bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted detection of cancer at the cellular level during biopsy by near-infrared confocal laser endomicroscopy
Authors: Kennedy Gregory T. , Azari Feredun S. , Bernstein Elizabeth , Nadeem Bilal , Chang Ashley , Segil Alix , Carlin Sean , Sullivan Neil T. , Encarnado Emmanuel , Desphande Charuhas , Kularatne Sumith , Gagare Pravin , Thomas Mini , Kucharczuk John C. , Christien Gaetan , Lacombe Francois , Leonard Kaela , Low Philip S. , Criton Aline , Singhal Sunil 
Published: May 2022

AbstractSuspicious nodules detected by radiography are often investigated by biopsy, but the diagnostic yield of biopsies of small nodules is poor. Here we report a method—NIR-nCLE—to detect cancer at the cellular level in real-time during biopsy. This technology integrates a cancer-targeted near-infrared (NIR) tracer with a needle-based confocal laser endomicroscopy (nCLE) system modified to detect NIR signal. We develop and test NIR-nCLE in preclinical models of pulmonary nodule biopsy including human specimens. We find that the technology has the resolution to identify a single cancer cell among normal fibroblast cells when co-cultured at a ratio of 1:1000, and can detect cancer cells in human tumors less than 2 cm in diameter. The NIR-nCLE technology rapidly delivers images that permit accurate discrimination between tumor and normal tissue by non-experts. This proof-of-concept study analyzes pulmonary nodules as a test case, but the results may be generalizable to other malignancies.
Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction
Authors: Wang Jingyao , Zhang Shihe , Lu Hongfang , Xu Heng 
Published: May 2022

AbstractMany eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the kinetic mechanisms of complex eukaryotic gene regulation.
Zeolite-confined subnanometric PtSn mimicking mortise-and-tenon joinery for catalytic propane dehydrogenation
Authors: Ma Sicong , Liu Zhi-Pan 
Published: May 2022

AbstractHeterogeneous catalysts are often composite materials synthesized via several steps of chemical transformation, and thus the atomic structure in composite is a black-box. Herein with machine-learning-based atomic simulation we explore millions of structures for MFI zeolite encapsulated PtSn catalyst, demonstrating that the machine-learning enhanced large-scale potential energy surface scan offers a unique route to connect the thermodynamics and kinetics within catalysts’ preparation procedure. The functionalities of the two stages in catalyst preparation are now clarified, namely, the oxidative clustering and the reductive transformation, which form separated Sn4O4 and PtSn alloy clusters in MFI. These confined clusters have high thermal stability at the intersection voids of MFI because of the formation of “Mortise-and-tenon Joinery”. Among, the PtSn clusters with high Pt:Sn ratios (>1:1) are active for propane dehydrogenation to propene, ∼103 in turnover-of-frequency greater than conventional Pt3Sn metal. Key recipes to optimize zeolite-confined metal catalysts are predicted.
Robust and tunable Weyl phases by coherent infrared phonons in ZrTe5
Authors: Aryal Niraj , Jin Xilian , Li Qiang , Liu Mengkun , Tsvelik A. M. , Yin Weiguo 
Published: May 2022

AbstractUltrafast control of structural and electronic properties of various quantum materials has recently sparked great interest. In particular, photoinduced switching between distinct topological phases has been considered a promising route to realize quantum computers. Here we use first-principles and effective Hamiltonian methods to show that in ZrTe5, lattice distortions corresponding to all three types of zone-center infrared optical phonon modes can drive the system from a topological insulator to a Weyl semimetal. Thus achieved Weyl phases are robust, highly tunable, and one of the cleanest due to the proximity of the Weyl points to the Fermi level and a lack of other carriers. We also find that Berry curvature dipole moment, induced by the dynamical inversion symmetry breaking, gives rise to various nonlinear effects that oscillate with the amplitude of the phonon modes. These nonlinear effects present an ultrafast switch for controlling the Weyltronics-enabled quantum system.
Chromatin structure predicts survival in glioma patients
Authors: Garrett Matthew C. , Albano Rebecca , Carnwath Troy , Shah Sanjit , Woo Daniel , Lamba Michael , Plas David R. , Paranjpe Aditi , Roskin Krishna , Zhao Chuntao , Lu Richard 
Published: May 2022

AbstractThe pathological changes in epigenetics and gene regulation that accompany the progression of low-grade to high-grade gliomas are under-studied. The authors use a large set of paired atac-seq and RNA-seq data from surgically resected glioma specimens to infer gene regulatory relationships in glioma. Thirty-eight glioma patient samples underwent atac-seq sequencing and 16 samples underwent additional RNA-seq analysis. Using an atac-seq/RNA-seq correlation matrix, atac-seq peaks were paired with genes based on high correlation values (|r2| > 0.6). Samples clustered by IDH1 status but not by grade. Surprisingly there was a trend for IDH1 mutant samples to have more peaks. The majority of peaks are positively correlated with survival and positively correlated with gene expression. Constructing a model of the top six atac-seq peaks created a highly accurate survival prediction model (r2 = 0.68). Four of these peaks were still significant after controlling for age, grade, pathology, IDH1 status and gender. Grade II, III, and IV (primary) samples have similar transcription factors and gene modules. However, grade IV (recurrent) samples have strikingly few peaks. Patient-derived glioma cultures showed decreased peak counts following radiation indicating that this may be radiation-induced. This study supports the notion that IDH1 mutant and IDH1 wildtype gliomas have different epigenetic landscapes and that accessible chromatin sites mapped by atac-seq peaks tend to be positively correlated with expression. The data in this study leads to a new model of treatment response wherein glioma cells respond to radiation therapy by closing open regions of DNA.
A neuromuscular model of human locomotion combines spinal reflex circuits with voluntary movements
Authors: Ramadan Rachid , Geyer Hartmut , Jeka John , Schöner Gregor , Reimann Hendrik 
Published: May 2022

AbstractExisting models of human walking use low-level reflexes or neural oscillators to generate movement. While appropriate to generate the stable, rhythmic movement patterns of steady-state walking, these models lack the ability to change their movement patterns or spontaneously generate new movements in the specific, goal-directed way characteristic of voluntary movements. Here we present a neuromuscular model of human locomotion that bridges this gap and combines the ability to execute goal directed movements with the generation of stable, rhythmic movement patterns that are required for robust locomotion. The model represents goals for voluntary movements of the swing leg on the task level of swing leg joint kinematics. Smooth movements plans towards the goal configuration are generated on the task level and transformed into descending motor commands that execute the planned movements, using internal models. The movement goals and plans are updated in real time based on sensory feedback and task constraints. On the spinal level, the descending commands during the swing phase are integrated with a generic stretch reflex for each muscle. Stance leg control solely relies on dedicated spinal reflex pathways. Spinal reflexes stimulate Hill-type muscles that actuate a biomechanical model with eight internal joints and six free-body degrees of freedom. The model is able to generate voluntary, goal-directed reaching movements with the swing leg and combine multiple movements in a rhythmic sequence. During walking, the swing leg is moved in a goal-directed manner to a target that is updated in real-time based on sensory feedback to maintain upright balance, while the stance leg is stabilized by low-level reflexes and a behavioral organization switching between swing and stance control for each leg. With this combination of reflex-based stance leg and voluntary, goal-directed control of the swing leg, the model controller generates rhythmic, stable walking patterns in which the swing leg movement can be flexibly updated in real-time to step over or around obstacles.
Age-related cognitive effects of the COVID-19 pandemic restrictions and associated mental health changes in Germans
Authors: Menze Inga , Mueller Patrick , Mueller Notger G. , Schmicker Marlen 
Published: May 2022

AbstractRestrictive means to reduce the spread of the COVID-19 pandemic have not only imposed broad challenges on mental health but might also affect cognitive health. Here we asked how restriction-related changes influence cognitive performance and how age, perceived loneliness, depressiveness and affectedness by restrictions contribute to these effects. 51 Germans completed three assessments of an online based study during the first lockdown in Germany (April 2020), a month later, and during the beginning of the second lockdown (November 2020). Participants completed nine online cognitive tasks of the MyBrainTraining and online questionnaires about their perceived strain and impact on lifestyle factors by the situation (affectedness), perceived loneliness, depressiveness as well as subjective cognitive performance. The results suggested a possible negative impact of depressiveness and affectedness on objective cognitive performance within the course of the lockdown. The younger the participants, the more pronounced these effects were. Loneliness and depressiveness moreover contributed to a worse evaluation of subjective cognition. In addition, especially younger individuals reported increased distress. As important educational and social input has partly been scarce during this pandemic and mental health problems have increased, future research should also assess cognitive long-term consequences.
Helical Indexing in Real Space
Authors: Sun Chen , Gonzalez Brenda , Jiang Wen 
Published: May 2022

AbstractBiological structures with helical symmetries of distinct twist, rise, and axial symmetry are abundant and span a wide range of organisms and functions. Performing de novo helical indexing remains challenging because of the steep learning curve involved in Fourier space layer lines. The unknown amount of out-of-plane tilt and the existence of multiple conformations of the helices further complicate indexing. In this work, we introduce a real-space indexing method that leverages the prior knowledge of the tilt and in-plane angles of the helical filaments/tubes, robust ab initio 3D reconstruction capabilities in single particle cryo-EM to obtain asymmetric reconstructions, and automatic indexing of helical parameters directly from the asymmetric density maps. We validated this approach using data from multiple helical structures of distinct helical symmetries, diameters, flexibility, data qualities, and heterogeneous states. The fully automated tool we introduce for real space indexing, HI3D, uses the 2D lattice in the autocorrelation of the cylindrical projection of a 3D density map to identify the helical symmetry. HI3D can often successfully determine the helical parameters of a suboptimal 3D density map, including ab initio single particle asymmetric reconstructions and sub-tomogram averages, with intermediate evidence that can also help assess the map quality. Furthermore, this open-source HI3D is usable independently as a Web application that can be accessed free of installation. With these methods, de novo helical indexing will be significantly more accessible to researchers investigating structures of helical filaments/tubes using cryo-EM.
Conventional and digital Ki67 evaluation and their correlation with molecular prognosis and morphological parameters in luminal breast cancer
Authors: Pons Laura , Hernández-León Laura , Altaleb Ahmad , Ussene Esperança , Iglesias Roman , Castillo Ana , Rodríguez-Martínez Paula , Castella Eva , Quiroga Vanesa , Felip Eudald , Cirauqui Beatriz , Margelí Mireia , Fernández Pedro Luis 
Published: May 2022

AbstractDigital counting methods were developed to decrease the high intra- and inter-observer variability of immunohistochemical markers such as Ki67, with most presenting a good correlation coefficient (CC). Since Ki67 is one of the major contributors to Oncotype DX, it is conceivable that Ki67 expression and the recurrence score (RS) obtained by the multigene panel are positively correlated. We decided first to test to what extent conventional and digital Ki67 quantification methods correlate in daily practice and, second, to determine which of these methods correlates better with the prognostic capacity of the Oncotype DX test. Both Ki67 evaluations were performed in 89 core biopsies with a diagnosis of estrogen receptor (ER) positive HER2-negative breast cancer (BC). Cases were, thus, classified twice for surrogate subtype: first by conventional analysis and then by digital evaluation. The Oncotype RS was obtained in 55 cases that were subsequently correlated to Ki67 evaluation by both methods. Conventional and digital Ki67 evaluation showed good concordance and correlation (CC = 0.81 (95% CI 0.73–0.89)). The correlation of Oncotype DX risk groups and surrogate derived subtypes was slightly higher for the digital technique (rs = 0.46, p < 0.01) compared to the conventional method (rs = 0.39, p < 0.01), even though both were statistically significant. In conclusion, we show that digital evaluation could be an alternative to conventional counting, and also has advantages for predicting the risk established by the Oncotype DX test in ER-positive BC. This study also supports the importance of an accurate Ki67 analysis which can influence the decision to submit ER-positive HER2-negative BC to prognostic molecular platforms.
Characterising the unity and diversity of executive functions in a within-subject fMRI study
Authors: Saylik Rahmi , Williams Adrian L. , Murphy Robin A. , Szameitat Andre J. 
Published: May 2022

AbstractBehavioural studies investigating the relationship between Executive Functions (EFs) demonstrated evidence that different EFs are correlated with each other, but also that they are partially independent from each other. Neuroimaging studies investigating such an interrelationship with respect to the functional neuroanatomical correlates are sparse and have revealed inconsistent findings. To address this question, we created four tasks derived from the same basic paradigm, one each for updating, inhibition, switching, and dual-tasking. We assessed brain activity through functional magnetic resonance imaging (fMRI) in twenty-nine participants while they performed the four EF tasks plus control tasks. For the analysis, we first determined the neural correlates of each EF by subtracting the respective control tasks from the EF tasks. We tested for unity in EF tasks by calculating the conjunction across these four “EF-minus-control” contrasts. This identified common areas including left lateral frontal cortices [middle and superior frontal gyrus (BA 6)], medial frontal cortices (BA 8) as well as parietal cortices [inferior and superior parietal lobules (BA 39/7)]. We also observed areas activated by two or three EF tasks only, such as frontoparietal areas [e.g., SFG (BA8) right inferior parietal lobule (BA 40), left precuneus (BA 7)], and subcortical regions [bilateral thalamus (BA 50)]. Finally, we found areas uniquely activated for updating [bilateral MFG (BA 8) and left supramarginal gyrus (BA 39)], inhibition (left IFG BA 46), and dual-tasking [left postcentral gyrus (BA 40)]. These results demonstrate that the functional neuroanatomical correlates of the four investigated EFs show unity as well as diversity.
Developmental differences in the impact of perceptual salience on short-term memory performance and meta-memory skills
Authors: Pedale Tiziana , Mastroberardino Serena , Capurso Michele , Macrì Simone , Santangelo Valerio 
Published: May 2022

AbstractIn everyday life, individuals are surrounded by many stimuli that compete to access attention and memory. Evidence shows that perceptually salient stimuli have more chances to capture attention resources, thus to be encoded into short-term memory (STM). However, the impact of perceptual salience on STM at different developmental stages is entirely unexplored. Here we assessed STM performance and meta-memory skills of 6, 10, and 18 years-old participants (total N = 169) using a delayed match-to-sample task. On each trial, participants freely explored a complex (cartoon-like) scene for 4 s. After a retention interval of 4 s, they discriminated the same/different position of a target-object extracted from the area of maximal or minimal salience of the initially-explored scene. Then, they provided a confidence judgment of their STM performance, as an index of meta-memory skills. When taking into account ‘confident’ responses, we found increased STM performance following targets at maximal versus minimal salience only in adult participants. Similarly, only adults showed enhanced meta-memory capabilities following maximal versus minimal salience targets. These findings documented a late development in the impact of perceptual salience on STM performance and in the improvement of metacognitive capabilities to properly judge the content of one’s own memory representation.
Pseudorapidity dependence of the bulk properties of hadronic medium in pp collisions at 7 TeV
Authors: Ajaz Muhammad , Haj Ismail Abd Al Karim , Waqas Muhammad , Suleymanov Mais , AbdelKader Atef , Suleymanov Rustam 
Published: May 2022

AbstractThe measured charged particle $$p_T$$

p
T

spectra in proton-proton collisions obtained by the CMS experiment at CERN is compared with the simulation results of EPOS–LHC and Pythia8.24 models at 7 TeV center-of-mass energy. The Pythia8.24 model describes the experimental data very well, particularly in the high $$p_T$$

p
T

region. The model also predicts the $$p_T$$

p
T

spectra for $$|$$
|
$$\eta $$
η
$$|$$
|
< 2.4 at 0 $$\le $$
≤
$$p_T$$

p
T

$$\le $$
≤
6 $$\text {GeV/}c$$

GeV/
c

. The EPOS–LHC model underpredicts the $$p_T$$

p
T

spectra from 0.1 to 2 $$\text {GeV/}c$$

GeV/
c

in all $$\eta $$
η
bins for about 20% and the $$p_T$$

p
T

spectrum from 0.1 to 4.2 $$\text {GeV/}c$$

GeV/
c

for $$|$$
|
$$\eta $$
η
$$|$$
|
< 2.4 by about 15% while reasonably predicts well for $$p_T$$

p
T

> 4.2 $$\text {GeV/}c$$

GeV/
c

within the experimental errors. Furthermore, to get information about collective properties of the hadronic matter, modified Hagedorn function with embedded transverse flow velocity and thermodynamically consistent Tsallis distribution functions are used to fit the experimental data and simulated results. The values of $$\chi ^2/ndf$$

χ
2

/
n
d
f

show that the functions fit the data and simulation results well. The parameter extracted by the functions: $$\beta _T$$

β
T

, $$T_0$$

T
0

, and $$T_{eff}$$

T

eff

decreases with increasing $$\eta $$
η
. The decrease in $$\beta _T$$

β
T

with increasing $$\eta $$
η
is due to the large energy deposition in lower rapidity bins producing rapid expansion due to large pressure gradient resulting quick expansion of the fireball. Similarly, large energy transfer in the lower pseudo-rapidity bin results in higher degree of excitation of the system which results larger values of $$T_0$$

T
0

and $$T_{eff}$$

T

eff

. The values of the fit constant $$N_0$$

N
0

increase with $$\eta $$
η
where the values of $$N_0$$

N
0

extracted from Pythia8.24 are closer to the data than the EPOS–LHC model. The Pythia8.24 model has better prediction than the EPOS–LHC model which might be connected to its flow-like features and color re-connections resulting from different Parton interactions in the initial and final state.
Oyster reef restoration facilitates the recovery of macroinvertebrate abundance, diversity, and composition in estuarine communities
Authors: Searles Adam R. , Gipson Emily E. , Walters Linda J. , Cook Geoffrey S. 
Published: May 2022

AbstractHistoric declines in oyster populations have resulted in diminished production of ecosystem services and habitat function in many estuaries. Due to the important role of oysters in ecosystem function, scientists and resource managers have employed oyster reef restoration to mitigate declines, recover essential ecosystem services, and better habitat function. Yet, there are knowledge gaps regarding the impact of restoration efforts on ecologically valuable mid-trophic level organisms inhabiting these systems. To address this knowledge gap, here we quantify macroinvertebrate species abundance, community diversity, and composition on experimental restored oyster reefs before and after restoration, and from live (positive control) and dead (negative control) reefs in the Indian River Lagoon, Florida. Species diversity and composition on restored reefs shifted towards states similar to live (positive control) reefs within 12 months of restoration. Recovery of species abundance occurred within 18 months of restoration. The results presented herein quantify the effect of restoration on resident macroinvertebrates and provide timelines of recovery for each attribute of these communities. Further, this study presents an actionable and transferable framework for identifying effective single-species metrics of restoration success across ecosystems. The application of this framework will provide managers and researchers with tools to improve the efficiency and efficacy of post-restoration monitoring. By doing so, this study contributes significantly to the improvement of broader restoration practices in an era of unprecedented habitat loss.