bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes
Authors: Asleh Karama , Negri Gian Luca , Spencer Miko Sandra E. , Colborne Shane , Hughes Christopher S. , Wang Xiu Q. , Gao Dongxia , Gilks C. Blake , Chia Stephen K. L. , Nielsen Torsten O. , Morin Gregg B. 
Published: February 2022

AbstractDespite advances in genomic classification of breast cancer, current clinical tests and treatment decisions are commonly based on protein level information. Formalin-fixed paraffin-embedded (FFPE) tissue specimens with extended clinical outcomes are widely available. Here, we perform comprehensive proteomic profiling of 300 FFPE breast cancer surgical specimens, 75 of each PAM50 subtype, from patients diagnosed in 2008-2013 (n = 178) and 1986-1992 (n = 122) with linked clinical outcomes. These two cohorts are analyzed separately, and we quantify 4214 proteins across all 300 samples. Within the aggressive PAM50-classified basal-like cases, proteomic profiling reveals two groups with one having characteristic immune hot expression features and highly favorable survival. Her2-Enriched cases separate into heterogeneous groups differing by extracellular matrix, lipid metabolism, and immune-response features. Within 88 triple-negative breast cancers, four proteomic clusters display features of basal-immune hot, basal-immune cold, mesenchymal, and luminal with disparate survival outcomes. Our proteomic analysis characterizes the heterogeneity of breast cancer in a clinically-applicable manner, identifies potential biomarkers and therapeutic targets, and provides a resource for clinical breast cancer classification.
Xrn1 is a deNADding enzyme modulating mitochondrial NAD-capped RNA
Authors: Sharma Sunny , Yang Jun , Grudzien-Nogalska Ewa , Shivas Jessica , Kwan Kelvin Y. , Kiledjian Megerditch 
Published: February 2022

AbstractThe existence of non-canonical nicotinamide adenine diphosphate (NAD) 5′-end capped RNAs is now well established. Nevertheless, the biological function of this nucleotide metabolite cap remains elusive. Here, we show that the yeast Saccharomyces cerevisiae cytoplasmic 5′-end exoribonuclease Xrn1 is also a NAD cap decapping (deNADding) enzyme that releases intact NAD and subsequently degrades the RNA. The significance of Xrn1 deNADding is evident in a deNADding deficient Xrn1 mutant that predominantly still retains its 5′-monophosphate exonuclease activity. This mutant reveals Xrn1 deNADding is necessary for normal growth on non-fermenting sugar and is involved in modulating mitochondrial NAD-capped RNA levels and may influence intramitochondrial NAD levels. Our findings uncover a contribution of mitochondrial NAD-capped RNAs in overall NAD regulation with the deNADding activity of Xrn1 fulfilling a central role.
Impact of charge noise on electron exchange interactions in semiconductors
Authors: Keith D. , Gorman S. K. , He Y. , Kranz L. , Simmons M. Y. 
Published: February 2022

AbstractThe electron exchange interaction is a promising medium for the entanglement of single-spin qubits in semiconductors as it results in high-speed two-qubit gates. The quality of such entangling gates is reduced by the presence of noise caused by nearby defects acting as two-level fluctuators. To date, the effect of charge noise has been calculated assuming a Gaussian distribution of exchange interaction frequencies between the qubits equivalent to a linear coupling of charge noise with the exchange interaction. In reality the coupling can differ significantly from this linear-coupling approximation depending on the inter-qubit tunnel coupling, detuning of the qubit system, and the magnitude of charge noise. We derive analytical expressions for the frequency spectra of exchange oscillations that encompasses both linear and non-linear coupling to charge-noise. The resulting decoherence times and decay profiles of the exchange oscillations vary considerably. When compared with recent experiments our model shows that non-linear charge-noise coupling is significant and requires consideration to characterise and optimise exchange-based entangling gates.
Stabilizing multiple topological fermions on a quantum computer
Authors: Koh Jin Ming , Tai Tommy , Phee Yong Han , Ng Wei En , Lee Ching Hua 
Published: February 2022

AbstractIn classical and single-particle settings, non-trivial band topology always gives rise to robust boundary modes. For quantum many-body systems, however, multiple topological fermions are not always able to coexist, since Pauli exclusion prevents additional fermions from occupying the limited number of available topological modes. In this work, we show, through IBM quantum computers, how one can robustly stabilize more fermions than the number of topological modes through specially designed 2-fermion interactions. Our demonstration hinges on the realization of BDI- and D-class topological Hamiltonians on transmon-based quantum hardware, and relied on a tensor network-aided circuit recompilation approach. We also achieved the full reconstruction of multiple-fermion topological band structures through iterative quantum phase estimation (IQPE). All in all, our work showcases how advances in quantum algorithm implementation enable noisy intermediate-scale quantum (NISQ) devices to be exploited for topological stabilization beyond the context of single-particle topological invariants.
A database of common vampire bat reports
Authors: Van de Vuurst Paige , Díaz M. Mónica , Rodríguez-San Pedro Annia , Allendes Juan Luis , Brown Natalie , Gutiérrez Juan David , Zarza Heliot , de Oliveira Stefan V. , Cárdenas-Canales Elsa , Barquez Rubén M. , Escobar Luis E. 
Published: February 2022

AbstractThe common vampire bat (Desmodus rotundus) is a sanguivorous (i.e., blood-eating) bat species distributed in the Americas from northern Mexico southwards to central Chile and Argentina. Desmodus rotundus is one of only three mammal species known to feed exclusively on blood, mainly from domestic mammals, although large wildlife and occasionally humans can also serve as a food source. Blood feeding makes D. rotundus an effective transmissor of pathogens to its prey. Consequently, this species is a common target of culling efforts by various individuals and organizations. Nevertheless, little is known about the historical distribution of D. rotundus. Detailed occurrence data are critical for the accurate assessment of past and current distributions of D. rotundus as part of ecological, biogeographical, and epidemiological research. This article presents a dataset of D. rotundus historical occurrence reports, including >39,000 locality reports across the Americas to facilitate the development of spatiotemporal studies of the species. Data are available at https://doi.org/10.6084/m9.figshare.15025296.
Carbon fibres as potential bone implants with controlled doxorubicin release
Authors: Chudoba Dorota , Łudzik Katarzyna , Jażdżewska Monika 
Published: February 2022

AbstractThis work presents the structural characterisation of carbon fibres obtained from the carbonization of flax tow at 400°C (CFs400°C) and 1000°C (CFs1000°C) and the thermodynamic and kinetic studies of adsorption of Doxorubicin (Dox) on the fibres. The characteristic of carbon fibres and their drug adsorption and removal mechanism were investigated and compared with that of natural flax tow. All fibres were fully characterized by scanning electron microscopy (SEM), Fourier transforms infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), specific surface area analysis and Boehm titration. The results demonstrated the highest adsorption properties of CFs400°C at 323 K (qmax = 275 mg g−1). The kinetic data followed the pseudo-second-order kinetic model more closely, whereas the Dubinin–Radushkevich model suitably described isotherms for all fibres. Calculated parameters revealed that the adsorption process of Dox ions is spontaneous and mainly followed by physisorption and a pore-filling mechanism. The removal efficiency for carbon fibres is low due to the effect of pore-blocking and hydrophobic hydration. However, presented fibres can be treated with a base for further chemical surface modification, increasing the adsorption capacity and controlling the release tendency.
Using publicly available transcriptomic data to identify mechanistic and diagnostic biomarkers in azoospermia and overall male infertility
Authors: Omolaoye Temidayo S. , Hachim Mahmood Yaseen , du Plessis Stefan S. 
Published: February 2022

AbstractAzoospermia, which is the absence of spermatozoa in an ejaculate occurring due to defects in sperm production, or the obstruction of the reproductive tract, affects about 1% of all men and is prevalent in up to 10–15% of infertile males. Conventional semen analysis remains the gold standard for diagnosing and treating male infertility; however, advances in molecular biology and bioinformatics now highlight the insufficiency thereof. Hence, the need to widen the scope of investigating the aetiology of male infertility stands pertinent. The current study aimed to identify common differentially expressed genes (DEGs) that might serve as potential biomarkers for non-obstructive azoospermia (NOA) and overall male infertility. DEGs across different datasets of transcriptomic profiling of testis from human patients with different causes of infertility/ impaired spermatogenesis and/or azoospermia were explored using the gene expression omnibus (GEO) database. Following the search using the GEOquery, 30 datasets were available, with 5 meeting the inclusion criteria. The DEGs for datasets were identified using limma R packages through the GEO2R tool. The annotated genes of the probes in each dataset were intersected with DEGs from all other datasets. Enriched Ontology Clustering for the identified genes was performed using Metascape to explore the possible connection or interaction between the genes. Twenty-five DEGs were shared between most of the datasets, which might indicate their role in the pathogenesis of male infertility. Of the 25 DEGs, eight genes (THEG, SPATA20, ROPN1L, GSTF1, TSSK1B, CABS1, ADAD1, RIMBP3) are either involved in the overall spermatogenic processes or at specific phases of spermatogenesis. We hypothesize that alteration in the expression of these genes leads to impaired spermatogenesis and, ultimately, male infertility. Thus, these genes can be used as potential biomarkers for the early detection of NOA.
Artificial double inversion recovery images can substitute conventionally acquired images: an MRI-histology study
Authors: Bouman Piet M. , Steenwijk Martijn D. , Geurts Jeroen J. G. , Jonkman Laura E. 
Published: February 2022

AbstractCortical multiple sclerosis lesions are disease-specific, yet inconspicuous on magnetic resonance images (MRI). Double inversion recovery (DIR) images are sensitive, but often unavailable in clinical routine and clinical trials. Artificially generated images can mitigate this issue, but lack histopathological validation. In this work, artificial DIR images were generated from postmortem 3D-T1 and proton-density (PD)/T2 or 3D-T1 and 3D fluid-inversion recovery (FLAIR) images, using a generative adversarial network. All sequences were scored for cortical lesions, blinded to histopathology. Subsequently, tissue samples were stained for proteolipid protein (myelin) and scored for cortical lesions type I-IV (leukocortical, intracortical, subpial and cortex-spanning, respectively). Histopathological scorings were then (unblinded) compared to MRI using linear mixed models. Images from 38 patients (26 female, mean age 64.3 ± 10.7) were included. A total of 142 cortical lesions were detected, predominantly subpial. Histopathology-blinded/unblinded sensitivity was 13.4/35.2% for artificial DIR generated from T1-PD/T2, 14.1/41.5% for artificial DIR from T1-FLAIR, 17.6/49.3% for conventional DIR and 10.6/34.5% for 3D-T1. When blinded to histopathology, there were no differences; with histopathological feedback at hand, conventional DIR and artificial DIR from T1-FLAIR outperformed the other sequences. Differences between histopathology-blinded/unblinded sensitivity could be minified through adjustment of the scoring criteria. In conclusion, artificial DIR images, particularly generated from T1-FLAIR could potentially substitute conventional DIR images when these are unavailable.
Effectiveness of wireless emergency alerts for social distancing against COVID-19 in Korea
Authors: Yeon Dahye , Kwak Myunghwan , Chung Ji-Bum 
Published: February 2022

AbstractThis study aimed to evaluate the effectiveness of wireless emergency alerts (WEAs) on social distancing policy. The Republic of Korea has been providing information to the public through WEAs using mobile phones. This study used five data sets: WEA messages, news articles including the keyword “COVID-19,” the number of confirmed COVID-19 patients, public foot traffic data, and the government’s social distancing level. The WEAs were classified into two topics—“warning” and “guidance”—using a random forest model. The results of the correlation analysis and further detailed analysis confirmed that the “warning” WEA topic and number of news articles significantly affected public foot traffic. However, the “guidance” topic was not significantly associated with public foot traffic. In general, the Korean government’s WEAs were effective at encouraging the public to follow social distance recommendations during the COVID-19 pandemic. In particular, the “warning” WEA topic, by providing information about the relative risk directly concerning the recipients, was significantly more effective than the “guidance” topic.
Expression of genes and localization of enzymes involved in polyunsaturated fatty acid synthesis in rabbit testis and epididymis
Authors: Castellini Cesare , Mattioli Simona , Moretti Elena , Cotozzolo Elisa , Perini Francesco , Dal Bosco Alessandro , Signorini Cinzia , Noto Daria , Belmonte Giuseppe , Lasagna Emiliano , Brecchia Gabriele , Collodel Giulia 
Published: February 2022

AbstractThe metabolism of polyunsaturated fatty acids (PUFAs) plays an important role in male reproduction. Linoleic and alpha-linolenic acids need to be provided in the diet and they are converted into long chain polyunsaturated fatty acids by steps of elongation and desaturation, exerted by elongases 2 (ELOVL2) and 5 (ELOVL5) and Δ5- (FADS1) and Δ6-desaturase (FADS2). This study aims to assess the gene expression and localization of enzymes involved in the synthesis of n-3 and n-6 long-chain PUFAs in control rabbits and those fed diets containing 10% extruded flaxseed. Enzyme and PUFA localization were assessed in the testes and epididymis by immunofluorescence. Testes showed high gene expression of FADS2, ELOVL2 and ELOVL5 and low expression of FADS1. Intermediate metabolites, enzymes and final products were differently found in Leydig, Sertoli and germinal cells. FADS2 was localized in interstitial cells and elongated spermatids; ELOVL5 in meiotic cells; FADS1 was evident in interstitial tissue, Sertoli cells and elongated spermatids; ELOVL2 in interstitial cells. Epididymal vesicles were positive for FADS1, ELOVL2 and ELOVL5 as well as docosahexaenoic, eicosapentaenoic, and arachidonic acids. This knowledge of fatty acids (FA) metabolism in spermatogenesis and the influence of diet on FA profile could help identify causes of male infertility, suggesting new personalized therapy.
Validating Automatic Diadochokinesis Analysis Methods Across Dysarthria Severity and Syllable Task in Amyotrophic Lateral Sclerosis
Authors: Tanchip Chelsea , Guarin Diego L. , McKinlay Scotia , Barnett Carolina , Kalra Sanjay , Genge Angela , Korngut Lawrence , Green Jordan R. , Berry James , Zinman Lorne , Yadollahi Azadeh , Abrahao Agessandro , Yunusova Yana 
Published: February 2022

Purpose:
Oral diadochokinesis (DDK) is a standard dysarthria assessment task. To extract automatic and semi-automatic DDK measurements, numerous DDK analysis algorithms based on acoustic signal processing are available, including amplitude based, spectral based, and hybrid. However, these algorithms have been predominantly validated in individuals with no perceptible to mild dysarthria. The behavior of these algorithms across dysarthria severity is largely unknown. Likewise, these algorithms have not been tested equally for various syllable types. The goal of this study was to evaluate the performance of five common DDK algorithms as a function of dysarthria severity, considering syllable types.

Method:
We analyzed 282 DDK recordings of /ba/, /pa/, and /ta/ from 145 participants with amyotrophic lateral sclerosis. Recordings were stratified into mild, moderate, or severe dysarthria groups based on individual performance on the Speech Intelligibility Test. Analysis included manual and automatic estimation of the number of syllables, DDK rate, and cycle-to-cycle temporal variability (cTV). Validation metrics included Bland–Altman mixed-effects limits of agreement between manual and automatic syllable counts, recall and precision between manual and automatic syllable boundary detection, and Kendall's tau-b correlations between manual and algorithm-detected DDK rate and cTV.

Results:

The amplitude-based algorithm (absolute energy) yielded the strongest correlations with manual analysis across all severity groups for DDK rate (
τ
b
= 0.7–0.84) and cTV (
τ
b
= 0.7–0.84) and the narrowest limits of agreement (−5.92 to 7.12 syllable difference). Moreover, this algorithm also provided the highest mean recall and precision across severity groups for /ba/ and /pa/, but with significantly more variation for/ta/.

Conclusions:
Algorithms based on signal energy analysis appeared to be the most robust for DDK analysis across dysarthria severity and syllable types; however, it remains prone to error against severe dysarthria and alveolar syllable context. Further development is needed to address this important issue.
RISSNet: Retain low‐light image details and improve the structural similarity net
Authors: Zhao Junbo , Chen Hongyang , Zeng Shangyou , Ma Chengxu 
Published: February 2022

AbstractImages taken under low light conditions cause people's sensory vision to fall into blind areas, and the essential properties of objects are hidden in the dark. There are many excellent algorithms that can adjust the brightness of high and low light region, but they still have room for improvement in realizing the function of denoising and similarity restoration of internal attributes of objects. Inspired by the work principle of human retina, the image is decomposed into two modules, firstly, the enhancement network which is guided by the Attention Mask module completed the enhancement by the U‐net network structure. In this structural network, an RISS module is designed here to effectively reduce the loss of image feature information, so as to improve the structural similarity of reconstructed images. Full convolutional network is used to maintain the position relation of illumination feature information. This network is trained on LOL‐dataset, and the experimental results prove that the network can recover images with different illuminations. In the later stage, the effectiveness of this method is verified by the subjective and objective comparison with other methods on different datasets. This method can not only realize the function of low‐light image enhancement, but also the function of image similarity restoration and image denoising.
Edge‐aware image outpainting with attentional generative adversarial networks
Authors: Li Xiaoming , Zhang Hengzhi , Feng Lei , Hu Jing , Zhang Rongguo , Qiao Qiang 
Published: February 2022

AbstractImage outpainting aims at extending the field of view of an existing image. While image inpainting has achieved great success with the deep learning technology, image outpainting still receive less attention. The main challenge is how to generate high‐quality extended images with clear texture and highly consistent semantic information. In order to solve the problem of the effect of invalid pixels on the generated image and the distance of effective pixels is too far. This paper proposes a two‐stage image outpainting method (the EA method), which consists of an edge generation stage and an edge transformation stage. In this paper, the convolutional block attention module (CBAM) is introduced into the generation network to focus on spatial and channel feature and the improved VAE‐GAN structure is used to generate the extended image for more realistic semantics. The EA method is evaluated on the CelebA, Pairs‐streetview and homemade landscapes dataset, and show that the results contain high‐quality textures as well as faithfully extend the semantics. The average PSNR, SSIM, FID index of the EA method on the three datasets is 22.7961, 0.7061, 6.8553 and show that it outperforms existing algorithms in both quantitative and qualitative analysis.
Eruptions from coronal bright points: A spectroscopic view by IRIS of a mini-filament eruption, QSL reconnection, and reconnection-driven outflows
Authors: Madjarska Maria S. , Mackay Duncan H. , Galsgaard Klaus , Wiegelmann Thomas , Xie Haixia 
Published: February 2022

Context. Our study investigates a mini-filament eruption associated with cancelling magnetic fluxes. The eruption originates from a small-scale loop complex commonly known as a coronal bright point (CBP). The event is uniquely recorded in both the imaging and spectroscopic data taken with the Interface Region Imaging Spectrograph (IRIS).
Aims. The investigation aims to gain a better understanding of the physical processes driving these ubiquitous small-scale eruptions.
Methods. We analysed IRIS spectroscopic and slit-jaw imaging observations as well as images taken in the extreme-ultraviolet channels of the Atmospheric Imaging Assembly (AIA) and line-of-sight magnetic-field data from the Helioseismic Magnetic Imager (HMI) on board the Solar Dynamics Observatory. As the observations can only indicate the possible physical processes at play, we also employed a non-linear force-free field (NLFFF) relaxation approach based on the HMI magnetogram time series. This allowed us to further investigate the evolution of the magnetic-field structures involved in the eruption process.
Results. We identified a strong small-scale brightening as a micro-flare in a CBP, recorded in emission from chromospheric to flaring plasmas. The mini-eruption is manifested via the ejection of hot (CBP loops) and cool (mini-filament) plasma recorded in both the imaging and spectroscopic data. The micro-flare is preceded by the appearance of an elongated bright feature in the IRIS slit-jaw 1400 Å images, located above the polarity inversion line. The micro-flare starts with an IRIS pixel size brightening and propagates bi-directionally along the elongated feature. We detected, in both the spectral and imaging IRIS data and AIA data, strong flows along and at the edges of the elongated feature; we believe that these represent reconnection outflows. Both edges of the elongated feature that wrap around the edges of the erupting MF evolve into a J-type shape, creating a sigmoid appearance. A quasi-separatrix layer (QSL) is identified in the vicinity of the polarity inversion line by computing the squashing factor, Q, in different horizontal planes of the NLFFF model.
Conclusions. This CBP spectro-imaging study provides further evidence that CBPs represent downscaled active regions and, as such, they may make a significant contribution to the mass and energy balance of the solar atmosphere. They are the sources of all range of typical active-region features, including magnetic reconnection along QSLs, (mini-)filament eruptions, (micro-)flaring, reconnection outflows, etc. The QSL reconnection site has the same spectral appearance as the so-called explosive events identified by strong blue- and red-shifted emission, thus providing an answer to an outstanding question regarding the true nature of this spectral phenomenon.