bluuebunny/crossref_metadata_2025 huggingface dataset:
Immune thrombocytopenia with clinical significance in systemic lupus erythematosus: a retrospective cohort study of 90 patients
Authors: Roussotte Mickaël , Gerfaud-Valentin Mathieu , Hot Arnaud , Audia Sylvain , Bonnotte Bernard , Thibault Thomas , Lobbes Hervé , Le Guenno Guillaume , Goulabchand Radjiv , Cathebras Pascal , Varron Loig , Dufour Jean François , Deroux Alban , Compain Caroline , Baudet Antoine , Karkowski Ludovic , Pérard Laurent , Ebbo Mikael , Lega Jean-Christophe , Sève Pascal
Published: December 2021

Objectives

To describe the characteristics, treatment and outcome of patients with immune thrombocytopenia with clinical significance (ITPCS) associated with SLE.

Methods

This retrospective multicentre study included SLE patients who experienced ≥1 ITPCS (defined as ITP with attributable bleeding disorders and/or a platelet count <30×109/l). Other causes of secondary thrombocytopenia were excluded. Major bleeding event (MBG) was defined as Khellaf score >8 and/or WHO score >2.

Results

A total of 90 patients were included, the median (range) follow-up duration was 80 (6–446) months. ITP was diagnosed before SLE in 25 patients. They presented a high rate of autoimmune haemolytic anaemia (15%), antiphospholipid antibody (62%) and antiphospholipid syndrome (19%). The 25 (28%) patients who experienced MBG had significantly more bleedings at ITP diagnosis and higher bleeding scores, and serositis and thrombosis during follow-up. They required significantly more treatment lines, transfusions and hospitalizations. The 11 (12%) patients who experienced no bleeding event presented a significantly more restricted SLE phenotype (cutaneous and/or articular). Patients received a mean (range) of 4.2 (1–11) treatment lines. Corticosteroids and HCQ allowed ITPCS overall response in one-third of patients. The median relapse-free survival of rituximab (n = 34), AZA (n = 19), MMF (n = 8), thrombopoietin-receptor agonists (n = 16) and splenectomy (n = 19) were 53, 31.5, 61, 24.5 and 78 months, respectively. Four patients experienced thrombotic events after splenectomy and one occurred under thrombopoietin-receptor agonist treatment.

Conclusion

SLE-ITCS patients displayed a high rate of haematological abnormalities and MBG patients exhibited higher morbidity. Management of thrombocytopenia was highly heterogeneous and many options seem viable.
Narcolepsy with intermediate cerebrospinal level of hypocretin-1
Authors: Postiglione Emanuela , Barateau Lucie , Pizza Fabio , Lopez Régis , Antelmi Elena , Rassu Anna-Laura , Vandi Stefano , Chenini Sofiene , Mignot Emmanuel , Dauvilliers Yves , Plazzi Giuseppe
Published: December 2021

Study Objectives

To describe the phenotype of narcolepsy with intermediate cerebrospinal fluid hypocretin-1 levels (CSF hcrt-1).

Methods

From 1600 consecutive patients with narcolepsy from Bologna and Montpellier sleep centers, we selected patients with intermediate CSF hcrt-1 levels (110–200 pg/mL). Clinical, neurophysiological, and biological data were contrasted for the presence of cataplexy, human leukocyte haplotype (HLA)-DQB1*06:02, and median CSF hcrt-1 levels (149.34 pg/mL).

Results

Forty-five (55% males, aged 35 ± 17 years) patients (2.8% of all cases) were included. Thirty-three (73%) were HLA-DQB1*06:02, 29 (64%) reported cataplexy (21, 72.4% with typical features), and 5 (11%) had presumed secondary etiology. Cataplexy was associated with other core narcolepsy symptoms, increased sleep onset rapid eye movement periods, and nocturnal sleep disruption. Cataplexy and irrepressible daytime sleep were more frequent in HLA-DQB1*06:02 positive patients. Lower CSF hcrt-1 levels were associated with hallucinations.

Conclusions

Narcolepsy with intermediate CSF hcrt-1 level is a rare condition with heterogeneous phenotype. HLA-DQB1*06:02 and lower CSF hcrt-1 were associated with typical narcolepsy features, calling for future research to distinguish incomplete from secondary narcolepsy forms.
“We Have to Build Trust”: Intimate Partner Violence Risk Assessment with Immigrant and Refugee Survivors
Authors: Messing Jill , Wachter Karin , AbiNader Millan , Ward-Lasher Allison , Njie-Carr Veronica , Sabri Bushra , Murray Sarah , Noor-Oshiro Amelia , Campbell Jacquelyn
Published: December 2021

Intimate partner violence (IPV) research highlights unique immigration-related risk factors, abusive tactics, and barriers to seeking help. With the aim of developing practice-informed guidance, data from nine focus groups (N = 57) were analyzed thematically to examine practitioners’ experiences and approaches to risk assessment with survivors of IPV who are immigrants and refugees. Participants noted the importance of fostering relationships and trust in client disclosure and assessment of risk. Participants highlighted using a conversation-based approach; carefully chosen words; and open-ended, indirect, and probing questions to help clients feel at ease and generate information regarding risk. Additionally, practitioners emphasized the importance of conducting risk assessment and client education in concert with safety and service planning. However, safety and service planning must account for variations in context and language, as well as social pressures to keep families together. The adaptation of risk assessments to reflect immigrant experiences is a critical step forward. Nevertheless, listening to practitioners with expertise serving immigrant and refugee IPV survivors and developing additional guidance on how to use risk assessment tools and engage survivors are paramount to expanding relevant and responsive domestic violence services for diverse groups.
Addressing Social Workers’ Stress, Burnout, and Resiliency: A Qualitative Study with Supervisors
Authors: Mack Brenda M
Published: December 2021

Social work can be a purpose-driven, fulfilling profession of helping others, creating change, and fighting against injustice. It can also include regular exposure to the pain and suffering of others, extensive documentation requirements, and crisis management. Often when social workers are feeling overly stressed, supervisors play a critical role in addressing their health and wellness. Supervisors use a variety of approaches to raise supervisees’ awareness about the signs and symptoms of stress and burnout. They can make a positive difference in the lives of their supervisees by creating opportunities to discuss work-related challenges. There are both proactive and responsive options for supervisors to consider when cultivating resiliency with social workers. This exploratory study included 24 supervisors who described their approaches to addressing supervisees’ stress, burnout, and resiliency. Findings highlight the importance of relationships, communication, self-care, work–life balance, and resources for well-being. Implications emphasize the supervisory process, intrapersonal and interpersonal capacity building, and the National Association of Social Workers’ call to action in addressing self-care for those in the profession. The resiliency-focused strategies and suggestions offered are meant to support supervisors in their role of building and maintaining a healthy workforce.
Parameter Values for Estimation of Internal Doses from Ingestion of Radioactive Fallout from Nuclear Detonations
Authors: Thiessen Kathleen M. , Hoffman F. Owen , Bouville André , Anspaugh Lynn R. , Beck Harold L. , Simon Steven L.
Published: December 2021

This paper suggests values or probability distributions for a variety of parameters used in estimating internal doses from radioactive fallout due to ingestion of food. Parameters include those needed to assess the interception and initial retention of radionuclides by vegetation, translocation of deposited radionuclides to edible plant parts, root uptake by plants, transfer of radionuclides from vegetation into milk and meat, transfer of radionuclides into non-agricultural plants and wildlife, and transfer from food and drinking water to mother's milk (human breast milk). The paper includes discussions of the weathering half-life for contamination on plant surfaces, biological half-lives of organisms, food processing (culinary factors), and contamination of drinking water. As appropriate, and as information exists, parameter values or distributions are specific for elements, chemical forms, plant types, or other relevant characteristics. Information has been obtained from the open literature and from publications of the International Atomic Energy Agency. These values and probability distributions are intended to be generic; they should be reviewed for applicability to a given location, time period, or season of the year, as appropriate. In particular, agricultural practices and dietary habits may vary considerably both with geography and over time in a given location.
Complex foraging behaviours in wild birds emerge from social learning and recombination of components
Authors: Wild S. , Chimento M. , McMahon K. , Farine D. R. , Sheldon B. C. , Aplin L. M.
Published: December 2021

Recent well-documented cases of cultural evolution towards increasing efficiency in non-human animals have led some authors to propose that other animals are also capable of cumulative cultural evolution, where traits become more refined and/or complex over time. Yet few comparative examples exist of traits increasing in complexity, and experimental tests remain scarce. In a previous study, we introduced a foraging innovation into replicate subpopulations of great tits, the ‘sliding-door puzzle’. Here, we track diffusion of a second ‘dial puzzle’, before introducing a two-step puzzle that combines both actions. We mapped social networks across two generations to ask if individuals could: (1) recombine socially-learned traits and (2) socially transmit a two-step trait. Our results show birds could recombine skills into more complex foraging behaviours, and naïve birds across both generations could learn the two-step trait. However, closer interrogation revealed that acquisition was not achieved entirely through social learning—rather, birds socially learned components before reconstructing full solutions asocially. As a consequence, singular cultural traditions failed to emerge, although subpopulations of birds shared preferences for a subset of behavioural variants. Our results show that while tits can socially learn complex foraging behaviours, these may need to be scaffolded by rewarding each component.

This article is part of a discussion meeting issue ‘The emergence of collective knowledge and cumulative culture in animals, humans and machines’.
A somatosensory computation that unifies limbs and tools
Authors: Miller Luke E. , Fabio Cécile , de Vignemont Frédérique , Roy Alice , Medendorp W. Pieter , Farnè Alessandro
Published: December 2021

It is often claimed that tools are embodied by the user, but whether the brain actually repurposes its body-based computations to perform similar tasks with tools is not known. A fundamental computation for localizing touch on the body is trilateration. Here, the location of touch on a limb is computed by integrating estimates of the distance between sensory input and its boundaries (e.g., elbow and wrist of the forearm). As evidence of this computational mechanism, tactile localization on a limb is most precise near its boundaries and lowest in the middle. We show that the brain repurposes trilateration to localize touch on a tool. In a large sample of participants, we found that localizing touch on a tool produced the signature of trilateration, with highest precision close to the base and tip of the tool. A computational model of trilateration provided a good fit to the observed localization behavior. To further demonstrate the computational plausibility of repurposing trilateration, we implemented it in a three-layer neural network that was based on principles of probabilistic population coding. This network determined hit location in tool-centered coordinates by using a tool’s unique pattern of vibrations when contacting an object. Simulations demonstrated the expected signature of trilateration, in line with the behavioral patterns. Our results have important implications for how trilateration may be implemented by somatosensory neural populations. We conclude that trilateration is a fundamental spatial computation that unifies limbs and tools.
Clonal hematopoiesis is associated with protection from Alzheimer’s disease
Authors: Bouzid Hind , Belk Julia A. , Jan Max , Qi Yanyan , Sarnowski Chloé , Wirth Sara , Ma Lisa , Chrostek Matthew , Ahmad Herra , Nachun Daniel , Yao Winnie ,   NHLBI Trans-omics for Precision Medicine (TOPMed) Consortium, Beiser Alexa , Bick Alexander G. , Bis Joshua C. , Fornage Myriam , Longstreth William T. , Lopez Oscar L. , Natarajan Pradeep , Psaty Bruce M. , Satizabal Claudia L. , Weinstock Joshua , Larson Eric B. , Crane Paul K. , Keene C. Dirk , Seshadri Sudha , Satpathy Ansuman T. , Montine Thomas J. , Jaiswal Siddhartha
Published: December 2021

Clonal hematopoiesis of indeterminate potential (CHIP) is a pre-malignant expansion of mutated blood stem cells that also associates with non-hematological disorders. Here, we tested whether CHIP was associated with Alzheimer’s disease (AD). Surprisingly, we found that CHIP carriers had reduced risk of AD dementia or AD neuropathologic features in multiple cohorts. The same mutations found in blood were also detected in the microglia-enriched fraction of brain in 7 out of 8 CHIP carriers. Single-cell chromatin accessibility profiling of brain-derived nuclei in two CHIP carriers revealed that the mutated cells were indistinguishable from microglia and comprised between 42-77% of the total microglial pool. These results suggest a role for mutant, marrow-derived cells in attenuating risk of AD, possibly by supplementing a failing microglial system during aging.
Structure of the 5’ untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune system via the human oligoadenylate synthase 1†
Authors: Bignon Emmanuelle , Miclot Tom , Terenzi Alessio , Barone Giampaolo , Monari Antonio
Published: December 2021

2’-5’-Oligoadenylate synthetase 1 (OAS1) is one of the key enzymes driving the innate immune system response to SARS-CoV-2 infection whose activity has been related to COVID-19 severity. In particular, OAS1 is a sensor of endogenous RNA that triggers the 2’-5’ oligoadenylate/RNase L pathway in response to viral infections, ultimately activating the RNA-Lyase which cleaves endogenous and exogenous RNA impeding the viral maturation. Upon SARS-CoV-2 infection, OAS1 is responsible for the recognition of viral RNA and has been shown to possess a particularly high sensitivity for the 5’-untranslated (5’-UTR) RNA region, which is organized in a double-strand stem loop motif (SLA). Since the structure of the nucleic acid/protein complex has not been resolved, here we report its structure obtained by molecular modeling, including enhanced sampling approaches. We also pinpoint that the SL1 region enhances the interaction network with the enzyme, promoting specific hydrogen bonds, absent in normal double strand RNA fragments, hence rationalizing the high affinity for OAS1.
De-novo generation of novel phenotypically active molecules for Chagas disease from biological signatures using AI-driven generative chemistry
Authors: Pikusa Michal , René Olivier , Williams Sarah , Chen Yen-Liang , Martin Eric , Godinez William J. , Rao Srinivasa P S , Guiguemde W. Armand , Nigsch Florian
Published: December 2021

Designing novel molecules with targeted biological activities and optimized physicochemical properties is a challenging endeavor in drug discovery. Recent developments in artificial intelligence have enhanced the early steps of de novo drug design and compound optimization. Herein, we present a generative adversarial network trained to design new chemical matter that satisfies a given biological signature. Our model, called pqsar2cpd, is based on the activity of compounds across multiple assays obtained via pQSAR (profile-quantitative structure–activity relationships). We applied pqsar2cpd to Chagas disease and designed a novel molecule that was experimentally confirmed to inhibit growth of parasites in vitro at low micromolar concentrations. Altogether, this approach bridges chemistry and biology into one single framework for the design of novel molecules with promising biological activity.
2½-minute 3D 7T 31P-MRSI of the human heart using concentric rings (CRT)
Authors: Clarke William , Hingerl Lukas , Strasser Bernhard , Bogner Wolfgang , Valkovič Ladislav , Rodgers Christopher T
Published: December 2021

A 3D density-weighted concentric ring trajectory (CRT) MRSI sequence is implemented for cardiac 31P-MRS at 7T.

The point-by-point k-space sampling of traditional phase-encoded CSI sequences severely restricts the minimum scan time at higher spatial resolutions. Our proposed CRT sequence implements a stack of concentric rings trajectory, with a variable number of rings and planes spaced to optimise the density of k-space weighting. This creates flexibility in acquisition time, allowing acquisitions substantially faster than traditional phase-encoded CSI sequences, while retaining high SNR.

We first characterise the signal-to-noise ratio and point spread function of the CRT sequence in phantoms. We then evaluate it at five different acquisition times and spatial resolutions in the hearts of five healthy participants at 7T. These different sequence durations are compared with existing published 3D acquisition-weighted CSI sequences with matched acquisition times and spatial resolutions. To minimise the effect of noise on the short acquisitions, low-rank denoising of the spatio-temporal data was also performed after acquisition.

The proposed sequence measures 3D localised PCr/ATP ratios of the human myocardium in 2.5 minutes, 2.6 times faster than the minimum scan time for the acquisition-weighted phase-encoded CSI. Alternatively, in the same scan time a 1.7-times smaller nominal voxel volume can be achieved. Low-rank denoising reduced the variance of measured PCr/ATP ratios by 11% across all protocols. The faster acquisitions permitted by 7T CRT 31P-MRSI could make cardiac stress protocols or creatine kinase rate measurements (which involve repeated scans) more tolerable for patients without sacrificing spatial resolution.
Sensory convergence in the world’s largest cavefish diversification: patterns of neuromast evolution, distribution and associated behaviour in Sinocyclocheilus
Authors: Chen Bing , Mao Tingru , Liu Yewei , Dai Wenzhang , Li Xianglin , Rajput Amrapali P. , Yang Jian , Gross Joshua B. , Meegaskumbura Madhava
Published: December 2021

The genus Sinocyclocheilus represents the largest freshwater cavefish genus in the world. This emerging model system is endemic to the southern Chinese karstic landscape, and demonstrates multiple adaptations for caves (troglomorphism), with eye-degeneration being the most pronounced. The less-apparent lateral line system, which is often expanded in cave-dwellers, has been studied in other cavefish systems, but never in the context of this diversification. Here we investigated the distribution and evolution of cephalic neuromasts in 26 Sinocyclocheilus species. We used live-staining and behavioural assays, and interpreted results in a phylogenetic context. We show that asymmetry in neuromast features and the rate of evolution is greater in cave-adapted species. Ancestral state reconstructions show that most Sinocyclocheilus are right-biased with some scatter, and show convergence of neuromast phenotypes. There is substantial variation in cephalic neuromast distribution patterns between and (to a lesser extent) within species. Behavioural assays show blind species have a distinctive wall-following behaviour. We explain these patterns in the context of the deep evolutionary history associated with this karstic region, other organismal traits, and habitat occupation of these remarkable diversifications of fishes. Interestingly, some of these neuromast patterns and behaviour show convergence with other phylogenetically distant cavefish systems.
Coral larvae suppress the heat stress response during the onset of symbiosis thereby decreasing their odds of survival
Authors: Kitchen Sheila A. , Jiang Duo , Harii Saki , Satoh Noriyuki , Weis Virginia M. , Shinzato Chuya
Published: December 2021

The endosymbiosis between most corals and their photosynthetic dinoflagellate partners begins early in the host life history, when corals are larvae or juvenile polyps. The capacity of coral larvae to buffer climate-induced stress while in the process of symbiont acquisition could come with physiological trade-offs that alter larval behavior, development, settlement and survivorship. Here we examined the joint effects of thermal stress and symbiosis onset on colonization dynamics, survival, metamorphosis and host gene expression of Acropora digitifera larvae. We found that thermal stress decreased symbiont colonization of hosts by 50% and symbiont density by 98.5% over two weeks. Temperature and colonization also influenced larval survival and metamorphosis in an additive manner, where colonized larvae fared worse or prematurely metamorphosed more often than non-colonized larvae under thermal stress. Transcriptomic responses to colonization and thermal stress treatments were largely independent, while the interaction of these treatments revealed contrasting expression profiles of genes that function in the stress response, immunity, inflammation and cell cycle regulation. The combined treatment either canceled or lowered the magnitude of expression of heat-stress responsive genes in the presence of symbionts, revealing a physiological cost to acquiring symbionts at the larval stage with elevated temperatures. In addition, host immune suppression, a hallmark of symbiosis onset under ambient temperature, turned to immune activation under heat stress. Thus, by integrating the physical environment and biotic pressures that mediate pre-settlement event in corals, our results suggest that colonization may hinder larval survival and recruitment creating isolated, genetically similar populations under projected climate scenarios.
A novel camera trap design for studying wildlife in mountain glacier ecosystems yields new insight for glacier biodiversity in the Pacific Northwest, USA
Authors: Hotaling Scott , Boersma Jordan , Paprocki Neil A. , Anderson Alissa , Whiles Logan , Ogburn Lucy , Kasper Sophia , White Catharine , Thornton Daniel H. , Wimberger Peter
Published: December 2021

Context

The global recession of glaciers and perennial snowfields is reshaping mountain ecosystems. Beyond physical changes to the landscape and altered downstream hydrology, the implications of glacier decline for biodiversity are poorly known. Before predictions can be made about how climate change will affect wildlife in glacier-associated ecosystems, a more thorough accounting of the role that glaciers play in species’ life histories is needed. However, typical approaches for documenting wildlife presence and behavior—remote camera traps—are difficult to use in glaciated terrain due to limited options for securing them (e.g., no trees) and dramatic seasonal changes in snowpack.

Aims

In this study, we sought to test a novel camera trap designed for glaciated mountain ecosystems. We also aimed to use this approach to gain insight into wildlife and human usage of a mountain glacier in western North America.

Methods

We deployed an elevational transect of uniquely designed camera traps along the western margin of the Paradise Glacier, a rapidly receding mountain glacier on the south side of Mount Rainier, WA, USA. Our simple camera trap design consisted of a wildlife camera attached to a camouflaged cylindrical cooler filled with snow and rocks.

Key results

Our camera design proved ideal for a mountain glacier ecosystem and from June to September 2021, we detected at least 16 vertebrate species (seven birds, nine mammals) over 770 trap nights using glacier-associated habitats. Humans, primarily skiers, were the most common species detected, but we also recorded 99 observations of wildlife (birds and mammals). These included three species of conservation concern in Washington: wolverine (Gulo gulo), Cascade red fox (Vulpes vulpes cascadensis), and white-tailed ptarmigan (Lagopus leucura).

Conclusions

Collectively, our results provide proof-of-concept for a novel camera trap design that is ideal for treeless, perennially snow-covered landscapes and revealed a rich diversity of wildlife using mountain glacier habitat in the Pacific Northwest. We highlight the global need for similar studies to better understand the true scale of biodiversity that will be impacted by glacier recession in mountain ecosystems.
Time-Varying Mortality Risk Suggests Increased Impact of Thrombosis in Hospitalized Covid-19 Patients
Authors: Lengerich Benjamin J. , Nunnally Mark E. , Aphinyanaphongs Yin , Caruana Rich
Published: December 2021

Treatment protocols, treatment availability, disease understanding, and viral characteristics have changed over the course of the Covid-19 pandemic; as a result, the risks associated with patient comorbidities and biomarkers have also changed. We add to the ongoing conversation regarding inflammation, hemostasis and vascular function in Covid-19 by performing a time-varying observational analysis of over 4000 patients hospitalized for Covid-19 in a New York City hospital system from March 2020 to August 2021 to elucidate the changing impact of thrombosis, inflammation, and other risk factors on in-hospital mortality. We find that the predictive power of biomarkers of thrombosis risk have increased over time, suggesting an opportunity for improved care by identifying and targeting therapies for patients with elevated thrombophilic propensity.
IGF1 Receptor Regulates Upward Firing Rate Homeostasis via the Mitochondrial Calcium Uniporter
Authors: Katsenelson Maxim , Shapira Ilana , Abbas Eman , Styr Boaz , Aïd Saba , Holzenberger Martin , Rizzoli Silvio , Slutsky Inna
Published: December 2021

Regulation of firing rate homeostasis constitutes a fundamental property of central neural circuits. While intracellular Ca2+ has long been hypothesized to be a feedback control signal, the molecular machinery enabling network-wide homeostatic response remains largely unknown. Here we show that deletion of insulin-like growth factor-1 receptor (IGF1R), a well-known regulator of neurodevelopment and ageing, limits firing rate homeostasis in response to inactivity, without altering the baseline firing rate distribution. Disruption of both synaptic and intrinsic homeostatic plasticity contributed to deficient firing rate homeostatic response. At the cellular level, a fraction of IGF1Rs was localized in mitochondria with the mitochondrial calcium uniporter complex (MCUc). IGF1R deletion suppressed spike burst-evoked mitochondrial Ca2+ (mitoCa2+) by weakening mitochondria-to-cytosol Ca2+ coupling. MCUc overexpression in IGF1R-deficient neurons rescued the deficits in spike-to-mitoCa2+ coupling and firing rate homeostasis. Our findings highlight IGF1R as a key regulator of the integrated homeostatic response by tuning mitochondrial temporal filtering. Decline in mitochondrial reliability for burst transfer may drive dysregulation of firing rate homeostasis in ageing and brain disorders associated with aberrant IGF1R / MCUc signaling.
ForestScanner: A mobile application for measuring and mapping trees with LiDAR-equipped iPhone and iPad
Authors: Tatsumi Shinichi , Yamaguchi Keiji , Furuya Naoyuki
Published: December 2021

Ground-based light detection and ranging (LiDAR) is becoming increasingly popular as an alternative means to conventional forest inventory methods. By gauging the distances to multiple points on the surrounding object surfaces, LiDAR acquires 3D point clouds from which tree sizes and spatial distributions can be rapidly estimated. However, the high cost and specialized skills associated with LiDAR technologies have put them out of reach for many potential users.

We here introduce ForestScanner, a free, mobile application that allows LiDAR-based forest inventories by means of iPhone or iPad with a built-in LiDAR sensor. ForestScanner does not require any manual analysis of 3D point clouds. As the user scans trees with an iPhone/iPad, ForestScanner estimates the stem diameters and spatial coordinates based on real-time instance segmentation and circle fitting. The users can visualize, check, and share the scanning resultsin situ.

By using ForestScanner, we measured the stem diameters and spatial coordinates of 672 trees within a 1 ha plot in 1 h 39 min with an iPhone and in 1 h 38 min with an iPad (diameter ≥5 cm; detection rate = 100%). The diameters measured by ForestScanner and a diameter tape were in good agreement; R2=0.963 for iPhone and R2=0.961 for iPad. ForestScanner and a conventional surveying system showed almost identical results for tree mapping (assessed by the spatial distances among trees within 0.04 ha subplots); Mantel R2=0.999 for both iPhone and iPad. ForestScanner reduced the person-hours required for measuring diameters to 25.7%, mapping trees to 9.3%, and doing both to 6.8% of the person-hours taken using a dimeter tape and the conventional surveying system.

Our results indicate that ForestScanner enables cost-, labor-, and time-efficient forest inventories. The application can increase the accessibility to LiDAR for non-experts (e.g., students, citizen scientists) and enhance resource assessments and biodiversity monitoring in forests worldwide.
Presence and the global implications of plastics in wild commercial fish in the Alboran Sea
Authors: López-Martínez Sergio , Perez-Rubín Cipriano , Gavara Rafael , Handcock Rebecca , Rivas Marga L
Published: December 2021

The presence of plastic in the environment has become a major problem for marine megafauna. The identification of the global micro and mesoplastic uptake by commercial fish populations may allow for a better understanding of their impact. This study aims to: (i) determine the presence and composition of plastic in two pelagic fish (Engraulis encrasicolus and Scomber scombrus) and two demersal species (Scyliorinus canicula and Mullus barbatus) from the Alboran Sea (western Mediterranean) to quantify the relationship between plastic prevalence and habitat and feeding behavior in the selected fish species, (ii) compare local measurements made of the presence of plastics ingested by these four fish species with published values from a across their range literature review, and (iii) identify the methodologies used in similar studies of plastic pollution in fish. Across their range, the highest occurrence of plastics was found in E. encrasicolus, which contrasts to that found in S. scombrus at the Alboran sea. Material analysis of the collected data showed the most predominant fiber color was black and the predominant plastic polymer was polyethylene. The increasing emerging risk of plastics and the levels of macro- and micro-plastic ingested by seafood in this study support the suggest that quantifying plastic presence and composition may be essential as a food safety measure.
Functional coupling between TRPV4 channel and TMEM16F modulates human trophoblast fusion
Authors: Zhang Yang , Liang Pengfei , Shan Ke Zoe , Feng Liping , Chen Yong , Liedtke Wolfgang , Yang Huanghe
Published: December 2021

TMEM16F, a Ca2+-activated phospholipid scramblase (CaPLSase), is critical for placental trophoblast syncytialization, HIV infection, and SARS-CoV2-mediated syncytialization. How TMEM16F is activated during cell fusion is unclear. Here, we used trophoblasts as a model for cell fusion and demonstrated that Ca2+influx through Ca2+permeable transient receptor potential vanilloid channel TRPV4 is critical for TMEM16F activation and subsequent human trophoblast fusion. GSK1016790A, a TRPV4 specific agonist, robustly activates TMEM16F in trophoblasts. Patch-clamp electrophysiology demonstrated that TRPV4 and TMEM16F are functionally coupled within Ca2+microdomains in human trophoblasts. Pharmacological inhibition or gene silencing of TRPV4 hindered TMEM16F activation and subsequent trophoblast syncytialization. Our study uncovers the functional expression of TRPV4 and a physiological activation mechanism of TMEM16F in human trophoblasts, thus providing us with novel strategies to regulate CaPLSase activity as a critical checkpoint of physiologically- and disease-relevant cell fusion events.
Two Stages of Speech Envelope Tracking in Human Auditory Cortex Modulated by Speech Intelligibility
Authors: Xu Na , Zhao Baotian , Luo Lu , Zhang Kai , Shao Xiaoqiu , Luan Guoming , Wang Qian , Hu Wenhan , Wang Qun
Published: December 2021

The envelope is essential for speech perception. Recent studies have shown that cortical activity can track the acoustic envelope. However, whether the tracking strength reflects the extent of speech intelligibility processing remains controversial. Here, using stereo-electroencephalogram (sEEG) technology, we directly recorded the activity in human auditory cortex while subjects listened to either natural or noise-vocoded speech. These two stimuli have approximately identical envelopes, but the noise-vocoded speech does not have speech intelligibility. We found two stages of envelope tracking in auditory cortex: an early high-γ (60-140 Hz) power stage (delay ≈ 49 ms) that preferred the noise-vocoded speech, and a late θ (4-8 Hz) phase stage (delay ≈ 178 ms) that preferred the natural speech. Furthermore, the decoding performance of high-γ power was better in primary auditory cortex than in non-primary auditory cortex, consistent with its short tracking delay. We also found distinct lateralization effects: high-γ power envelope tracking dominated left auditory cortex, while θ phase showed better decoding performance in right auditory cortex. In sum, we suggested a functional dissociation between high-γ power and θ phase: the former reflects fast and automatic processing of brief acoustic features, while the latter correlates to slow build-up processing facilitated by speech intelligibility.
Conformational variation in enzyme catalysis: A structural study on catalytic residues
Authors: Riziotis Ioannis G. , Ribeiro António J. M. , Borkakoti Neera , Thornton Janet M.
Published: December 2021

Conformational variation in catalytic residues can be captured as alternative snapshots in enzyme crystal structures. Addressing the question of whether active site flexibility is an intrinsic and essential property of enzymes for catalysis, we present a comprehensive study on the 3D variation of active sites of 925 enzyme families, using explicit catalytic residue annotations from the Mechanism and Catalytic Site Atlas and structural data from the Protein Data Bank. Through weighted pairwise superposition of the functional atoms of active sites, we captured structural variability at single-residue level and examined the geometrical changes as ligands bind or as mutations occur. We demonstrate that catalytic centres of enzymes can be inherently rigid or flexible to various degrees according to the function they perform, and structural variability most often involves a subset of the catalytic residues, usually those not directly involved in the formation or cleavage of bonds. Moreover, data suggest that 2/3 of active sites are flexible, and in half of those, flexibility is only observed in the side chain. The goal of this work is to characterise our current knowledge of the extent of flexibility at the heart of catalysis and ultimately place our findings in the context of the evolution of catalysis as enzymes evolve new functions and bind different substrates.
In silicoand functional characterisation of an ultra-rareCFTRmutation identifies novel lasso motif interactions regulating channel gating
Authors: Wong Sharon L. , Awatade Nikhil T. , Astore Miro A. , Allan Katelin M. , Carnell Michael J. , Slapetova Iveta , Chen Po-chia , Capraro Alexander , Fawcett Laura K. , Whan Renee M. , Griffith Renate , Ooi Chee Y. , Kuyucak Serdar , Jaffe Adam , Waters Shafagh A.
Published: December 2021

Characterisation of I37R – a novel mutation in the lasso motif of ABC-transporter CFTR, a chloride channel – was conducted by theratyping using CFTR potentiators which increase channel gating activity and correctors which repair protein trafficking defects. I37R-CFTR function was characterised using intestinal current measurements (ICM) in rectal biopsies, forskolin-induced swelling (FIS) in intestinal organoids and short circuit current measurements (Isc) in organoid-derived monolayers from an individual with I37R/F508del CFTR genotype. We demonstrated that the I37R-CFTR mutation results in a residual function defect amenable to treatment with potentiators and type III, but not to type I, correctors. Molecular dynamics of I37R-CFTR using an extended model of the phosphorylated, ATP-bound human CFTR identified an altered lasso motif conformation which results in an unfavourable strengthening of the interactions between the lasso motif, the regulatory (R) domain and the transmembrane domain two (TMD2). In conclusion, structural and functional characterisation of the I37R-CFTRmutation increases understanding of CFTR channel regulation and provides a potential pathway to access CFTR modulator treatments for individuals with CF caused by ultra-rareCFTRmutations.
PTRN-1/CAMSAP and NOCA-2/NINEIN are required for microtubule polarity in Caenorhabditis elegans dendrites
Authors: He Liu , van Beem Lotte , Hoogenraad Casper C. , Harterink Martin
Published: December 2021

The neuronal microtubule cytoskeleton is key to establish axon-dendrite polarity. Dendrites are characterized by the presence of minus-end out microtubules, however the mechanisms that organize these microtubules minus-end out is still poorly understood. Here, we characterized the role of two microtubule minus-end related proteins in this process in Caenorhabditis elegans, the microtubule minus-end stabilizing protein CAMSAP (PTRN-1) and a NINEIN homologue (NOCA-2). We found that CAMSAP and NINEIN function in parallel to mediate microtubule organization in dendrites. During dendrite outgrowth, RAB-11 positive vesicles localized to the dendrite tip function as a microtubule organizing center (MTOC) to nucleate microtubules. In the absence of either CAMSAP or NINEIN, we observed a low penetrance MTOC vesicles mis-localization to the cell body, and a nearly fully penetrant phenotype in double mutant animals. This suggests that both proteins are important for localizing the MTOC vesicles to the growing dendrite tip to organize microtubules minus-end out. Whereas NINEIN localizes to the MTOC vesicles where it is important for the recruitment of the microtubule nucleator γ-tubulin, CAMSAP localizes around the MTOC vesicles and is co-translocated forward with the MTOC vesicles upon dendritic growth. Together, these results indicate that microtubule nucleation from the MTOC vesicles and microtubule stabilization are both important to localize the MTOC vesicles distally to organize dendritic microtubules minus-end out.
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
Authors: Symer David E. , Akagi Keiko , Geiger Heather M. , Song Yang , Li Gaiyun , Emde Anne-Katrin , Xiao Weihong , Jiang Bo , Corvelo André , Toussaint Nora C. , Li Jingfeng , Agrawal Amit , Ozer Enver , El-Naggar Adel K. , Du Zoe , Shewale Jitesh B. , Stache-Crain Birgit , Zucker Mark , Robine Nicolas , Coombes Kevin R. , Gillison Maura L.
Published: December 2021

Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes. The HPV oncoproteins E6 and E7 are necessary but insufficient for cancer formation, indicating that additional secondary genetic events are required. Here, we investigate potential oncogenic impacts of virus integration. Analysis of 105 HPV-positive oropharyngeal cancers by whole-genome sequencing detects virus integration in 77%, revealing five statistically significant sites of recurrent integration near genes that regulate epithelial stem cell maintenance (i.e., SOX2, TP63, FGFR, MYC) and immune evasion (i.e., CD274). Genomic copy number hyperamplification is enriched 16-fold near HPV integrants, and the extent of focal host genomic instability increases with their local density. The frequency of genes expressed at extreme outlier levels is increased 86-fold within ±150 kb of integrants. Across 95% of tumors with integration, host gene transcription is disrupted via intragenic integrants, chimeric transcription, outlier expression, gene breaking, and/or de novo expression of noncoding or imprinted genes. We conclude that virus integration can contribute to carcinogenesis in a large majority of HPV-positive oropharyngeal cancers by inducing extensive disruption of host genome structure and gene expression.
Arithmetic properties of (2, 3)-regular overcubic bipartitions
Authors: Nayaka S. Shivaprasada
Published: December 2021

Purpose

Let b¯2,3(n), which enumerates the number of (2, 3)-regular overcubic bipartition of n. The purpose of the paper is to describe some congruences modulo 8 for b¯2,3(n). For example, for each α ≥ 0 and n ≥ 1, b¯2,3(8n+5)≡0(mod8), b¯2,3(2⋅3α+3n+4⋅3α+2)≡0(mod8).

Design/methodology/approach

H.C. Chan has studied the congruence properties of cubic partition function a(n), which is defined by ∑n=0∞a(n)qn=1(q;q)∞(q2;q2)∞.

Findings

To establish several congruence modulo 8 for b¯2,3(n), here the author keeps to the classical spirit of q-series techniques in the proofs.

Originality/value

The results established in the work are extension to those proved in ℓ-regular cubic partition pairs.
Opportunism, bounded rationality and governance choices in exploration alliances: the moderating role of boundary spanners' guanxi
Authors: Lin Liang-Hung , Ho Yu-Ling
Published: December 2021

Purpose

By distinguishing opportunism-based and bounded rationality-based transaction costs, the study examines how firms use equity/relational governance and boundary spanners' guanxi to govern their exploration alliances in a transaction cost economizing way.

Design/methodology/approach

This study used a survey methodology for data collection, and the sample consists of 150 exploration alliances formed by large Taiwanese information and electronic firms.

Findings

Findings of this study show that exploration alliances incur considerable transaction costs and require high-level equity control and relational governance. The positive exploration of alliance-equity ownership relationship will be weakened by boundary spanners' guanxi when guanxi serves to harmonize conflicts and mitigate opportunism-based transaction costs, thereby reducing the need for using costly equity ownership to govern exploration alliances. In contrast, the positive exploration alliance-relational governance relationship will be amplified when guanxi becomes a source of legitimacy in the Chinese guanxi institution. This relation-augmenting effect will drive more relational governance because guanxi and relational governance together allow alliance managers to obtain sufficient legitimacy in the formation of a common dominant frame, thereby mitigating bounded rationality-based transaction costs.

Originality/value

By distinguishing various moderating effects of boundary spanners' guanxi and separating transaction costs into two forms, this study contributes to the existing literature as well as advances our understanding of alliance governance decisions in the Chinese business environment.
Motion control of the two joint planar robotic manipulators through accelerated Dai–Liao method for solving system of nonlinear equations
Authors: Halilu Abubakar Sani , Majumder Arunava , Waziri Mohammed Yusuf , Ahmed Kabiru , Awwal Aliyu Muhammed
Published: December 2021

Purpose

The purpose of this research is to propose a new choice of nonnegative parameter t in Dai–Liao conjugate gradient method.

Design/methodology/approach

Conjugate gradient algorithms are used to solve both constrained monotone and general systems of nonlinear equations. This is made possible by combining the conjugate gradient method with the Newton method approach via acceleration parameter in order to present a derivative-free method.

Findings

A conjugate gradient method is presented by proposing a new Dai–Liao nonnegative parameter. Furthermore the proposed method is successfully applied to handle the application in motion control of the two joint planar robotic manipulators.

Originality/value

The proposed algorithm is a new approach that will not either submitted or publish somewhere.
Barriers and enablers to health and social services for older prisoners transitioning to community
Authors: Hagos Amanuel Kidane , Withall Adrienne , Ginnivan Natasha Ann , Snoyman Phillip , Butler Tony
Published: December 2021

Purpose

When properly designed and implemented, prison-to-community transition programs targeting older prisoners could potentially save resources, reduce reoffending rates and contribute to improved public protection and safety. However, older prisoners transitioning to community are often neglected and overlooked, and thus, interventions targeted to address their needs are limited. The purpose of this study was to identify barriers and enablers to health and social services for older prisoners transitioning to community.

Design/methodology/approach

A qualitative study was conducted using focus group discussions with corrections officers, community corrections officers and parole officers (n = 32) in four correctional centres, two community corrections offices (CCOs) and one parole unit in New South Wales (NSW) in 2019. The authors used thematic analysis to analyse the findings.

Findings

The study identified three main themes relating to barriers and enablers: organisational, social and economic and individual and family and seven sub-themes: planning the transition, communication, assisting prisoners, transition programs, officers’ knowledge and scope of work, social and economic issues and offenders’ conditions

Research limitations/implications

The processes required to ensure effective prison-to-community transition of older prisoners are not well-developed suggesting the need for more systemic and organised mechanisms. Implications of the barriers and enablers for policy, research and practice are discussed.

Originality/value

This study identified a composite of barriers and enablers to health and social services for older prisoners in NSW prisons and CCOs.
Which professional skills value more under digital transformation?
Authors: Paklina Sofia , Shakina Elena
Published: December 2021

Purpose

This study seeks to explore the demand side of the labour market influenced by the digital revolution. It aims at identifying the new composition of skills and their value as implicitly manifested by employers when they look for the new labour force. The authors analyse the returns to computing skills based on text mining techniques applied to the job advertisements.

Design/methodology/approach

The methodology is based on the hedonic pricing model with the Heckman correction to overcome the sample selection bias. The empirical part is based on a large data set that includes more than 9m online vacancies on one of the biggest job boards in Russia from 2006 to 2018.

Findings

Empirical evidence for both negative and positive returns to computing skills and their monetary values is found. Importantly, the authors also have found both complementary and substitutional effects within and between non-domain (basic) and domain (advanced) subgroups of computing skills.

Originality/value

Apart from the empirical evidence on the value of professional computing skills and their interrelations, this study provides the important methodological contribution on applying the hedonic procedure and text mining to the field of human resource management and labour market research.