bluuebunny/crossref_metadata_2025 huggingface dataset:
Characteristics, Hospital Length of Stay, and Readmissions Among Individuals Undergoing Abdominal Ostomy Surgery
Authors: Schott Laura L. , Eaves Deanna , Inglese Gary , Sinha Meenal
Published: November 2022

PURPOSE:

The purpose of this study was to examine patient characteristics, length of stay (LOS), hospital revisits, and complications of patients undergoing abdominal ostomy surgery.

DESIGN:

Retrospective cohort study.

SUBJECTS AND SETTING:

Data were extracted from the PINC AI Healthcare Database (PHD), a large archive that stores data from 25% of all US inpatient hospital discharges. Patients were admitted to 658 hospitals in the United States between December 1, 2017, and November 30, 2018. The sample comprised 27,658 adult patients; 15,512 underwent creation of a colostomy, 10,207 underwent ileostomy construction, and 1930 had a urostomy procedure. Their median age was 64 years (interquartile range [IQR] = 19 years). Emergent admission type was 71.2% for patients who underwent a colostomy procedure, 49.4% for ileostomy, and 9.9% for urostomy. The majority of patients underwent open surgery (77.7%); 22.3% of procedures used an endoscopic approach.

METHODS:

Patients were identified as having undergone abdominal ostomy surgery via ICD-10-PCS (International Classification of Diseases, Tenth Revision, Procedure Coding System) procedure codes. Demographic, visit, hospital and clinical characteristics, LOS, and hospital revisits (ie, readmissions and emergency department [ED]) were captured for qualifying patients. Data were evaluated using unadjusted descriptive analyses.

RESULTS:

The median LOS of 9 days (IQR = 9 days) varied by ostomy surgery; the cumulative postsurgical LOS was 7 days (IQR = 5 days). The most frequent underlying diagnoses resulting in ostomy surgery were diverticulitis of the large bowel (19.6%) managed by colostomy, colorectal cancer managed by ileostomy (22.5%), or urothelial cancer managed by urostomy (78.1%). Slightly less than a quarter (23.7%) of patients were discharged home without home care, 43.0% went home with home healthcare, and 29.6% were discharged to a non–acute care facility. Hospital readmission within 120 days of discharge was 36.3% for patients with a colostomy, 52.3% for those with an ileostomy, and 34.6% for patients with a urostomy. Ostomy complications were identified as the reason for readmission in 62.4% of patients. Slightly more than 1 in 5 patients (20.7%) had a subsequent ED visit within 120 days, 39.7% of which involved ostomy complication.

CONCLUSIONS:

Characteristics of patients undergoing abdominal stoma surgery varied based on underlying diagnosis and ostomy type. The median hospital LOS was more than 1 week. Patients experienced high rates of healthcare utilization (hospital admission or ED visits) during the 120 days following surgery.
Longevity of a solitary mole-rat species and its implications for the assumed link between sociality and longevity in African mole-rats (Bathyergidae)
Authors: Dammann P. , Šaffa G. , Šumbera R.
Published: November 2022

Sociality and cooperative breeding are associated with enhanced longevity in insects and birds, but whether this is also true for mammals is still subject to debate. African mole-rats (Bathyergidae) have recently been claimed to be the only mammalian family in which such an association may exist because cooperatively breeding bathyergids seem to be substantially longer lived than solitary bathyergids. However, although ample longevity data are available for several social bathyergids, almost nothing is known about mortality distribution and lifespan in solitary bathyergids. Here we present robust long-term data on the longevity of a solitary African mole-rat, the silvery mole-rat
Heliophobius argenteocinereus
. Our findings show that this species is much longer-lived than previously believed. Nonetheless, our comparative analysis suggests that sociality has indeed a positive effect on longevity in this family. We argue that the extreme longevity seen particularly in social bathyergids is probably caused by a combination of subterranean lifestyle and cooperative breeding.
Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance in Salmonella enterica subsp. enterica serovar Heidelberg
Authors: Hetman Benjamin M. , Pearl David L. , Barker Dillon O. R. , Robertson James , Nash John H. E. , Reid-Smith Richard , Agunos Agnes , Carrillo Catherine , Topp Edward , Van Domselaar Gary , Parmley E. Jane , Bharat Amrita , Mulvey Michael , Allen Vanessa , Taboada Eduardo N.
Published: November 2022

Antimicrobial resistance (AMR) has become a critical threat to public health worldwide. The use of antimicrobials in food and livestock agriculture, including the production of poultry, is thought to contribute to the dissemination of antibiotic resistant bacteria (ARB) and the genes and plasmids that confer the resistant phenotype (ARG). However, the relative contribution of each of these processes to the emergence of resistant pathogens in poultry production and their potential role in the transmission of resistant pathogens in human infections, requires a deeper understanding of the dynamics of ARB and ARG in food production and the factors involved in the increased risk of transmission.
Temporal Associations of Plasma Levels of the Secreted Phospholipase A2Family and Mortality in Severe COVID-19
Authors: Lu Eric , Hara Aki , Sun Shudong , Hallmark Brian , Snider Justin M. , Seeds Michael C. , Watkins Joseph C. , McCall Charles E. , Zhang Hao Helen , Yao Guang , Chilton Floyd H.
Published: November 2022

Previous research suggests that group IIA secreted phospholipase A2(sPLA2-IIA) plays a role in and predicts severe COVID-19 disease. The current study reanalyzed a longitudinal proteomic data set to determine the temporal (days 0, 3 and 7) relationship between the levels of several members of a family of sPLA2isoforms and the severity of COVID-19 in 214 ICU patients. The levels of six secreted PLA2isoforms, sPLA2-IIA, sPLA2-V, sPLA2-X, sPLA2-IB, sPLA2-IIC, and sPLA2-XVI, increased over the first 7 ICU days in those who succumbed to the disease. sPLA2-IIA outperformed top ranked cytokines and chemokines as predictors of patient outcome. A decision tree corroborated these results with day 0 to day 3 kinetic changes of sPLA2-IIA that separated the death and severe categories from the mild category and increases from day 3 to day 7 significantly enriched the lethal category. In contrast, there was a time-dependent decrease in sPLA2-IID and sPLA2-XIIB in patients with severe or lethal disease, and these two isoforms were at higher levels in mild patients. Taken together, proteomic analysis revealed temporal sPLA2patterns that reflect the critical roles of sPLA2isoforms in severe COVID-19 disease.
Characterizing the blood stage antimalarial activity of tafenoquine in healthy volunteers experimentally infected withPlasmodium falciparum
Authors: Barber Bridget E. , Abd-Rahman Azrin N. , Webster Rebecca , Potter Adam J. , Llewellyn Stacey , Marquart Louise , Sahai Nischal , Leelasena Indika , Birrell Geoffrey W. , Edstein Michael D. , Shanks G. Dennis , Wesche David , Moehrle Joerg J. , McCarthy James S.
Published: November 2022

Background

The long acting 8-aminoquinoline tafenoquine may be a good candidate for mass drug administration if it exhibits sufficient blood stage antimalarial activity at doses low enough to be tolerated by glucose 6-phosphate dehydrogenase (G6PD) deficient individuals.

Methods

Healthy G6PD-normal adults were inoculated withPlasmodium falciparum3D7-infected erythrocytes on day 0. Different single oral doses of tafenoquine were administered on day 8. Parasitemia, and concentrations of tafenoquine and the 5,6-orthoquinone metabolite in plasma/whole blood/urine were measured and standard safety assessments performed. Curative artemether-lumefantrine therapy was administered if parasite regrowth occurred, or on day 48±2. Outcomes were parasite clearance kinetics, pharmacokinetic and pharmacokinetic/pharmacodynamic (PK/PD) parameters from modelling, and dose simulations in a theoretical endemic population.

Results

Twelve participants were inoculated and administered 200 mg (n=3), 300 mg (n=4), 400 mg (n=2), or 600 mg (n=3) tafenoquine. The parasite clearance half-life with 400 mg or 600 mg (5.4 h and 4.2 h respectively) was faster than with 200 mg or 300 mg (11.8 h and 9.6 h respectively). Parasite regrowth occurred after dosing with 200 mg (3/3 participants) and 300 mg (3/4 participants), but not after 400 mg or 600 mg. Simulations using the PK/PD model predicted that 460 mg and 540 mg would clear parasitaemia by a factor of 106and 109, respectively, in a 60 kg adult.

Conclusions

Although a single dose or tafenoquine exhibits potentP. falciparumblood stage antimalarial activity, the estimated doses to effectively clear asexual parasitemia will require prior screening to exclude G6PD deficiency.

Main point

A single oral dose of tafenoquine is effective against blood stagePlasmodium falciparuminfection. However, as the estimated dose to clear asexual parasitaemia is ≥460 mg (in adults), prior screening for glucose 6-phosphate dehydrogenase deficiency will be required.
EEG-LLAMAS: an open source, low latency, EEG-fMRI neurofeedback platform
Authors: Levitt Joshua , Yang Zinong , Williams Stephanie D. , Lütschg Espinosa Stefan E. , Garcia-Casal Allan , Lewis Laura D.
Published: November 2022

Simultaneous EEG-fMRI is a powerful multimodal technique for imaging the brain, but its use in neurofeedback experiments has been limited by EEG noise caused by the MRI environment. Neurofeedback studies typically require analysis of EEG in real time, but EEG acquired inside the scanner is heavily contaminated with ballistocardiogram (BCG) artifact, a high-amplitude artifact locked to the cardiac cycle. Although techniques for removing BCG artifacts do exist, they are either not suited to real-time, low-latency applications, such as neurofeedback, or have limited efficacy. We propose and validate a new open-source BCG removal software called EEG-LLAMAS (Low Latency Artifact Mitigation Acquisition Software), which adapts and advances existing artifact removal techniques for low-latency experiments. We first used simulations to validate LLAMAS in data with known ground truth. We found that LLAMAS performed better than the best publicly-available real-time BCG removal technique, optimal basis sets (OBS), in terms of its ability to recover EEG waveforms, power spectra, and slow wave phase. To determine whether LLAMAS would be effective in practice, we then used it to conduct real-time EEG-fMRI recordings in healthy adults, using a steady state visual evoked potential (SSVEP) task. We found that LLAMAS was able to recover the SSVEP in real time, and recovered the power spectra collected outside the scanner better than OBS. We also measured the latency of LLAMAS during live recordings, and found that it introduced a lag of less than 50ms on average. The low latency of LLAMAS, coupled with its improved artifact reduction, can thus be effectively used for EEG-fMRI neurofeedback. This platform enables closed-loop experiments which previously would have been prohibitively difficult, such as those that target short-duration EEG events, and is shared openly with the neuroscience community.
Uncharacterized protein c17orf80: a novel interactor of human mitochondrial nucleoids
Authors: Potter Alisa , Hangas Anu , Goffart Steffi , Huynen Martijn A. , Cabrera-Orefice Alfredo , Spelbrink Johannes N.
Published: November 2022

Molecular functions of many human proteins remain unstudied, despite the demonstrated association with diseases or pivotal molecular structures, such as mitochondrial DNA (mtDNA). This small genome is crucial for proper functioning of mitochondria, the energy-converting organelles. In mammals, mtDNA is arranged into macromolecular complexes called nucleoids that serve as functional stations for its maintenance and expression. Here, we aimed to explore an uncharacterized protein c17orf80, which was previously detected close to the nucleoid components by proximity-labelling mass spectrometry. To investigate the subcellular localization and function of c17orf80, we took an advantage of immunofluorescence microscopy, interaction proteomics and several biochemical assays. We demonstrate that c17orf80 is a mitochondrial membrane-associated protein that interacts with nucleoids even when mtDNA replication is inhibited. In addition, we show that c17orf80 is not essential for mtDNA maintenance and mitochondrial gene expression in cultured human cells. These results provide a basis for uncovering the molecular function of c17orf80 and the nature of its association with nucleoids, possibly leading to new insights about mtDNA and its expression.
Deep RNA-seq of male and female murine sensory neuron subtypes after nerve injury
Authors: Barry Allison M , Zhao Na , Yang Xun , Bennett David L , Baskozos Georgios
Published: November 2022

Dorsal root ganglia (DRG) neurons have been well described for their role in driving both acute and pain. Although nerve injury is known to cause transcriptional dysregulation, how this differs across neuronal subtypes and the impact of sex is unclear. Here, we study the deep transcriptional profiles of multiple murine DRG populations in early and late pain states while considering sex. We have exploited currently available transgenics to label numerous subpopulations for fluorescent activated cell sorting (FACS) and subsequent transcriptomic analysis. Using bulk tissue samples, we are able to circumvent the issues of low transcript coverage and drop-outs seen with single cell datasets. This increases our power to detect novel and even subtle changes in gene expression within neuronal subtypes and discuss sexual dimorphism at the neuronal subtype level. We have curated this resource into an accessible database for other researchers (https://livedataoxford.shinyapps.io/drg-directory/). We see both stereotyped and unique subtype signatures in injured states after nerve injury at both an early and late timepoint. While all populations contribute to a general injury signature, subtype enrichment changes can also be seen. Within populations, there is not a strong intersection of sex and injury, but previously unknown sex differences in naïve states-particularly in Aβ-RA + Aδ-LTMRs - still contribute to differences in injured neurons.
EEG and pupillometric signatures of working memory overload
Authors: Kosachenko Alexandra I. , Kasanov Dauren , Kotyusov Alexander I. , Pavlov Yuri G.
Published: November 2022

Understanding the physiological correlates of cognitive overload has implications for gauging the limits of human cognition, for developing novel methods to define cognitive overload, and for mitigating the negative outcomes associated with overload. Most previous psychophysiological studies manipulated verbal working memory load in a narrow range (an average load of 5 items). It is unclear, however, how the nervous system responds to working memory load exceeding typical capacity limits. The objective of the current study was to characterize the central and autonomic nervous system changes associated with memory overload, by means of combined recording of EEG and pupillometry. Eighty-six participants were presented with a digit span task involving the serial auditory presentation of items. Each trial consisted of sequences of either 5, 9, or 13 digits, each separated by 2 seconds. Both theta activity and pupil size, after the initial rise, expressed a pattern of a short plateau and a decrease with reaching the state of memory overload, indicating that pupil size and theta possibly have similar neural mechanisms. Based on the described above triphasic pattern of pupil size temporal dynamics, we concluded that cognitive overload causes physiological systems to reset, and to release effort. Although memory capacity limits were exceeded and effort was released (as indicated by pupil dilation), alpha continued to decrease with increasing memory load. These results suggest that associating alpha with the focus of attention and distractor suppression is not warranted.
BrainAGE: Revisited and reframed machine learning workflow
Authors: Kalc Polona , Dahnke Robert , Hoffstaedter Felix , Gaser Christian ,   Alzheimer’s Disease Neuroimaging Initiative
Published: November 2022

Since the introduction of the BrainAGE method (Franke et al., 2010), novel machine learning methods of brain age prediction have continued to emerge. The idea of estimating the chronological age from magnetic resonance images proved to be an interesting field of research due to the relative simplicity of its interpretation and its potential use as a biomarker of brain health. We revised our previous BrainAGE approach, originally utilising relevance vector regression (RVR), and substituted it with Gaussian process regression (GPR), which enables more stable processing of larger datasets, such as the UK Biobank (UKB). In addition, we extended the global BrainAGE approach to regional BrainAGE, providing spatially specific scores for 5 brain lobes per hemisphere. We tested the performance of the new algorithms under several different conditions and investigated their validity on the ADNI and schizophrenia samples, as well as on a synthetic dataset of neocortical thinning. The results show an improved performance of the reframed global model on the UKB sample with a mean absolute error (MAE) of less than 2 years and a significant difference in BrainAGE between healthy participants and patients with Alzheimer’s disease and schizophrenia. Moreover, the workings of the algorithm show meaningful effects for a simulated neocortical atrophy dataset. The regional BrainAGE model performed well on two clinical samples, showing disease-specific patterns for different levels of impairment. The results demonstrate that the new improved algorithms provide reliable and valid brain age estimations.
A method for generating user-defined circular single-stranded DNA from plasmid DNA using Golden Gate intramolecular ligation
Authors: Strawn Isabell K. , Steiner Paul J. , Newton Matilda S. , Whitehead Timothy A.
Published: November 2022

Construction of user-defined long circular single stranded DNA (cssDNA) and linear single stranded DNA (lssDNA) is important for various biotechnological applications. Many current methods for synthesis of these ssDNA molecules do not scale to multi-kilobase constructs. Here we present a robust methodology for generating user-defined cssDNA employing Golden Gate assembly, a nickase, and exonuclease degradation. Our technique is demonstrated for three plasmids with insert sizes ranging from 2.1-3.4 kb, requires no specialized equipment, and can be accomplished in five hours with a yield of 33-43 % of the theoretical. To produce lssDNA, we evaluated different CRISPR-Cas9 cleavage conditions and report a 52 ± 8% cleavage efficiency of cssDNA. Our method presented here can make ssDNA readily available to biotechnology researchers.
Single-molecule tracking reveals the functional allocation,in vivointeractions and spatial organization of universal transcription factor NusG
Authors: el Sayyed Hafez , Pambos Oliver J. , Stracy Mathew , Gottesman Max E. , Kapanidis Achillefs N.
Published: November 2022

Bacterial gene expression is highly regulated to allow cells to grow and adapt. Much regulation occurs during transcription elongation, where RNA polymerase (RNAP) extends nascent RNA transcripts aided by global and universally-conserved elongation factor NusG. NusG modulates transcription by inhibiting pausing and backtracking; promoting anti-termination on ribosomal RNA (rrn) operons; coupling transcription with translation on mRNA genes; and stimulating Rho-dependent termination on toxic genes. Despite extensive work on NusG, its functional allocation and spatial distributionin vivois unknown. Here, we addressed these long-standing questions using single-molecule tracking and super-resolution imaging of NusG in liveE. colicells. We found that, under conditions of moderate growth, NusG is mainly present as a population that associates indirectly with the chromosome via RNAP in transcription elongation complexes, and a slowly diffusing population we identified as a NusG complex with the 30S ribosomal subunit; this complex offers a “30S-guided” path for NusG to enter transcription elongation. Only ~10% of total NusG was fast-diffusing, with the mobility of this population suggesting that free NusG interacts non-specifically with DNA for >50% of the time. Using antibiotics and deletion mutants, we showed that most chromosome-associated NusG is involved inrrnanti-termination and in transcriptiontranslation coupling. NusG involvement inrrnanti-termination was mediated via its participation in phase-separated transcriptional condensates. Our work illuminates the diverse activities of a central regulator while offering a guide on how to dissect the roles of multi-functional machines using in vivo imaging.
Pisces: A multi-modal data augmentation approach for drug combination synergy prediction
Authors: Xu Hanwen , Lin Jiacheng , Woicik Addie , Liu Zixuan , Ma Jianzhu , Zhang Sheng , Poon Hoifung , Wang Liewei , Wang Sheng
Published: November 2022

Drug combination therapy is promising for cancer treatment through simultaneously reducing resistance and improving efficacy. Machine learning approaches to drug combination response prediction can prioritize experiments and discover new combinations, but require lots of training data in order to fit the nonlinearity of synergistic effect. Here, we propose Pisces, a novel machine learning approach for drug combination synergy prediction. The key idea of Pisces is to augment the sparse drug combination dataset by creating multiple views for each drug combination based on its different modalities. We combined eight different modalities of a single drug to create 64 augmented views for a pair of drugs, effectively expanding the size of the original data 64 times. Pisces obtained state-of-the-art results on cell-line-based drug synergy prediction, xenograft-based drug synergy prediction, and drug-drug interaction prediction. By interpreting Pisces’s predictions using a genetic interaction network, we further identified a breast cancer drug-sensitive pathway from BRCA cell lines in GDSC. We validated this pathway on an independent TCGA-BRCA tumor dataset and found that patients with this pathway activated had substantially longer survival time. Collectively, Pisces effectively predicts drug synergy and drug-drug interactions through augmenting the original dataset 64 times, and can be broadly applied to various biological applications that involve a pair of drugs.
Haptoglobin buffers lipopolysaccharides to safeguard against aberrant NFκB activation
Authors: Zein Laura , Grossmann Josina , Swoboda Helena , Borgel Christina , Wilke Bernhard , Awe Stephan , Nist Andrea , Stiewe Thorsten , Stehling Oliver , Freibert Sven-Andreas , Adhikary Till , Chung Ho-Ryun
Published: November 2022

It has remained yet unclear which soluble factors regulate the anti-inflammatory macrophage phenotype observed in both homeostasis and tumourigenesis. We show here that haptoglobin, a major serum pro-tein with elusive immunoregulatory properties, binds and buffers serum-borne bacterial lipopolysaccharides to attenuate activation of NFκB in macrophages. Haptoglobin binds different lipopolysaccharides with low micromolar affinities. Given its abundance, haptoglobin constitutes a buffer for lipopolysaccharides, shielding them to safeguard against aberrant inflammatory reactions caused by small fluctuations. Concordantly, NFκB activation by haptoglobin-associated lipopolysaccharides was delayed relative to stimulation with pure lipopolysaccharide. Our findings warrant evaluation of therapeutic benefits of haptoglobin for inflammatory conditions and re-evaluation of purification strategies. Finally, they allow to elucidate mechanisms of enhanced immunosuppression by oncofetal haptoglobin.
Neurogenetic identification of mosquito sensory neurons
Authors: Konopka Joanna K. , Task Darya , Poinapen Danny , Potter Christopher J.
Published: November 2022

Anophelesmosquitoes, as vectors for the malaria parasite, are a global threat to human health. To find and bite a human, they utilize neurons within their sensory appendages. However, the identity and quantification of sensory appendage neurons are lacking. Here we use a neurogenetic approach to label all neurons inAnopheles coluzziimosquitoes. We utilize the Homology Assisted CRISPR Knock-in (HACK) approach to generate aT2A-QF2wknock-in of the synaptic genebruchpilot. We use a membrane-targeted GFP reporter to visualize the neurons in the brain and to quantify neurons in all major chemosensory appendages (antenna, maxillary palp, labella, tarsi). By comparing labeling of brp>GFP and Orco>GFP mosquitoes, we predict the extent of neurons expressing Ionotropic Receptors or other chemosensory receptors. This work introduces a valuable genetic tool for the functional analysis ofAnophelesmosquito neurobiology and initiates characterization of the sensory neurons that guide mosquito behavior.

Graphical Abstract
Whole-brain afferent input mapping to functionally distinct brainstem noradrenaline cell types
Authors: Sulkes Cuevas Jessica , Watanabe Mayumi , Uematsu Akira , Johansen Joshua P.
Published: November 2022

The locus coeruleus (LC) is a small region in the pons and the main source of noradrenaline (NA) to the forebrain. While traditional models suggested that all LC-NA neurons project indiscriminately throughout the brain, accumulating evidence indicates that these cells can be heterogeneous based on their anatomical connectivity and behavioral functionality and exhibit distinct coding modes. How LC-NA neuronal subpopulations are endowed with unique functional properties is unclear. Here, we used a viral-genetic approach for mapping anatomical connectivity at different levels of organization based on inputs and outputs of defined cell classes. Specifically, we studied the whole-brain afferent inputs onto two functionally distinct LC-NA neuronal subpopulations which project to amygdala or medial prefrontal cortex (mPFC). We found that the global input distribution is similar for both LC-NA neuronal subpopulations. However, finer analysis demonstrated important differences in inputs from specific brain regions. Moreover, sex related differences were apparent, but only in inputs to amygdala-projecting LC-NA neurons. These findings reveal a cell type and sex specific afferent input organization which could allow for context dependent and target specific control of NA outflow to forebrain structures involved in emotional control and decision making.
Supramodal Shape Representation in the Human Brain
Authors: Xu Yangwen , Vignali Lorenzo , Sigismondi Federica , Crepaldi Davide , Bottini Roberto , Collignon Olivier
Published: November 2022

We can sense an object’s shape by vision or touch. Previous studies suggested that the inferolateral occipitotemporal cortex (ILOTC) implements supramodal shape representations as it responds more to seeing or touching objects than shapeless textures. However, such activation in the anterior portion of the ventral visual pathway could be due to the conceptual representation of an object or visual imagery triggered by touching an object. We addressed these possibilities by directly comparing shape and conceptual representations in early blind (who lack visual experience/imagery) and sighted participants. We found that bilateral ILOTC in both groups showed stronger activation during a shape verification task than during a conceptual verification task made on the names of the same manmade objects. Moreover, the distributed activity in the ILOTC encoded shape similarity but not conceptual association among objects. Besides the ILOTC, we also found shape representation in both groups’ bilateral ventral premotor cortices and intraparietal sulcus, a frontoparietal circuit relating to object grasping and haptic processing. In contrast, the conceptual verification task activated both groups’ left perisylvian brain network relating to language processing, and, interestingly, the cuneus in early blind participants only. The ILOTC had stronger functional connectivity to frontoparietal circuit than to the left perisylvian network, forming a modular structure specialized in shape representation. Our results conclusively support that the ILOTC selectively implements shape representation independently of visual experience, and this unique functionality likely comes from its privileged connection to the frontoparietal haptic circuit.
The shadowing effect of initial expectation on learning asymmetry
Authors: Sun Jingwei , Ni Yinmei , Li Jian
Published: November 2022

Evidence for positivity and optimism bias abounds in high-level belief updates. However, no consensus has been reached regarding whether learning asymmetries exists in more elementary forms of updates such as reinforcement learning (RL). In RL, the learning asymmetry concerns the sensitivity difference in incorporating positive and negative prediction errors (PE) into value estimation, namely the asymmetry of learning rates associated with positive and negative PEs. Although RL has been established as a canonical framework in interpreting agent and environment interactions, the direction of the learning rate asymmetry remains controversial. Here, we propose that part of the controversy stems from the fact that people may have different value expectations before entering the learning environment. Such default value expectation influences how PEs are calculated and consequently biases subjects’ choices. We test this hypothesis in two learning experiments with stable or varying reinforcement probabilities, across monetary gains, losses and gain-loss mixtures environments. Our results consistently support the model incorporating asymmetric learning rates and initial value expectation, highlighting the role of initial expectation in value update and choice preference. Further simulation and model parameter recovery analyses confirm the unique contribution of initial value expectation in accessing learning rate asymmetry.

Author Summary

While RL model has long been applied in modeling learning behavior, where value update stands in the core of the learning process, it remains controversial whether and how learning is biased when updating from positive and negative PEs. Here, through model comparison, simulation and recovery analyses, we show that accurate identification of learning asymmetry is contingent on taking into account of subjects’ default value expectation in both monetary gain and loss environments. Our results stress the importance of initial expectation specification, especially in studies investigating learning asymmetry.
Multi-session tDCS paired with passive mobilisation increases thalamo-cortical coupling during command following
Authors: Aloi Davide , Jalali Roya , Calzolari Sara , Lafanechere Melanie , Miall R. Chris , Fernández-Espejo Davinia
Published: November 2022

Background

Therapeutic options for patients with prolonged disorder of consciousness (PDOC) are limited. PDOC patients often exhibit a dissociation between their retained level of (covert) cognitive ability and their (overt) behavioural responses (cognitive-motor dissociation; CMD). This is linked to reduced coupling between thalamus and the primary motor cortex.

Objective

To assess whether pairing tDCS with a concurrent passive mobilisation protocol (designed to be feasible in PDOC) can influence thalamo-M1 dynamics and whether these changes are enhanced after multiple stimulation sessions.

Methods

We used Dynamic Causal Modelling (DCM) on functional magnetic resonance imaging (fMRI) data from 22 healthy participants to assess tDCS changes on effective connectivity within motor network areas during command-following.

Results

We found that a single anodal tDCS session (paired with passive mobilisation of the thumb) decreased self-inhibition in the motor cortex, with five sessions further enhancing this effect. In addition, anodal tDCS increased thalamo-M1 excitation as compared to cathodal stimulation, with the effects maintained after 5 sessions. In turn, cathodal tDCS had opposing effects on these connections after one session but became more similar to anodal after 5.

Conclusions

Together, our results suggest that pairing anodal tDCS with passive mobilisation across multiple sessions may facilitate behavioural command-following in PDOC patients with CMD. More broadly, they offer a mechanistic window into the neural underpinnings of the cumulative effects of multi-session tDCS.
Prior movement of one arm facilitates motor adaptation in the other
Authors: Gippert M. , Leupold S. , Heed T. , Howard I. S. , Villringer A. , Nikulin V. V. , Sehm B.
Published: November 2022

Many movements in daily life are embedded in motion sequences that involve more than one limb, demanding the motor system to monitor and control different body parts in quick succession. During such movements, systematic changes in the environment or the body might require motor adaptation of specific segments. However, previous motor adaptation research has focused primarily on motion sequences produced by a single limb, or on simultaneous movements of several limbs. For example, adaptation to opposing force fields is possible in unimanual reaching tasks when the direction of a prior or subsequent movement is predictive of force field direction. It is unclear, however, whether multi-limb sequences can support motor adaptation processes in a similar way. In the present study, we investigated whether reaches can be adapted to different force fields in a bimanual motor sequence when the information about the perturbation is associated with the prior movement direction of the other arm. In addition, we examined whether prior perceptual (visual or proprioceptive) feedback of the opposite arm contributes to force field-specific motor adaptation. Our key finding is that only active participation in the bimanual sequential task supports pronounced adaptation. This result suggests that active segments in bimanual motion sequences are linked across limbs. If there is a consistent association between movement kinematics of the linked and goal movement, the learning process of the goal movement can be facilitated. More generally, if motion sequences are repeated often, prior segments can evoke specific adjustments of subsequent movements.

Significance statement

Movements in a limb’s motion sequence can be adjusted based on linked movements. A prerequisite is that kinematics of the linked movements correctly predict which adjustments are needed. We show that use of kinematic information to improve performance is even possible when a prior linked movement is performed with a different limb. For example, a skilled juggler might have learned how to correctly adjust his catching movement of the left hand when the right hand performed a throwing action in a specific way. Linkage is possibly a key mechanism of the human motor system for learning complex bimanual skills. Our study emphasizes that learning of specific movements should not be studied in isolation but within their motor sequence context.
Quantitative assessment of association between noncoding variants and transcription factor binding
Authors: Ouyang Ningxin , Boyle Alan P.
Published: November 2022

Association fine-mapping of molecular traits is an essential method for understanding the impact of genetic variation. Sequencing-based assays, including RNA-seq, DNase-seq and ChIP-seq, have been widely used to measure different cellular traits and enabled genome-wide mapping of quantitative trait loci (QTLs). The disruption of cis-regulatory sequence, often occurring through variation within transcription factor binding motifs, has been strongly associated with gene dysregulation and human disease. We recently developed a computational method, TRACE, for transcription factor binding footprint prediction. TRACE integrates chromatin accessibility and transcription factor binding motifs to produce quantitative scores that describe the binding affinity of a TF for a specific TFBS locus. Here we have extended this method to incorporate variant data for 57 Yoruban individuals. Using genome-wide chromatin-accessibility data and human TF binding motifs, we have generated precise, genome-wide predictions of individual-specific transcription factor binding footprints. Subsequent association mapping between these footprints and nearby regulatory variants yielded numerous footprint-variant pairs with significant evidence for correlation, which we call footprint-QTLs (fpQTLs). fpQTLs appear to affect TF binding in a distance-dependent manner and share significant overlap with known dsQTLs and eQTLs. fpQTLs provide a rich resource for the study of regulatory variants, both within and outside known TFBSs, leading to improved functional interpretation of noncoding variation.
BioSAXS at European Synchrotron Radiation Facility – Extremely Brilliant Source: BM29 with an upgraded source, detector, robot, sample environment, data collection and analysis software
Authors: Tully Mark D. , Kieffer Jerome , Brennich Martha E. , Cohen Aberdam Raphael , Florial Jean Baptiste , Hutin Stephanie , Oscarsson Markus , Beteva Antonia , Popov Anton , Moussaoui Dihia , Theveneau Pascal , Papp Gergely , Gigmes Jonathan , Cipriani Florent , McCarthy Andrew , Zubieta Chloe , Mueller-Dieckmann Christoph , Leonard Gordon , Pernot Petra
Published: November 2022

As part of its Extremely Brilliant Source (EBS) upgrade project, the ESRF's BM29 BioSAXS beamline was subject to a significant upgrade and refurbishment. In addition to the replacement of the beamline's original bending magnet source by a two-pole wiggler, leading to an increase in brilliance by a factor of 60, the sample environment of the beamline was almost completely refurbished: a vacuum-compatible Pilatus3 X 2M with a sensitive area of 253.7 mm × 288 mm and frame rates up to 250 Hz was installed, increasing the active area available and thus the q-scaling of scattering images taken; the sample changer was replaced with an upgraded version, allowing more space for customizable sample environments and the installation of two new sample exposure units; the software associated with the beamline was also renewed. In addition, the layout and functionality of the BSXCuBE3 (BioSAXS Customized Beamline Environment) data acquisition software was redesigned, providing an intuitive `user first' approach for inexperienced users, while at the same time maintaining more powerful options for experienced users and beamline staff. Additional features of BSXCuBE3 are queuing of samples; either consecutive sample changer and/or SEC-SAXS (size-exclusion chromatography small-angle X-ray scattering) experiments, including column equilibration were also implemented. Automatic data processing and analysis are now managed via Dahu, an online server with upstream data reduction, data scaling and azimuthal integration built around PyFAI (Python Fast Azimuthal Integration), and data analysis performed using the open source FreeSAS. The results of this automated data analysis pipeline are displayed in ISPyB/ExiSAXS. The upgraded BM29 has been in operation since the post-EBS restart in September 2020, and here a full description of its new hardware and software characteristics together with examples of data obtained are provided.
Five-year plan and agricultural productivity in China
Authors: Han Yali , Paudel Krishna P. , Wan Junyi , He Qinying
Published: November 2022

Purpose

China's economy has transformed from a high-speed growth phase to a high-quality development phase. The agriculture sector has grown substantially since the economic reform in 1978. Considering the five-year plan (FYP) as a collection of policies, this study explores the relationship between the FYP and agricultural total factor productivity (TFP).

Design/methodology/approach

This study uses 31 provincial-level panel data of the five FYPs from 1996 to 2020. The data envelopment analysis (DEA) is used to compute Malmquist productivity indexes. The authors analyze the temporal and spatial changes and convergences of China's agricultural TFP, and investigate the impact of economic planning on China's agricultural TFP and its regional difference.

Findings

There is a slow but upward growth trend in China's agricultural TFP. The technical change has played a leading role in the growth of China's agricultural TFP. The agricultural TFP of all provinces has shown a “catch-up” effect and is developing toward their respective steady-state levels. The regional difference in productivity growth among the eastern, central and western regions exists. Test results show that the FYP has a positive effect on the agricultural TFP, and the effect has obvious regional heterogeneity. The FYP also plays a positive role in the gross value of agricultural output, and the impact effect is greater than that on the improvement of agricultural productivity.

Originality/value

There are many forms of industrial policy in China, among which the FYP is the guiding document of industrial policy, which makes a systematic plan for industrial development in the subsequent five years. The development objectives, guidelines and overall deployment for agriculture in the FYP not only describe the general context of China's agricultural development but also show the key ideas of agricultural development. Therefore, this study explores its impact on agricultural quality development from the perspective of FYP. The results provide evidence for examining the governance performance of the government and the objective evaluation and restraint of the FYP. As agriculture moves toward the stage of high-quality development, the Chinese government should strengthen the critical guiding role of the FYP and pay attention to quality indicators such as technical progress, efficiency improvement and regional coordination in the formulation of the FYP.
Analysis of key factors influencing green highway project development focusing on network interaction and project success: evidence from China
Authors: Huang Ning , Du Qiang , Zou Patrick X.W. , Huang Youdan
Published: November 2022

Purpose

This study aims to analyze the interaction and key factors within the network of factors influencing the success of green highway projects.

Design/methodology/approach

Through literature review and interviews with experienced project managers, this study identified 33 influencing factors from the perspectives of stakeholders and life cycle. The interaction between these influencing factors was determined by surveying different experts, most of whom have participated in green highway projects in China. Then, social network analysis (SNA) was used to explore the impact and control ability of different factors.

Findings

According to the prioritization of these factors, the results showed that some key factors were identified, especially incremental cost, lack of standards and regulations, development of innovative technologies and materials, public awareness and environmental protection behavior. Finally, some meaningful suggestions were put forward for different influencing factors of green highway projects.

Research limitations/implications

While the key influencing factors of the green highway projects have been identified by considering the interrelationships between different factors, the specific influencing paths and levels of different factors are not analyzed, more studies and methods should be conducted on this area in the future.

Practical implications

This finding of factors influencing the success of green highway projects which is useful for managers to overcome various obstacles encountered in similar projects. Moreover, considering the interaction among the influencing factors enables managers to make systematic and efficient decisions.

Social implications

Developing green highways have been perceived as a major innovation to help achieve the synergy of environmental protection, economic development and social responsibility. Studying the key factors influencing the success of green highway projects and putting forward targeted suggestions are crucial for promoting the environmental protection transformation of highway construction.

Originality/value

Compared with most studies on the identification of key influencing factors of construction projects, this research emphasized the interaction between different factors within the system in the analysis process. The findings could provide useful references to promote the successful implementation of green highway projects.
Evolution of construction risk management research: historiography and keyword co-occurrence analysis
Authors: Zhao Xianbo
Published: November 2022

Purpose

This study collected the bibliographic data of 2034 journal articles published in 2000–2021 from Web of Science (WoS) core collection database and adopted two bibliometric analysis methods, namely historiography and keyword co-occurrence, to identify the evolution trend of construction risk management (CRM) research topics.

Design/methodology/approach

CRM has been a key issue in construction management research, producing a big number of publications. This study aims to undertake a review of the global CRM research published from 2000 to 2021 and identify the evolution of the research topics relating to CRM.

Findings

This study found that risk analysis methods have shifted from simply ranking risks in terms of their relative importance or significance toward examining the interrelationships among risks, and that the objects of CRM research have shifted from generic construction projects toward specified types of construction projects (e.g. small projects, underground construction projects, green buildings and prefabricated projects). In addition, researchers tend to pay more attention to an individual risk category (e.g. political risk, safety risk and social risk) and integrate CRM into cost, time, quality, safety and environment management functions with the increasing adoption of various information and communication technologies.

Research limitations/implications

This study focused on the journal articles in English in WoS core collection database only, thus excluding the publications in other languages, not indexed by WoS and conference proceedings. In addition, the historiography focused on the top documents in terms of document strength and thus ignored the role of the documents whose strengths were a little lower than the threshold.

Originality/value

This review study is more inclusive than any prior reviews on CRM and overcomes the drawbacks of mere reliance on either bibliometric analysis results or subjective opinions. Revealing the evolution process of the CRM knowledge domain, this study provides an in-depth understanding of the CRM research and benefits industry practitioners and researchers.