bluuebunny/crossref_metadata_2025 huggingface dataset:
Psychometric properties of pain measurements for people living with dementia: a COSMIN systematic review
Authors: Smith Toby O. , Harvey Karmen
Published: May 2022

Purpose

Detecting pain in older people with dementia is challenging. Consequentially, pain is often under-reported and under-treated. There remains uncertainty over what measures should be promoted for use to assess pain in this population. The purpose of this paper is to answer this question.

Methods

A search of clinical trials registered on the ClinicalTrial.gov and ISRCTN registries was performed to identify outcome measures used to assess pain in people with dementia. Following this, a systematic review of published and unpublished databases was performed to 01 November 2021 to identify papers assessing the psychometric properties of these identified measures. Each paper and measure was assessed against the COSMIN checklist. A best evidence synthesis analysis was performed to assess the level of evidence for each measure.

Results

From 188 clinical trials, nine outcome measures were identified. These included: Abbey Pain Scale, ALGOPLUS, DOLOPLUS-2, Facial Action Coding System, MOBID-2, self-reported pain through the NRS or VAS/thermometer or Philadelphia Geriatric Pain Intensity Scale, PACSLAC/PACSLAC-2, Pain Assessment in Advanced Dementia (PAINAD), and Checklist for non-verbal pain behavior (CNPI). From these, 51 papers (5924 people with dementia) were identified assessing the psychometric properties of these measures. From these, there was strong- and moderate-level evidence to support the use of the facial action coding system, PACSLAC and PACSLAC-II, CNPI, DOLOPLUS-2, ALGOPLUS, MOBID, and MOBID-2 tools for the assessment of pain with people living with dementia.

Conclusion

Whilst these reflect measurement tools used in research, further consideration on how these reflect clinical practice should be considered.

PROSPERO registration

CRD42021282032
Effects of the Follicular Menstrual Phase on Forearm Vascular Conductance in Abdominal Obese Premenopausal Women During Graded Handgrip Exercise
Authors: Restaino Robert M. , Cradock Kenwyn , Barlow Matthew A.
Published: May 2022

Purpose

Previous studies have reported a sympatholytic action of estrogen on the vasculature in response to increased sympathetic outflow, an effect most notable during exercise, providing for necessary increases in blood flow to working muscle. In contrast, elevated concentrations of progesterone can inhibit this action of estrogen, impairing increases in blood flow. We hypothesize that the peak concentration of estrogen during the proliferative portion of the follicular phase of the menstrual cycle in female humans will increase vascular conductance during exercise when the effects of progesterone are negligible. In addition, we hypothesize that overweight abdominally obese females will have an attenuated conductance response to dynamic exercise during the same menstrual phase.

Methods

Participants engaged in graded forearm exercise using an isotonic handgrip dynometer with sequential increases in resistance at a cadence of 30 contractions/minute until task failure. They performed exercise at time points of the menstrual cycle corresponding to low concentrations of both sex hormones and elevated estrogen, while progesterone remained low. Blood flow and vascular conductance were measured using Doppler ultrasound.

Results

This revealed a trend that abdominal obese women during a phase of low estrogen had a lower overall blood flow and vascular conductance response than healthy controls at matching resistance stages during rest and exercise. This group difference was attenuated during the proliferative phase with elevated circulating estrogen. There is not a statistically significant interaction between Ovarian Phase and Weight group (P = 0.778).

Conclusion

The results indicate that overweight women are at a disadvantage during exercise in increasing blood flow to working muscles, which can be detrimental to overall fitness improvement during the early and potentially late follicular phase of the menstrual cycle.
Everything You Need to Know About OCD
Authors: Drummond Lynne M. , Edwards Laura J.
Published: May 2022

Do you ever find yourself overwhelmed by troublesome and persistent thoughts that make you feel anxious? Do you feel an urge to wash your hands repeatedly, or check appliances over and over, to help ease your anxiety? Do you feel panicked about what might happen if you did not perform these rituals? You may be struggling with Obsessive Compulsive Disorder (OCD). OCD is a common, yet distressing condition, but one that is responsive to modern treatments. Everything You Need to Know About OCD gives you a comprehensive insight in to this condition, how to spot symptoms of it in yourself or a loved one, and outlines the treatment options available. The book features self-help chapters that guide you through Graded Exposure therapy, a highly effective psychological treatment for OCD. These chapters will equip you with strategies to banish unwanted thoughts and help you regain control of your life.
Rare stromatoporoids from the Lower Devonian (Emsian) of Nevada, and their biostratigraphic and paleobiogeographic significance
Authors: Stock Carl W.
Published: May 2022

Two previously known species of stromatoporoids are reported from Nevada:Stromatoporella perannulata, from the Bartine Member of the McColley Canyon Formation (middle Emsian); andStictostroma moosense, from the Oxyoke Canyon Sandstone (uppermost Emsian). A new species,Syringodictyon nevadensen. sp., is described from the Coils Creek Member of the McColley Canyon Formation (upper Emsian).Stromatoporella perannulataalso occurs in Emsian-age strata on Ellesmere Island, arctic Canada, and in strata of Emsian and/or Eifelian age in Ontario, New York, Ohio, and Kentucky. Outside Nevada,Syringodictyonis confined to the Emsian of Ellesmere Island, and Emsian/Eifelian of Ontario and New York.Stictostroma moosenseis known from only the Emsian/Eifelian of Ontario.

It is concluded that the three Nevada specimens are Emsian in age. This implies that in other localities where two of the species,S.perannulataandS.moosense, occur in strata where the placement of the Emsian-Eifelian boundary is in question, it might be higher than previously thought. The presence of the two species, plusSyringodictyon, in both the Old World Realm (Nevada, arctic Canada) and the Eastern Americas Realm (Ontario, New York, Ohio, Kentucky), infers a selective marine connection between the two realms that was not available to other taxa. The breach in the inter-realm barrier most likely occurred as a shallow seaway across the Canadian Shield.

UUID:http://zoobank.org/e73023c6-88ca-4b4d-9b01-f74a75b99c43
A new genus of treeshrew and other micromammals from the middle Miocene hominoid locality of Ramnagar, Udhampur District, Jammu and Kashmir, India
Authors: Sehgal Ramesh Kumar , Singh Abhishek Pratap , Gilbert Christopher C. , Patel Biren A. , Campisano Christopher J. , Selig Keegan R. , Patnaik Rajeev , Singh Ningthoujam Premjit
Published: May 2022

The fossil record of treeshrews, hedgehogs, and other micromammals from the Lower Siwaliks of India is sparse. Here, we report on a new genus and species of fossil treeshrew, specimens of the hedgehogGalerix, and other micromammals from the middle Miocene (Lower Siwalik) deposits surrounding Ramnagar (Udhampur District, Jammu and Kashmir), at a fossil locality known as Dehari. The treeshrew from Dehari (Sivatupaia ramnagarensisn. gen. n. sp.) currently represents the oldest record of fossil tupaiids in the Siwaliks, extending their time range by ca. 2.5–4.0 Myr in the region. Dietary analyses suggest that the new tupaiid was likely adapted for a less mechanically challenging or more frugivorous diet compared to other extant and fossil tupaiids. The occurrence ofGalerixhas only been recently documented from the Indian Siwaliks and the Dehari specimens help establish the likely presence of a relatively large SiwalikGalerixspecies in the Ramnagar region. In addition to the new treeshrew and hedgehogs, new specimens of the rodentsKanisamys indicus,Sayimys sivalensis, and Murinae indet. from Dehari help confirm that age estimates for the Ramnagar region are equivalent to the Chinji Formation in Pakistan, most likely corresponding to the middle to upper part of the Chinji Formation.

UUID:http://zoobank.org/56fb160c-2df8-4cd3-be91-af4dc02d0979
The evolution of unprocessed food inflation in Turkey: an exploratory study on select products
Authors: Demirkılıç Serkan , Özertan Gökhan , Tekgüç Hasan
Published: May 2022

Food price increases stem from economic, agricultural, and political factors. Understanding the dynamics behind the food price formation process and assessing how potential factors contribute to food price changes will significantly affect policies formulated to manage food price increases. High food inflation rates have been a chronic problem in Turkey over the last decade, with unprocessed food prices rising faster than general price levels. In this article, we use exploratory analyses based on economic principles rather than econometric analyses. First, our results indicate that exchange rates are strongly associated with domestic food prices due to dependence on imported inputs. Second, deep-dive analyses on select products show that global price movements and pass-through prices from producer to consumer are not solely responsible for price increases.
A pairwise strategic network formation model with group heterogeneity: With an application to international travel
Authors: Hoshino Tadao
Published: May 2022

This study considers a network formation model in which each dyad of agents strategically determines the link status. Our model allows the agents to have unobserved group heterogeneity in the propensity of link formation. For the model estimation, we propose a three-step maximum likelihood method, in which the latent group structure is estimated using the binary segmentation algorithm in the second step. As an empirical illustration, we focus on the network data of international visa-free travels. The results indicate the presence of significant strategic complementarity and a certain level of degree heterogeneity in the network formation behavior.
When do different systems of government lead to similar power-sharing? The case of government formation
Authors: Silva Thiago N.
Published: May 2022

Recent studies provide evidence that the absence of a no-confidence procedure in presidential systems is crucial for understanding why the allocation of portfolios does not follow the same pattern in both parliamentary and presidential democracies. In this study, I argue that distinctions within presidential systems must be used to explain the substantial variation in the allocation of portfolios to presidential parties. I theorize that when the president is more dependent upon the legislature to make and enact policies, the balance of power in presidential cabinets is more likely to reflect the balance of power in the legislature. In this case, the presidential cabinet can resemble the proportional cabinets usually formed in parliamentary systems. With new data from 20 presidential democracies worldwide spanning more than 70 years, the results support the expectation of a greater formateur's advantage when presidents have greater institutionally-granted powers to influence the policy agenda in the legislature.
KIN CONFLICTS AND STASIS: CIVIL WAR ON PEUCE IN VALERIUS FLACCUS’ARGONAUTICA
Authors: Sanderson Elaine C.
Published: May 2022

While it is no secret that Valerius Flaccus’Argonauticaexplores civil-war themes at great length, the conflicts arising on the island of Peuce between the Colchians and the Argonauts and within the Argonautic party itself in the epic's final book (8.217–467) have been overlooked in critical studies of Valerian civil war. This article argues that Valerius presents the conflicts on Peuce as examples of civil war—emphasizing the bonds of kinship between the conflicting parties and illustrating effects of this discord using imagery of stasis and cosmic dissolution associated with civil war in the wider Latin literary tradition—and thus invites reflection on the development and manifestation of internecine strife within theArgonautica.
Right to Restitution under Illegal Contracts: Seeking Clarity in Ghana
Authors: Faakye Solomon
Published: May 2022

The law on the availability of restitution in the context of illegal contracts is unclear. Several irreconcilable approaches have been proposed at common law in search of a solution to the question of whether or not a party to an illegal contract who has benefitted from the contract has any right to restitution. This article examines the Ghanaian judicial approach and ascertains the extent to which it sheds light on this difficult issue. It does so by examining the evolution of judicial solutions in English common law and, in that context, evaluating the approaches adopted by the Ghanaian courts.
Exploring the role of macrophages in determining the pathogenesis of liver fluke infection
Authors: Quinteros Susel Loli , O'Brien Bronwyn , Donnelly Sheila
Published: May 2022

The food-borne trematodes, Opisthorchis viverrini and Clonorchis sinensis, are classified as group 1 biological carcinogens: definitive causes of cancer. By contrast, infections with Fasciola hepatica, also a food-borne trematode of the phylum Platyhelminthes, are not carcinogenic. This review explores the premise that the differential activation of macrophages during infection with these food-borne trematodes is a major determinant of the pathological outcome of infection. Like most helminths, the latter stages of infection with all 3 flukes induce M2 macrophages, a phenotype that mediates the functional repair of tissue damaged by the feeding and migratory activities of the parasites. However, there is a critical difference in how the development of pro-inflammatory M1 macrophages is regulated during infection with these parasites. While the activation of the M1 macrophage phenotype is largely suppressed during the early stages of infection with F. hepatica, M1 macrophages predominate in the bile ducts following infection with O. viverrini and C. sinensis. The anti-microbial factors released by M1 macrophages create an environment conducive to mutagenesis, and hence the initiation of tumour formation. Subsequently, the tissue remodelling processes induced by the M2 macrophages promote the proliferation of mutated cells, and the expansion of cancerous tissue. This review will also explore the interactions between macrophages and parasite-derived signals, and their contributions to the stark differences in the innate immune responses to infection with these parasites.
Does the impact of bereavement vary between same and different gender partnerships? A representative national, cross-sectional study
Authors: Timmins Liadh , Pitman Alexandra , King Michael , Gao Wei , Johnson Katherine , Yu Peihan , Braybrook Debbie , Roach Anna , Marshall Steve , Day Elizabeth , Rose Ruth , Clift Paul , Almack Kathryn , Yi Deok Hee , Bristowe Katherine , Harding Richard
Published: May 2022

Background

Data suggest poorer bereavement outcomes for lesbian, gay and bisexual people, but this has not been estimated in population-based research. This study compared bereavement outcomes for partners of same-gender and different-gender decedents.

Methods

In this population-based, cross-sectional survey of people bereaved of a civil partner or spouse 6–10 months previously, we used adjusted logistic and linear regression to investigate outcomes of interest: (1) positive screen on Inventory of Complicated Grief (ICG), (2) positive screen on General Health Questionnaire (GHQ), (3) grief intensity (ICG) and (4) psychiatric symptoms (GHQ-12).

Results

Among 233 same-gender partners and 329 of different-gender partners, 66.1% [95% confidence interval (CI) 60.0–72.2] and 59.2% [95% CI (53.9–64.6)] respectively screened positive for complicated grief on the ICG, whilst 76.0% [95% CI (70.5–81.5)] and 69.3% [95% CI (64.3–74.3)] respectively screened positive on the GHQ-12. Same-gender bereaved partners were not significantly more likely to screen positive for complicated grief than different-gender partners [adjusted odds ratio (aOR) 1.56, 95% CI (0.98–2.47)], p = 0.059, but same-gender bereaved partners were significantly more likely to screen for psychiatric caseness [aOR 1.67 (1.02, 2.71) p = 0.043]. We similarly found no significant association of partner gender with grief intensity [B = 1.86, 95% CI (−0.91to 4.63), p = 0.188], but significantly greater psychological distress for same-gender partners [B = 1.54, 95% CI (−0.69–2.40), p < 0.001].

Conclusions

Same-gender bereaved partners report significantly more psychological distress. In view of their poorer sub-clinical mental health, clinical and bereavement services should refine screening processes to identify those at risk of poor mental health outcomes.
RETHINKING THE RURAL IN ANCIENT MAYA STUDIES
Authors: Lamb Céline
Published: May 2022

This Special Section provides a glimpse into the vitality of rural investigations in the Maya area by presenting recent archaeological research and interpretive perspectives on the ancient rural Maya. This introduction serves to contextualize the articles of this Special Section within and outside of academic discourse and practice. I start by reviewing the common ways in which rural people and places are essentialized, to underscore that these now unpopular ideas continue to implicitly pervade research priorities, definitions, and interpretations. I then provide a brief historical summary of rural research in the Maya area and some of its significant contributions to our current understandings of ancient rural Maya peoples. Finally, drawing from rural studies, I argue for greater theorization of rurality—including how it was constituted, experienced, perhaps even perceived in the past, and its relationship to periurban, conurban, and urban life, and the continued existence and transformation of rural spaces and lifeways within increasingly urbanized societies. This introduction aims to invigorate further theoretical elaboration with regard to ancient Maya rurality and elicit archaeologists to place themselves and their work within the broader historical and cultural trends of how the rural is perceived and addressed.
‘Self-Coordination’ and Its Origins: Civil Servants and Regime Change in 1933 and 1918/19
Authors: O'Byrne Darren M.
Published: May 2022

This article situates civil servants’ responses to regime change in 1933 in their longer-term context. Focusing particularly on the process of ‘self-coordination’ – a term used by historians to describe and explain ministerial bureaucrats’ voluntary adaptation to changed political circumstances by implementing the Third Reich's policy agenda – it argues that this process was far from unique, being in fact the typical response to regime change throughout the twentieth century. By examining how civil servants facilitated regime change in 1918/19 and 1933 specifically, it also argues that the central pillar of the ‘self-coordination’ thesis – that it was informed by civil servants’ political or ideological beliefs – needs to be revisited. Indeed, the fact that many began their careers in Imperial Germany and served under both the Weimar Republic and National Socialism suggests that it was not only ideology that informed their actions. So, in conclusion, the essay looks at how bureaucratic organisations like government ministries function and, more importantly, how individuals function within them, presenting a different angle, based on organisational theory, from which to assess civil servants’ propensity to ‘self-coordinate’.
Assessing Hygienic Status, Sanitation Issues, and Associated Problems in Dambi Dollo Town, Oromia Regional State, Ethiopia
Authors: Eticha Tolera Kuma , Adisu Melkamu Tamiru
Published: May 2022

The pollutants discharged untreated into water bodies become a challenge in Ethiopia. This study aims to assess sanitation and hygiene status and the associated problems. A total of 500 households were selected using a systematic random sampling technique. Questionnaires, interviews, and site observation were employed. The absence of public and communal latrines had been seen as the constraint. The present study confirmed that waste disposal management has serious problems. In conclusion, these findings revealed that part of the households are living in communities with the town-owned poor sanitary facilities and that further studies are encouraged on waste disposal management.
Peri-conceptional diet patterns and the risk of gestational diabetes mellitus in South Indian women
Authors: Mahendra Anvesha , Kehoe Sarah H , Crozier Sarah R , Kumaran Kalyanaraman , Krishnaveni GV , Arun Nalini , Padmaja  , Kini Prakash , Taskeen Unaiza , Kombanda Krupa T , Johnson Matthew , Osmond Clive , Fall Caroline HD
Published: May 2022

Objective:

To identify peri-conceptional diet patterns among women in Bangalore and examine their associations with risk of gestational diabetes mellitus (GDM).

Design:

BAngalore Nutrition Gestational diabetes LifEstyle Study, started in June 2016, was a prospective observational study, in which women were recruited at 5–16 weeks’ gestation. Peri-conceptional diet was recalled at recruitment, using a validated 224-item FFQ. GDM was assessed by a 75-g oral glucose tolerance test at 24–28 weeks’ gestation, applying WHO 2013 criteria. Diet patterns were identified using principal component analysis, and diet pattern–GDM associations were examined using multivariate logistic regression, adjusting for ‘a priori’ confounders.

Setting:

Antenatal clinics of two hospitals, Bangalore, South India.

Participants:

Seven hundred and eighty-five pregnant women of varied socio-economic status.

Results:

GDM prevalence was 22 %. Three diet patterns were identified: (a) high-diversity, urban (HDU) characterised by diverse, home-cooked and processed foods was associated with older, more affluent, better-educated and urban women; (b) rice-fried snacks-chicken-sweets (RFCS), characterised by low diet diversity, was associated with younger, less-educated, and lower-income, rural and joint families; and (c) healthy, traditional vegetarian (HTV), characterised by home-cooked vegetarian and non-processed foods, was associated with less-educated, more affluent, and rural and joint families. The HDU pattern was associated with a lower GDM risk (adjusted odds ratio (aOR): 0·80/sd, 95 % CI (0·64, 0·99), P = 0·04) after adjusting for confounders. BMI was strongly related to GDM risk and possibly mediated diet–GDM associations.

Conclusions:

The findings support global recommendations to encourage women to attain a healthy pre-pregnancy BMI and increase diet diversity. Both healthy and unhealthy foods in the patterns indicate low awareness about healthy foods and a need for public education.
Pre-pregnancy exposure to arsenic in diet and non-cardiac birth defects
Authors: Suhl Jonathan , Conway Kristin M , Rhoads Anthony , Langlois Peter H , Feldkamp Marcia L , Michalski Adrian M , Oleson Jacob J , Sidhu Alpa , Kancherla Vijaya , Obrycki John , Mazumdar Maitreyi , Romitti Paul A ,   the National Birth Defects Prevention Study
Published: May 2022

Objectives:

To explore associations between maternal pre-pregnancy exposure to arsenic in diet and non-cardiac birth defects.

Design:

This is a population-based, case–control study using maternal responses to a dietary assessment and published arsenic concentration estimates in food items to calculate average daily total and inorganic arsenic exposure during the year before pregnancy. Assigning tertiles of total and inorganic arsenic exposure, logistic regression analysis was used to estimate OR for middle and high tertiles, compared to the low tertile.

Setting:

US National Birth Defects Prevention Study, 1997–2011.

Participants:

Mothers of 10 446 children without birth defects and 14 408 children diagnosed with a non-cardiac birth defect.

Results:

Maternal exposure to total dietary arsenic in the middle and high tertiles was associated with a threefold increase in cloacal exstrophy, with weak positive associations (1·2–1·5) observed either in both tertiles (intercalary limb deficiency) or the high tertile only (encephalocele, glaucoma/anterior chamber defects and bladder exstrophy). Maternal exposure to inorganic arsenic showed mostly weak, positive associations in both tertiles (colonic atresia/stenosis, oesophageal atresia, bilateral renal agenesis/hypoplasia, hypospadias, cloacal exstrophy and gastroschisis), or the high (glaucoma/anterior chamber defects, choanal atresia and intestinal atresia stenosis) or middle (encephalocele, intercalary limb deficiency and transverse limb deficiency) tertiles only. The remaining associations estimated were near the null or inverse.

Conclusions:

This exploration of arsenic in diet and non-cardiac birth defects produced several positive, but mostly weak associations. Limitations in exposure assessment may have resulted in exposure misclassification. Continued research with improved exposure assessment is recommended to identify if these associations are true signals or chance findings.
Field and Synthetic Waveform Tests on Using Large‐Offset Seismic Streamer Data to Derive Shallow Seabed Shear‐Wave Velocity and Geotechnical Properties
Authors: Wege Sebastian , Legendre Cédric P. , Chi Wu‐Cheng , Wang Tan Kin , Kunath Pascal , Liu Char‐Shine
Published: May 2022

Characterizing properties of marine subsurface sediment helps with siting for offshore infrastructure. Shear‐wave velocity (Vs) provides information on the geotechnical properties of the seabed. We present our initial efforts to obtain a detailed two‐dimensional model of Vs for a large‐offset multi‐channel seismic (MCS) transect collected in shallow waters across the Taiwan Strait using surface waves excited by a large volume airgun. We derived the dispersion curves of the Scholte waves along the 37.5‐km‐long transect using the phase‐shift method and then conducted multimodal inversion to obtain a Vs model down to a depth of 150 m. To estimate the dynamic Poisson's ratio across the transect, we combined the Vs model with a compressional wave velocity model derived from the traditional MCS semblance velocity analysis. Lastly, we approximated the seismic attenuation of the profile. Our results show a large lateral variation in shear‐wave velocity. In the north, a low‐velocity zone with shear‐wave velocities of about 150 m/s was identified, while in the south, the shear‐wave velocity was found to be 300 m/s. With synthetic data, several sensitivity tests were performed to derive optimal parameters for offshore large‐offset streamer data. We particularly focused on the depth of the streamer and source and the water depth in combination with different seabed properties. Our results show that we can robustly derive the shear‐wave velocity, along with the Poisson's ratio, using large‐offset streamer data elsewhere based on the criteria we have tested using field and synthetic data sets.
Deposit‐Derived Block‐and‐Ash Flows: The Hazard Posed by Perched Temporary Tephra Accumulations on Volcanoes; 2018 Fuego Disaster, Guatemala
Authors: Risica Gilda , Rosi Mauro , Pistolesi Marco , Speranza Fabio , Branney Michael J.
Published: May 2022

The impact of hazardous pyroclastic density currents (PDCs) increases with runout distance, which is strongly influenced by the mass flux. This article shows that the mass flux of a PDC may derive not only from vent discharge during the eruption, but also from partly hot, temporary stores (accumulations) of aerated pyroclastic material perched high on the volcano. The unforeseen PDC at Fuego volcano (Guatemala) on 3 June 2018 happened c.1.5 hr after the eruption climax. It overran the village of San Miguel Los Lotes causing an estimated 400+ fatalities. Analysis of the facies architecture of the deposit combined with video footage shows that a pulsatory block‐and‐ash flow flowed down the Las Lajas valley and rapidly waxed, the runout briefly increasing to 12.2 km as it filled and then spilled out of river channels, entered a second valley where it devastated the village and became increasingly erosive, prior to waning. Paleomagnetic analysis shows that the PDC contained only 6% very hot (>590°C) clasts, 39% moderately hot (∼200°C–500°C) clasts, and 51% cool (<200°C) clasts. This reveals that the block‐and‐ash flow mostly derived from collapse of loose and partly hot pyroclastic deposits, stored high on the volcano, gradually accumulated during the last 2–3 years. Progressive collapse of unstable deposits supplied the block‐and‐ash flow, causing a bulk‐up process, waxing flow, channel overspill and unexpected runout. The study demonstrates that deposit‐derived pyroclastic currents from perched temporary tephra stores pose a particular hazard that is easy to overlook and requires a new, different approach to hazard assessment and monitoring.
Impacts of Assimilating GOES‐16 ABI Channels 9 and 10 Clear Air and Cloudy Radiance Observations With Additive Inflation and Adaptive Observation Error in GSI‐EnKF for a Case of Rapidly Evolving Severe Supercells
Authors: Johnson Aaron , Wang Xuguang , Jones Thomas
Published: May 2022

The unprecedentedly high space and time resolution of infrared radiance observations from GOES‐16 Advanced Baseline Imager (ABI) present an opportunity to improve analyses and short‐term forecasts of rapidly evolving convective‐scale processes such as the initiation and organization of severe supercell thunderstorms. Such a case is used for experiments aimed at better understanding the assimilation of ABI all‐sky radiance observations in GSI‐EnKF. Experiments assimilating ABI channel 10 are used to demonstrate and understand the impacts of implementing additive inflation and adaptive observation error for ABI radiance assimilation in GSI‐EnKF. The experiments using channel 10 are then compared to experiments using ABI channel 9 and both channels together. The impact of additive inflation is to increase lead time of one of the two supercells by about 20 min, and to enable improved prediction of the second supercell. The improvement occurs because the development of deepening cumulus is accelerated where ABI observes clouds to appear that are not present in the ensemble background forecast. The impact of the adaptive observation error is to increase the strength and persistence of the developing supercells in forecasts initialized from ensemble mean analyses. Compared to the ABI channel 10 radiance, ABI channel 9 provides 10 min of additional lead time for the second supercell, likely because it better constrains an upper‐level shortwave in clear air.
Pathways to Better Prediction of the MJO: 2. Impacts of Atmosphere‐Ocean Coupling on the Upper Ocean and MJO Propagation
Authors: Savarin Ajda , Chen Shuyi S.
Published: May 2022

This study investigates effects of atmosphere‐ocean coupling on MJO precipitation and eastward propagation, and upper ocean conditions during and after MJO passage. To explore pathways for improving MJO prediction, three model experiments are conducted using the Unified Wave Interface‐Coupled Model at convection‐permitting (4 km) resolution: (a) uncoupled atmosphere‐only, (b) coupled atmosphere‐ocean, and (c) coupled atmosphere‐ocean with improved air‐sea flux algorithm simulations. The model simulations are compared with observations from the DYNAMO field campaign in 2011. Both coupled atmosphere‐ocean simulations produced eastward propagation of the MJO where the uncoupled, atmosphere‐only simulation did not. The uncoupled model overestimates both precipitation and surface winds associated with the MJO, while coupled model simulations substantially reduce model bias. Improved air‐sea fluxes lead to systematic improvements in precipitation, winds, sea surface temperature, and the ocean mixed layer when compared to the original coupled simulation. This leads to further improvement of the MJO's eastward propagation speed compared with observations. Despite these improvements, the regional coupled simulations still have difficulty representing the extent of convectively suppressed conditions in the Indian Ocean after MJO passage, which indicates the importance of the large‐scale environment from lateral boundary conditions. Coupled model simulations also reveal some issues in the representation of upper ocean stratification in the ocean model, especially errors in salinity, which result in overestimation of the mixed layer depth after MJO passage.
Coral‐Based Sea Surface Salinity Reconstructions and the Role of Observational Uncertainties in Inferred Variability and Trends
Authors: Reed Emma V. , Thompson Diane M. , Anchukaitis Kevin J.
Published: May 2022

Climate observations in much of the tropical oceans are scarce during most of the 20th century, so paleoclimate proxies are needed to understand the full range of natural climate variability. Past proxy studies have focused primarily on sea surface temperatures, but there are comparatively few salinity reconstructions. Such reconstructions can extend our understanding of hydroclimate across the tropical oceans, including variability in precipitation, evaporation, and ocean circulation. Here we compile a network of salinity‐sensitive coral δ18O records, then apply a reduced‐space method based on empirical orthogonal function analysis to reconstruct annual tropical salinity anomalies over the 20th century. A comparison of surface salinity data sets, including reanalyzes (SODA2/3, Ocean ReAnalysis System 5 (ORAS5), Global Ocean Data Assimilation System) and objective analyses (Institute of Atmospheric Physics (IAP), EN4, Delcroix), show large discrepancies in the spatial structure, temporal evolution, and importance of the leading modes of variability. Two salinity data sets, IAP and ORAS5, are retained for climate reconstruction. Our coral‐based salinity reconstructions reveal significant long‐term trends over the 20th century, which are likely associated with hydrological cycle intensification and possibly a weakening of the Walker Circulation. These reconstructions also capture the spatial and temporal patterns of salinity anomalies associated with the El Niño‐Southern Oscillation, Interdecadal Pacific Oscillation, and Atlantic Multidecadal Oscillation. Ultimately, this approach can enhance our understanding of tropical hydroclimate prior to the observational era.
Early‐to‐Late Winter 20th Century North Atlantic Multidecadal Atmospheric Variability in Observations, CMIP5 and CMIP6
Authors: Bracegirdle Thomas J.
Published: May 2022

The strong multidecadal variability in North Atlantic (NA) winter atmospheric circulation is poorly understood and appears too weak in climate models. Recent research has shown peak atmospheric multidecadal variability over the NA in late winter, particularly March, linked to Atlantic multidecadal variability (AMV) of the ocean. Here a range of NA atmospheric circulation indices are assessed to provide a comprehensive picture of early‐to‐late winter low‐frequency variability and its representation in the latest generation of climate models (Coupled Model Intercomparison Project Phase 6 [CMIP6]). As found for CMIP5, CMIP6 models exhibit too‐weak multidecadal NA atmospheric variability compared to reanalysis data over the period 1862–2005. Consistent with previous research, the eastern part of the NA westerly jet (U700NA) exhibits peak low‐frequency variability in March. However, for NA‐wide jet speed and the NAO, low‐frequency variability and model‐reanalysis discrepancies are strongest in January and February, associated with too‐weak NA ocean‐atmosphere linkages.
Present‐Day Strike‐Slip Faulting and Thrusting of the Kepingtage Fold‐and‐Thrust Belt in Southern Tianshan: Constraints From GPS Observations
Authors: Li Jie , Yao Yuan , Li Rui , Yusan Sulitan , Li Guirong , Freymueller Jeffrey T. , Wang Qi
Published: May 2022

Across inherited complex fold‐and‐thrust belts (FTBs), shortening may be accommodated at different rates depending on structural style variations; such cases have rarely been documented We present the example of the Kepingtage FTB in southern Tianshan, which is bisected by the NNW‐trending left‐lateral strike‐slip Piqiang Fault (PQF) into eastern and western segments. The 1.45 ± 0.31–2.10 ± 0.42 mm/a shortening rate of the eastern segment is accommodated in a diffuse‐deformation pattern within the five‐row thrust‐anticlinal zone and the 2.36 ± 0.23–3.70 ± 0.59 mm/a shortening rate of the western segment is accommodated within the two‐row thrust‐anticlinal zone at the FTB front. To accommodate the latitudinal variability, the PQF exhibits a 2.30 ± 0.20–4.10 ± 0.40 mm/a segmentation strike‐slip rate. The 2.35 ± 0.33–4.20 ± 0.45 mm/a shortening rate of the Kepingtage FTB and southern Tianshan Fault is one‐third of the total convergence rate between the Tarim Basin and Kazakh Platform at 77°–79°E; hence, the complex Tianshan deformation occurred mainly at the FTB.
Elucidating the importance and regulation of key enhancers for human MEIS1 expression
Authors: Xiang Ping , Yang Xining , Escano Leo , Dhillon Ishpreet , Schneider Edith , Clemans-Gibbon Jack , Wei Wei , Wong Jasper , Wang Simon Xufeng , Tam Derek , Deng Yu , Yung Eric , Morin Gregg B. , Hoodless Pamela A. , Hirst Martin , Karsan Aly , Kuchenbauer Florian , Humphries R. Keith , Rouhi Arefeh
Published: May 2022

Myeloid ecotropic virus insertion site 1 (MEIS1) is essential for normal hematopoiesis and is a critical factor in the pathogenesis of a large subset of acute myeloid leukemia (AML). Despite the clinical relevance of MEIS1, its regulation is largely unknown. To understand the transcriptional regulatory mechanisms contributing to human MEIS1 expression, we created a knock-in green florescent protein (GFP) reporter system at the endogenous MEIS1 locus in a human AML cell line. Using this model, we have delineated and dissected a critical enhancer region of the MEIS1 locus for transcription factor (TF) binding through in silico prediction in combination with oligo pull-down, mass-spectrometry and knockout analysis leading to the identification of FLI1, an E-twenty-six (ETS) transcription factor, as an important regulator of MEIS1 transcription. We further show direct binding of FLI1 to the MEIS1 locus in human AML cell lines as well as enrichment of histone acetylation in MEIS1-high healthy and leukemic cells. We also observe a positive correlation between high FLI1 transcript levels and worse overall survival in AML patients. Our study expands the role of ETS factors in AML and our model constitutes a feasible tool for a more detailed understanding of transcriptional regulatory elements and their interactome.
Regulation of proton partitioning in kinase-activating acute myeloid leukemia and its therapeutic implication
Authors: Man Cheuk-Him , Zeng Xiaoyuan , Lam Wing , Ng Timothy C. C. , Kwok Tsz-Ho , Dang Kenny C. C. , Leung Thomas W. Y. , Ng Nelson K. L. , Lam Stephen S. Y. , Cher Chae-Yin , Leung Anskar Y. H.
Published: May 2022

Gain-of-function kinase mutations are common in AML and usually portend an inferior prognosis. We reported a novel mechanism whereby kinase mutants induced intracellular alkalization characteristic in oncogenesis. Thirteen kinases were found to activate sodium/hydrogen exchanger (NHE1) in normal hematopoietic progenitors, of which FLT3-ITD, KRASG12D, and BTK phosphorylated NHE1 maintained alkaline intracellular pH (pHi) and supported survival of AML cells. Primary AML samples with kinase mutations also showed increased NHE1 phosphorylation and evidence of NHE1 addiction. Amiloride enhanced anti-leukemic effects and intracellular distribution of kinase inhibitors and chemotherapy. Co-inhibition of NHE1 and kinase synergistically acidified pHi in leukemia and inhibited its growth in vivo. Plasma from patients taking amiloride for diuresis reduced pHi of leukemia and enhanced cytotoxic effects of kinase inhibitors and chemotherapy in vitro. NHE1-mediated intracellular alkalization played a key pathogenetic role in transmitting the proliferative signal from mutated-kinase and could be exploited for therapeutic intervention in AML.
FANCD2 maintains replication fork stability during misincorporation of the DNA demethylation products 5-hydroxymethyl-2’-deoxycytidine and 5-hydroxymethyl-2’-deoxyuridine
Authors: Peña-Gómez María José , Moreno-Gordillo Paula , Narmontė Milda , García-Calderón Clara B. , Rukšėnaitė Audronė , Klimašauskas Saulius , Rosado Iván V.
Published: May 2022

Fanconi anemia (FA) is a rare hereditary disorder caused by mutations in any one of the FANC genes. FA cells are mainly characterized by extreme hypersensitivity to interstrand crosslink (ICL) agents. Additionally, the FA proteins play a crucial role in concert with homologous recombination (HR) factors to protect stalled replication forks. Here, we report that the 5-methyl-2’-deoxycytidine (5mdC) demethylation (pathway) intermediate 5-hydroxymethyl-2’-deoxycytidine (5hmdC) and its deamination product 5-hydroxymethyl-2’-deoxyuridine (5hmdU) elicit a DNA damage response, chromosome aberrations, replication fork impairment and cell viability loss in the absence of FANCD2. Interestingly, replication fork instability by 5hmdC or 5hmdU was associated to the presence of Poly(ADP-ribose) polymerase 1 (PARP1) on chromatin, being both phenotypes exacerbated by olaparib treatment. Remarkably, Parp1−/− cells did not show any replication fork defects or sensitivity to 5hmdC or 5hmdU, suggesting that retained PARP1 at base excision repair (BER) intermediates accounts for the observed replication fork defects upon 5hmdC or 5hmdU incorporation in the absence of FANCD2. We therefore conclude that 5hmdC is deaminated in vivo to 5hmdU, whose fixation by PARP1 during BER, hinders replication fork progression and contributes to genomic instability in FA cells.
Rewritable two-dimensional DNA-based data storage with machine learning reconstruction
Authors: Pan Chao , Tabatabaei S. Kasra , Tabatabaei Yazdi S. M. Hossein , Hernandez Alvaro G. , Schroeder Charles M. , Milenkovic Olgica
Published: May 2022

DNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global error-correction redundancy.
PI(18:1/18:1) is a SCD1-derived lipokine that limits stress signaling
Authors: Thürmer Maria , Gollowitzer André , Pein Helmut , Neukirch Konstantin , Gelmez Elif , Waltl Lorenz , Wielsch Natalie , Winkler René , Löser Konstantin , Grander Julia , Hotze Madlen , Harder Sönke , Döding Annika , Meßner Martina , Troisi Fabiana , Ardelt Maximilian , Schlüter Hartmut , Pachmayr Johanna , Gutiérrez-Gutiérrez Óscar , Rudolph Karl Lenhard , Thedieck Kathrin , Schulze-Späte Ulrike , González-Estévez Cristina , Kosan Christian , Svatoš Aleš , Kwiatkowski Marcel , Koeberle Andreas
Published: May 2022

Cytotoxic stress activates stress-activated kinases, initiates adaptive mechanisms, including the unfolded protein response (UPR) and autophagy, and induces programmed cell death. Fatty acid unsaturation, controlled by stearoyl-CoA desaturase (SCD)1, prevents cytotoxic stress but the mechanisms are diffuse. Here, we show that 1,2-dioleoyl-sn-glycero-3-phospho-(1’-myo-inositol) [PI(18:1/18:1)] is a SCD1-derived signaling lipid, which inhibits p38 mitogen-activated protein kinase activation, counteracts UPR, endoplasmic reticulum-associated protein degradation, and apoptosis, regulates autophagy, and maintains cell morphology and proliferation. SCD1 expression and the cellular PI(18:1/18:1) proportion decrease during the onset of cell death, thereby repressing protein phosphatase 2 A and enhancing stress signaling. This counter-regulation applies to mechanistically diverse death-inducing conditions and is found in multiple human and mouse cell lines and tissues of Scd1-defective mice. PI(18:1/18:1) ratios reflect stress tolerance in tumorigenesis, chemoresistance, infection, high-fat diet, and immune aging. Together, PI(18:1/18:1) is a lipokine that links fatty acid unsaturation with stress responses, and its depletion evokes stress signaling.
Nitrogen represses haustoria formation through abscisic acid in the parasitic plant Phtheirospermum japonicum
Authors: Kokla Anna , Leso Martina , Zhang Xiang , Simura Jan , Serivichyaswat Phanu T. , Cui Songkui , Ljung Karin , Yoshida Satoko , Melnyk Charles W.
Published: May 2022

Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. The external environment including nutrient availability affects the extent of parasitism and to understand this phenomenon, we investigated the role of nutrients and found that nitrogen is sufficient to repress haustoria formation in the root parasite Phtheirospermum japonicum. Nitrogen increases levels of abscisic acid (ABA) in P. japonicum and prevents the activation of hundreds of genes including cell cycle and xylem development genes. Blocking ABA signaling overcomes nitrogen’s inhibitory effects indicating that nitrogen represses haustoria formation by increasing ABA. The effect of nitrogen appears more widespread since nitrogen also inhibits haustoria in the obligate root parasite Striga hermonthica. Together, our data show that nitrogen acts as a haustoria repressing factor and suggests a mechanism whereby parasitic plants use nitrogen availability in the external environment to regulate the extent of parasitism.
SpotClean adjusts for spot swapping in spatial transcriptomics data
Authors: Ni Zijian , Prasad Aman , Chen Shuyang , Halberg Richard B. , Arkin Lisa M. , Drolet Beth A. , Newton Michael A. , Kendziorski Christina
Published: May 2022

Spatial transcriptomics is a powerful and widely used approach for profiling the gene expression landscape across a tissue with emerging applications in molecular medicine and tumor diagnostics. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind RNA. Ideally, unique molecular identifiers (UMIs) at a spot measure spot-specific expression, but this is often not the case in practice due to bleed from nearby spots, an artifact we refer to as spot swapping. To improve the power and precision of downstream analyses in spatial transcriptomics experiments, we propose SpotClean, a probabilistic model that adjusts for spot swapping to provide more accurate estimates of gene-specific UMI counts. SpotClean provides substantial improvements in marker gene analyses and in clustering, especially when tissue regions are not easily separated. As demonstrated in multiple studies of cancer, SpotClean improves tumor versus normal tissue delineation and improves tumor burden estimation thus increasing the potential for clinical and diagnostic applications of spatial transcriptomics technologies.