-than-classical Grover search via quantum error detection and suppression
Authors: Pokharel Bibek , Lidar Daniel A. 
Published: February 2024

AbstractWe report better-than-classical success probabilities for a complete Grover quantum search algorithm on the largest scale demonstrated to date, of up to five qubits, using two different IBM platforms. This is enabled by error suppression via robust dynamical decoupling. Further improvements arise after the use of measurement error mitigation, but the latter is insufficient by itself for achieving better-than-classical performance. For two qubits, we demonstrate a 99.5% success probability via the use of the [[4, 2, 2]] quantum error-detection (QED) code. This constitutes a demonstration of quantum algorithmic breakeven via QED. Along the way, we introduce algorithmic error tomography (AET), a method that provides a holistic view of the errors accumulated throughout an entire quantum algorithm, filtered via the errors detected by the QED code used to encode the circuit. We demonstrate that AET provides a stringent test of an error model based on a combination of amplitude damping, dephasing, and depolarization.
The inherence bias in preschoolers’ explanations for achievement differences: replication and extension
Authors: Renoux Margaux , Goudeau Sébastien , Alexopoulos Theodore , Bouquet Cédric A. , Cimpian Andrei 
Published: February 2024

AbstractTwo studies examined how preschoolers (N = 610; French) explain differences in achievement. Replicating and extending previous research, the results revealed that children invoke more inherent factors (e.g., intelligence) than extrinsic factors (e.g., access to educational resources) when explaining why some children do better in school than others. This inherence bias in explanation can contribute to inequalities in education (e.g., the early-emerging disparities based on social class) by portraying them as fair and legitimate even when they are not.
Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities
Authors: Roider Tobias , Baertsch Marc A. , Fitzgerald Donnacha , Vöhringer Harald , Brinkmann Berit J. , Czernilofsky Felix , Knoll Mareike , Llaó-Cid Laura , Mathioudaki Anna , Faßbender Bianca , Herbon Maxime , Lautwein Tobias , Bruch Peter-Martin , Liebers Nora , Schürch Christian M. , Passerini Verena , Seifert Marc , Brobeil Alexander , Mechtersheimer Gunhild , Müller-Tidow Carsten , Weigert Oliver , Seiffert Martina , Nolan Garry P. , Huber Wolfgang , Dietrich Sascha 
Published: February 2024

AbstractThe redirection of T cells has emerged as an attractive therapeutic principle in B cell non-Hodgkin lymphoma (B-NHL). However, a detailed characterization of lymphoma-infiltrating T cells across B-NHL entities is missing. Here we present an in-depth T cell reference map of nodal B-NHL, based on cellular indexing of transcriptomes and epitopes, T cell receptor sequencing, flow cytometry and multiplexed immunofluorescence applied to 101 lymph nodes from patients with diffuse large B cell, mantle cell, follicular or marginal zone lymphoma, and from healthy controls. This multimodal resource revealed quantitative and spatial aberrations of the T cell microenvironment across and within B-NHL entities. Quantitative differences in PD1+TCF7− cytotoxic T cells, T follicular helper cells or IKZF3+ regulatory T cells were linked to their clonal expansion. The abundance of PD1+TCF7− cytotoxic T cells was associated with poor survival. Our study portrays lymphoma-infiltrating T cells with unprecedented comprehensiveness and provides a unique resource for the investigation of lymphoma biology and prognosis.
Clinical surveillance systems obscure the true cholera infection burden in an endemic region
Authors: Hegde Sonia T. , Khan Ashraful Islam , Perez-Saez Javier , Khan Ishtiakul Islam , Hulse Juan Dent , Islam Md Taufiqul , Khan Zahid Hasan , Ahmed Shakeel , Bertuna Taner , Rashid Mamunur , Rashid Rumana , Hossain Md Zakir , Shirin Tahmina , Wiens Kirsten E. , Gurley Emily S. , Bhuiyan Taufiqur Rahman , Qadri Firdausi , Azman Andrew S. 
Published: February 2024

AbstractOur understanding of cholera transmission and burden largely relies on clinic-based surveillance, which can obscure trends, bias burden estimates and limit the impact of targeted cholera-prevention measures. Serological surveillance provides a complementary approach to monitoring infections, although the link between serologically derived infections and medically attended disease incidence—shaped by immunological, behavioral and clinical factors—remains poorly understood. We unravel this cascade in a cholera-endemic Bangladeshi community by integrating clinic-based surveillance, healthcare-seeking and longitudinal serological data through statistical modeling. Combining the serological trajectories with a reconstructed incidence timeline of symptomatic cholera, we estimated an annual Vibrio cholerae O1 infection incidence rate of 535 per 1,000 population (95% credible interval 514–556), with incidence increasing by age group. Clinic-based surveillance alone underestimated the number of infections and reported cases were not consistently correlated with infection timing. Of the infections, 4 in 3,280 resulted in symptoms, only 1 of which was reported through the surveillance system. These results impart insights into cholera transmission dynamics and burden in the epicenter of the seventh cholera pandemic, where >50% of our study population had an annual V. cholerae O1 infection, and emphasize the potential for a biased view of disease burden and infection risk when depending solely on clinical surveillance data.
Development of statistical auto-segmentation method for diffusion restriction gray matter lesions in patients with newly diagnosed sporadic Creutzfeldt–Jakob disease
Authors: Heo Hwon , Park Ho Young , Suh Chong Hyun , Shim Woo Hyun , Lim Jae-Sung , Lee Jae-Hong , Kim Sang Joon 
Published: February 2024

AbstractQuantification of diffusion restriction lesions in sporadic Creutzfeldt-Jakob disease (sCJD) may provide information of the disease burden. We aim to develop an automatic segmentation model for sCJD and to evaluate the volume of disease extent as a prognostic marker for overall survival. Fifty-six patients (mean age ± SD, 61.2 ± 9.9 years) were included from February 2000 to July 2020. A threshold-based segmentation was used to obtain abnormal signal intensity masks. Segmented volumes were compared with the visual grade. The Dice similarity coefficient was calculated to measure the similarity between the automatic vs. manual segmentation. Cox proportional hazards regression analysis was performed to evaluate the volume of disease extent as a prognostic marker. The automatic segmentation showed good correlation with the visual grading. The cortical lesion volumes significantly increased as the visual grade aggravated (extensive: 112.9 ± 73.2; moderate: 45.4 ± 30.4; minimal involvement: 29.6 ± 18.1 mm3) (P < 0.001). The deep gray matter lesion volumes were significantly higher for positive than for negative involvement of the deep gray matter (5.6 ± 4.6 mm3vs. 1.0 ± 1.3 mm3,P < 0.001). The mean Dice similarity coefficients were 0.90 and 0.94 for cortical and deep gray matter lesions, respectively. However, the volume of disease extent was not associated with worse overall survival (cortical extent:P = 0.07; deep gray matter extent:P = 0.12).
Impact of modifiers on soil–water characteristics of graphite tailings
Authors: Du Changbo , Lu Xinxin , Yi Fu 
Published: February 2024

AbstractTo achieve integrated resource utilization of graphite tailings to improve their water-holding capacity, river silt and cow dung powder were added to graphite tailings as organic matter improvers. Improver ratios were designed using 4 g cow dung powder and 20, 30, and 50 g river silt. Soil–water characterization tests were performed using a combined tensiometer and filter paper method based on optimum density measurements. Analysis of the influence of river silt dosing on the soil–water characteristic curves of improved graphite tailing specimens was performed with data fitting using the Van Genuchten model. Here, we investigated the effect of river silt dosing on the internal pore structure and water-holding capacity of modified graphite tailing samples and verified the applicability of the model to graphite tailings. Our results demonstrate that the organic matter improver incorporated into graphite tailings can improve the internal structural compactness of graphite tailings, improving the water holding capacity. With an increase in river silt dosage, the saturated water content is larger, and the residual water content increases and then decreases. When river silt dosage is 30 g, the residual water content is the highest at a value of 3.32%. The van Genuchten model was highly accurate for assessing the graphite tailings. With an increase in river silt doping, the internal pore space first decreased and then increased, and the internal structure gradually became compact and loosened. The internal structure was in the optimal state in the experimental study when the dosage of cow dung powder was 4 g and the dosage of river silt was 30 g. The water holding capacity was optimal at this time. The results of this study provide a theoretical foundation for graphite-tailing-based mine reclamation and play a guiding role in exploring the value of the hydraulic characteristic index parameters when applying graphite tailings engineering.
Efficient, high-power, narrow-linewidth, continuous-wave quantum-dot semiconductor comb laser
Authors: Buyalo Mikhail , Gubenko Alexey , Mikhrin Sergey , Mikhrin Vladimir , Kovsh Alexey R. , Krishnamoorthy Ashok V. 
Published: February 2024

AbstractWe report a continuous-wave, O-band quantum-dot semiconductor comb laser for WDM optical interconnects exhibiting a 2.2 THz optical bandwidth with up to 89 comb wavelengths spaced at 25 GHz, over 30% peak ex-facet electrical-to-optical power conversion efficiency, up to 270 mW of usable laser power, relative intensity noise below − 135 dB/Hz per individual mode, individual laser mode linewidth of 140 kHz, mode beating linewidths of 50 kHz across all modes, and stable far-field output with 75% coupling efficiency to PM fiber in a butterfly package.
Environmental enrichment promotes adaptive responding during tests of behavioral regulation in male heterogeneous stock rats
Authors: Ishiwari Keita , King Christopher P. , Martin Connor D. , Tripi Jordan A. , George Anthony M. , Lamparelli Alexander C. , Chitre Apurva S. , Polesskaya Oksana , Richards Jerry B. , Solberg Woods Leah C. , Gancarz Amy M. , Palmer Abraham A. , Dietz David M. , Mitchell Suzanne H. , Meyer Paul J. 
Published: February 2024

AbstractOrganisms must regulate their behavior flexibly in the face of environmental challenges. Failure can lead to a host of maladaptive behavioral traits associated with a range of neuropsychiatric disorders, including attention deficit hyperactivity disorder, autism, and substance use disorders. This maladaptive dysregulation of behavior is influenced by genetic and environmental factors. For example, environmental enrichment produces beneficial neurobehavioral effects in animal models of such disorders. The present study determined the effects of environmental enrichment on a range of measures related to behavioral regulation using a large cohort of male, outbred heterogeneous stock (HS) rats as subjects. Subjects were reared from late adolescence onwards either in pairs in standard housing with minimal enrichment (n = 200) or in groups of 16 in a highly enriched environment consisting of a large multi-level cage filled with toys, running wheels, and shelters (n = 64). Rats were subjected to a battery of tests, including: (i) locomotor response to novelty, (ii) light reinforcement, (iii) social reinforcement, (iv) reaction time, (v) a patch-depletion foraging test, (vi) Pavlovian conditioned approach, (vii) conditioned reinforcement, and (viii) cocaine conditioned cue preference. Results indicated that rats housed in the enriched environment were able to filter out irrelevant stimuli more effectively and thereby regulate their behavior more efficiently than standard-housing rats. The dramatic impact of environmental enrichment suggests that behavioral studies using standard housing conditions may not generalize to more complex environments that may be more ethologically relevant.