Miracle-dz/UniFAR-FTUs huggingface dataset:
Focus on the emerging new fields of network physiology and network medicine

Despite the vast progress and achievements in systems biology and integrative physiology in the last decades, there is still a significant gap in understanding the mechanisms through which (i) genomic, proteomic and metabolic factors and signaling pathways impact vertical processes across cells, tissues and organs leading to the expression of different disease phenotypes and influence the functional and clinical associations between diseases, and (ii) how diverse physiological systems and organs coordinate their functions over a broad range of space and time scales and horizontally integrate to generate distinct physiologic states at the organism level. Two emerging fields, network medicine and network physiology, aim to address these fundamental questions. Novel concepts and approaches derived from recent advances in network theory, coupled dynamical systems, statistical and computational physics show promise to provide new insights into the complexity of physiological structure and function in health and disease, bridging the genetic and sub-cellular level with inter-cellular interactions and communications among integrated organ systems and sub-systems. These advances form first building blocks in the methodological formalism and theoretical framework necessary to address fundamental problems and challenges in physiology and medicine. This ‘focus on’ issue contains 26 articles representing state-of-the-art contributions covering diverse systems from the sub-cellular to the organism level where physicists have key role in laying the foundations of these new fields.
Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference

Advances in high-throughput sequencing have ushered in a new era of research into the gut microbiome and its role in human health and disease. However, due to the unique characteristics of microbiome survey data, their use for the detection of ecological interaction networks remains a considerable challenge, and a field of active methodological development. In this review, we discuss the landscape of existing statistical and experimental methods for detecting and characterizing microbial interactions, as well as the role that host and environmental metabolic signals play in mediating the behavior of these networks. Numerous statistical tools for microbiome network inference have been developed. Yet due to tool-specific biases, the networks identified by these methods are often discordant, motivating a need for the development of more general tools, the use of ensemble approaches, and the incorporation of prior knowledge into prediction. By elucidating the complex dynamics of the microbial interactome, we will enhance our understanding of the microbiome’s role in disease, more precisely predict the microbiome’s response to perturbation, and inform the development of future therapeutic strategies for microbiome-related disease. Impact statement This review provides a comprehensive description of experimental and statistical tools used for network analyses of the human gut microbiome. Understanding the system dynamics of microbial interactions may lead to the improvement of therapeutic approaches for managing microbiome-associated diseases. Microbiome network inference tools have been developed and applied to both cross-sectional and longitudinal experimental designs, as well as to multi-omic datasets, with the goal of untangling the complex web of microbe-host, microbe-environmental, and metabolism-mediated microbial interactions. The characterization of these interaction networks may lead to a better understanding of the systems dynamics of the human gut microbiome, augmenting our knowledge of the microbiome’s role in human health, and guiding the optimization of effective, precise, and rational therapeutic strategies for managing microbiome-associated disease.
Temporal Dynamics of Shape Processing Differentiate Contributions of Dorsal and Ventral Visual Pathways

Although shape perception is primarily considered a function of the ventral visual pathway, previous research has shown that both dorsal and ventral pathways represent shape information. Here, we examine whether the shape-selective electrophysiological signals observed in dorsal cortex are a product of the connectivity to ventral cortex or are independently computed. We conducted multiple EEG studies in which we manipulated the input parameters of the stimuli so as to bias processing to either the dorsal or ventral visual pathway. Participants viewed displays of common objects with shape information parametrically degraded across five levels. We measured shape sensitivity by regressing the amplitude of the evoked signal against the degree of stimulus scrambling. Experiment 1, which included grayscale versions of the stimuli, served as a benchmark establishing the temporal pattern of shape processing during typical object perception. These stimuli evoked broad and sustained patterns of shape sensitivity beginning as early as 50 msec after stimulus onset. In Experiments 2 and 3, we calibrated the stimuli such that visual information was delivered primarily through parvocellular inputs, which mainly project to the ventral pathway, or through koniocellular inputs, which mainly project to the dorsal pathway. In the second and third experiments, shape sensitivity was observed, but in distinct spatio-temporal configurations from each other and from that elicited by grayscale inputs. Of particular interest, in the koniocellular condition, shape selectivity emerged earlier than in the parvocellular condition. These findings support the conclusion of distinct dorsal pathway computations of object shape, independent from the ventral pathway.
Breast Cancer Screening and Care Among Black Sexual Minority Women: A Scoping Review of the Literature from 1990 to 2017.

INTRODUCTION Black women are more likely to be diagnosed at later stages of breast cancer compared with White women due to lower frequency of screening and lack of timely follow-up after abnormal screening results. Disparities in breast cancer screening, risk, and mortality are present within both Black women and sexual minority communities; however, there exists limited research concerning breast cancer care among Black sexual minority women. MATERIALS AND METHODS This scoping review examines the literature from 1990 to 2017 of the breast cancer care continuum among Black sexual minority women, including behavioral risk factors, screening, treatment, and survivorship. A total of 91 articles were identified through PubMed, PsycINFO, and CINAHL (Cumulative Index to Nursing and Allied Health Literature) databases. Fifteen articles were selected for data extraction, which met the criteria for including Black/African American women, discussing breast cancer care among both racial and sexual minorities, and being a peer-reviewed article. RESULTS The 15 articles were primarily within urban contexts, and defined sexual minorities as lesbian or bisexual women. Across all the studies, Black sexual minority women were highly under-represented, and key conclusions are not fully applicable to Black sexual minority women. Sexual minority women had a higher prevalence of breast cancer risk factors (i.e., nulliparity, fewer mammograms, higher alcohol intake, and lower oral contraceptive use). Furthermore, some studies noted homophobia from health providers as potential barriers to engagement in care for sexual minority women. CONCLUSIONS The lack of studies concerning Black sexual minority women in breast cancer care indicates the invisibility of a group that experiences multiple marginalized identities. More research is needed to capture the dynamics of the breast cancer care continuum for Black sexual minority women.
A well‐resolved transcriptomic phylogeny of the mite harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi) reveals signatures of Gondwanan vicariance

We explored the extent to which Gondwanan vicariance contributed to the circum‐Antarctic distribution of the mite harvestman family Pettalidae, a group of small, dispersal‐limited arachnids whose phylogeny has been poorly resolved, precluding rigorous biogeographic hypothesis testing.
Pulmonary arterial stent for pulmonary trunk stenosis after size-mismatched lung transplantation

To the Editor: Appropriate donor-to-recipient size matchpulmonary angiography, which demonstrated an open ing is of crucial importance in lung transplantation. anastomosis with severe stenosis of the distal right Although tailoring of the lung has been described as a successful means of overcoming size disparities, its merits and demerits remain unclear. Here, we present a case of recurrent hypoxemia after unmatched single lung transplantation. The causes of the hypoxemia were right middle lobe resection and the consequential pulmonary trunk stenosis that lead to unbalanced ventilation–blood flow ratio, which was diagnosed by pulmonary angiography and properly treated by the implantation of stents. The diagnostic protocol and treatment experience may have value for future clinical lung transplantations.
Selecting Future Climate Projections of Surface Solar Radiation in Japan

The ensemble average projections of the Coupled Model Inter-comparison Project Phase 5 (CMIP5) ensemble show future increases in shortwave radiation at the surface (SW) in Japan. We reveal that the Arctic Oscillation-like atmospheric circulation trends cause cloud cover decreases around Japan, leading to increases in the SW. In many cases, impact assessment studies use the outputs of only a few models due to limited research resources. We find that the four climate models used in the Japanese multisector impact assessment project, S-8, do not sufficiently capture the uncertainty ranges of the CMIP5 ensemble regarding the SW projections. Therefore, the impact assessments using the SW of these four models can be biased. We develop a novel method to select a better subset of models that are more widely distributed and are not biased, unlike the S-8 models. (Citation: Shiogama, H., R. Ito, Y. Imada, T. Nakaegawa, N. Hirota, N. N. Ishizaki, K. Takahashi, I. Takayabu, and S. Emori, 2020: Selecting future climate projections of surface solar radiation in Japan. SOLA, 16, 75−79, doi:10.2151/sola.2020-013.)
The Making of Contentious Political Space: The Transformation of Hong Kong’s Victoria Park

Space plays a vital role in structuring and forming social movements into particular shapes—especially via its physical settings, the representation constructed through dominant and alternative discourses, and protesters’ spatial practices therein. Geographers and urban theorists have long argued that public space is of paramount significance to collective actions. Yet we know less about how a sustainable, manageable, and iconic public space for continuous movement mobilization is created. This article uses Victoria Park, an iconic public space of contention in Hong Kong, as a case to examine how a contentious political space is made. Through archival research, we demonstrate how the Defend Diaoyutai Islands Movement of the 1970s transformed the park from an “empty” recreational space to a political space. People’s political actions made this transformation of the spatial order possible. Nonetheless, the British colonial government re-policed the spatial norms of the space, which in turn regulated both the government and protesters. The study affords significant opportunities for thinking about the spatial constraints of contentious politics.
Influence of Cost Strategy on Firm Performance

In today's complex and dynamic environment firm competitiveness is inevitable. This means therefore, that for better positioning and to remain ahead of rivals, firms can pursue suitable strategies especially being a cost leader. Empirical studies show that cost strategies influence competitiveness and growth of a firm (Tehrani, 2003). This study sought to determine the influence of cost strategy on the performance of manufacturing firms in Kenya. According to Porter (1995) firms that pursue cost leadership can achieve better competitive advantage leading to improved performance. Additionally, he asserts that firms are able to defend their market since lower cost can enable them earn better returns. Firms that adopt cost strategy, therefore, endeavor to lower cost in terms of production in the industry. The study utilized Porter's (1980) framework with the foundation of Dynamic capability theory by David Teece &amp; Gary Pisano in 1994 and stakeholders theory(Harrison, Bosse &amp; Phillips, 2010) and goal setting theory by Locke &amp; Latham (2006). The study adopted cross sectional descriptive survey, guided by positivist philosophy. This is because the study intended to observe a phenomenon and report it as it is. The study aimed to study all large manufacturers in Kenya. Data was collected using a structured questionnaire. Through use of percentages, mean scores and standard deviation the data was described. Regression analysis was used to test the hypothesis. The study found that cost strategy had a significant influence on the performance of manufacturing firms in Kenya.
Reliability of Measures Intended to Assess Threshold-Independent Hearing Disorders.

OBJECTIVES Recent animal studies have shown that noise exposure can cause cochlear synaptopathy without permanent threshold shift. Because the noise exposure preferentially damaged auditory nerve fibers that processed suprathreshold sounds (low-spontaneous rate fibers), it has been suggested that synaptopathy may underlie suprathreshold hearing deficits in humans. Recently, several researchers have suggested measures to identify the pathology or pathologies underlying suprathreshold hearing deficits in humans based on results from animal studies; however, the reliability of some of these measures have not been assessed. The purpose of this study was to assess the test-retest reliability of measures that may have the potential to relate suprathreshold hearing deficits to site(s)-of-lesion along the peripheral auditory system in humans. DESIGN Adults with audiometric normal hearing were tested on a battery of behavioral and physiologic measures that included (1) thresholds in quiet (TIQ), (2) thresholds in noise (TIN), (3) frequency-modulation detection threshold (FMDT), (4) word recognition in four listening conditions, (5) distortion-product otoacoustic emissions (DPOAE), (6) middle ear muscle reflex (MEMR), (7) tone burst-elicited auditory brainstem response (tbABR), and (8) speech-evoked ABR (sABR). Data collection for each measure was repeated over two visits separated by at least one week. The residuals of the correlation between the suprathreshold measures and TIQ serve as functional and quantitative proxies for threshold-independent hearing disorders because they represent the portion of the raw measures that is not dependent on TIQ. Reliability of the residual measures was assessed using intraclass correlation (ICC). RESULTS Reliability for the residual measures was good (ICC ≥ 0.75) for FMDT, DPOAEs, and MEMR. Residual measures showing moderate reliability (0.5 ≤ ICC < 0.75) were tbABR wave I amplitude, TIN, and word recognition in quiet, noise, and time-compressed speech with reverberation. Wave V of the tbABR, waves of the sABR, and recognition of time-compressed words had poor test-retest reliability (ICC < 0.5). CONCLUSIONS Reliability of residual measures was mixed, suggesting that care should be taken when selecting measures for diagnostic tests of threshold-independent hearing disorders. Quantifying hidden hearing loss as the variance in suprathreshold measures of auditory function that is not due to TIQ may provide a reliable estimate of threshold-independent hearing disorders in humans.
Pneumonia-Specific Escherichia coli with Distinct Phylogenetic and Virulence Profiles, France, 2012–2014

In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collections containing commensal and bacteremia isolates. The preponderant phylogenetic group was B2 (59.6%), and the predominant sequence type complex (STc) was STc73. STc127 and STc141 were overrepresented and STc95 underrepresented in pneumonia isolates compared with bacteremia isolates. Pneumonia isolates carried higher proportions of virulence genes sfa/foc, papGIII, hlyC, cnf1, and iroN compared with bacteremia isolates. Virulence factor gene content and antimicrobial drug resistance were higher in pneumonia than in commensal isolates. Genomic and phylogenetic characteristics of E. coli pneumonia isolates from critically ill patients indicate that they belong to the extraintestinal pathogenic E. coli pathovar but have distinguishable lung-specific traits.
Consolidation alters motor sequence-specific distributed representations

FMRI studies investigating the acquisition of sequential motor skills in humans have revealed learning-related functional reorganizations of the cortico-striatal and cortico-cerebellar motor systems in link with the hippocampus. Yet, the functional significance of these activity level changes is not fully understood as they convey the evolution of both sequence-specific knowledge and unspecific task expertise. Moreover, these changes do not specifically assess the occurrence of learning-related plasticity. To address these issues, we investigated local circuits tuning to sequence-specific information using multivariate distances between patterns evoked by consolidated or newly acquired motor sequences production. Results reveal that representations in dorsolateral striatum, prefrontal and secondary motor cortices are greater when executing consolidated sequences than untrained ones. By contrast, sequence representations in the hippocampus and dorsomedial striatum are less engaged. Our findings show, for the first time in humans, that complementary sequence-specific motor representations evolve distinctively during critical phases of skill acquisition and consolidation.
Endobronchial ultrasound-guided transbronchial needle aspiration under general anesthesia versus bronchoscopist-directed deep sedation: A retrospective analysis

Background: Different sedation strategies are used during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) for the diagnostic workup of lung cancer including general anesthesia (GA) and moderate sedation. However, no data are available about EBUS-TBNA under deep sedation (DS) with fiberoptic intubation directed by the investigator. Materials and Methods: A retrospective analysis of EBUS-TBNAs under GA (n = 160) or DS (n = 105) was performed. Results: Unadjusted diagnostic yield did not differ significantly between the groups (GA: 42.5% vs. DS: 53.3%P= 0.1018). Similar results were obtained when only patients with a final diagnosis of malignancy were analyzed (GA: 53.6% vs. DS: 61.5%P= 0.2675). Adverse events (AEs) occurred more often under DS (GA: 27.5% vs. DS: 59.1%P< 0.0001) due to more sedation-related problems whereas severe AEs tended to be higher under GA (GA: 7.5% vs. DS: 1.9%P= 0.0523). Conclusion: In summary, our data show that the diagnostic yield and the complication rate of EBUS-TBNA performed under DS are similar compared to GA. Hence, in an appropriate setting, EBUS-TBNA can be performed safely under DS.
A systematic review of reviews identifying UK validated dietary assessment tools for inclusion on an interactive guided website for researchers: www.nutritools.org

Abstract Background Health researchers may struggle to choose suitable validated dietary assessment tools (DATs) for their target population. The aim of this review was to identify and collate information on validated UK DATs and validation studies for inclusion on a website to support researchers to choose appropriate DATs. Design A systematic review of reviews of DATs was undertaken. DATs validated in UK populations were extracted from the studies identified. A searchable website was designed to display these data. Additionally, mean differences and limits of agreement between test and comparison methods were summarized by a method, weighting by sample size. Results Over 900 validation results covering 5 life stages, 18 nutrients, 6 dietary assessment methods, and 9 validation method types were extracted from 63 validated DATs which were identified from 68 reviews. These were incorporated into www.nutritools. org. Limits of agreement were determined for about half of validations. Thirty four DATs were FFQs. Only 17 DATs were validated against biomarkers, and only 19 DATs were validated in infant/children/adolescents. Conclusions The interactive www.nutritools. org website holds extensive validation data identified from this review and can be used to guide researchers to critically compare and choose a suitable DAT for their research question, leading to improvement of nutritional epidemiology research.
Distributive quality assurance and delivery of stereotactic ablative radiotherapy treatments amongst beam matched linear accelerators: A feasibility study

Abstract Purpose Beam matching occurs on all linacs to some degree and when two are more are matched to each other, patients are able to be transferred between machines. Quality assurance of plans can also be performed “distributively” on any of the matched linacs. The degree to which machines are matched and how this translates to like delivery of plans has been the focus of a number of studies. This concept has not yet been explored for stereotactic techniques which require a higher degree of accuracy. This study proposes beam matching criteria which allows for the distributive delivery and quality assurance of stereotactic body radiotherapy (SBRT) plans. Method Two clinically relevant and complex volumetric modulated arc therapy (VMAT) SBRT spine and lung plans were chosen as benchmarking cases. These were delivered on nine previously beam matched linacs with quality assurance performed through ArcCheck and film exposure in the sagittal plane. Measured doses were compared to their treatment planning system predictions through gamma analysis at a range of criteria. Results Despite differences in beam match parameters and variations in small fields, all nine linacs produced accurate deliveries with a tight deviation in the population sample. Pass rates were well above suggested tolerances at the recommended gamma criterion. Film was able to detect dose errors to a greater degree than ArcCheck. Conclusion Distributive quality assurance and delivery of stereotactic ablative radiotherapy treatments amongst beam matched linacs is certainly feasible provided the linacs are matched to a strict protocol like that suggested in this study and regular quality assurance is performed on the matched fleet. Distributive quality assurance and delivery of SBRT provides the possibility of efficiency gains for physicists as well as treatment staff.