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1.
Nature ; 617(7961): 629-636, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-37138085

RESUMO

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 µs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 µs, signifying the presence of a reduced intermediate, possibly a bound peroxide.


Assuntos
Oxigênio , Fotossíntese , Complexo de Proteína do Fotossistema II , Oxirredução , Oxigênio/química , Oxigênio/metabolismo , Complexo de Proteína do Fotossistema II/química , Complexo de Proteína do Fotossistema II/metabolismo , Prótons , Água/química , Água/metabolismo , Manganês/química , Manganês/metabolismo , Cálcio/química , Cálcio/metabolismo , Peróxidos/metabolismo
2.
Nature ; 592(7855): 571-576, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33790468

RESUMO

Biological invasions are responsible for substantial biodiversity declines as well as high economic losses to society and monetary expenditures associated with the management of these invasions1,2. The InvaCost database has enabled the generation of a reliable, comprehensive, standardized and easily updatable synthesis of the monetary costs of biological invasions worldwide3. Here we found that the total reported costs of invasions reached a minimum of US$1.288 trillion (2017 US dollars) over the past few decades (1970-2017), with an annual mean cost of US$26.8 billion. Moreover, we estimate that the annual mean cost could reach US$162.7 billion in 2017. These costs remain strongly underestimated and do not show any sign of slowing down, exhibiting a consistent threefold increase per decade. We show that the documented costs are widely distributed and have strong gaps at regional and taxonomic scales, with damage costs being an order of magnitude higher than management expenditures. Research approaches that document the costs of biological invasions need to be further improved. Nonetheless, our findings call for the implementation of consistent management actions and international policy agreements that aim to reduce the burden of invasive alien species.


Assuntos
Biodiversidade , Ecologia/economia , Ciência Ambiental/economia , Internacionalidade , Espécies Introduzidas/economia , Espécies Introduzidas/tendências , Animais , Mapeamento Geográfico , Invertebrados , Modelos Lineares , Plantas , Vertebrados
3.
Proc Natl Acad Sci U S A ; 121(21): e2318293121, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38753504

RESUMO

The antiquity of human dispersal into Mediterranean islands and ensuing coastal adaptation have remained largely unexplored due to the prevailing assumption that the sea was a barrier to movement and that islands were hostile environments to early hunter-gatherers [J. F. Cherry, T. P. Leppard, J. Isl. Coast. Archaeol. 13, 191-205 (2018), 10.1080/15564894.2016.1276489]. Using the latest archaeological data, hindcasted climate projections, and age-structured demographic models, we demonstrate evidence for early arrival (14,257 to 13,182 calendar years ago) to Cyprus and predicted that large groups of people (~1,000 to 1,375) arrived in 2 to 3 main events occurring within <100 y to ensure low extinction risk. These results indicate that the postglacial settlement of Cyprus involved only a few large-scale, organized events requiring advanced watercraft technology. Our spatially debiased and Signor-Lipps-corrected estimates indicate rapid settlement of the island within <200 y, and expansion to a median of 4,000 to 5,000 people (0.36 to 0.46 km-2) in <11 human generations (<300 y). Our results do not support the hypothesis of inaccessible and inhospitable islands in the Mediterranean for pre-agropastoralists, agreeing with analogous conclusions for other parts of the world [M. I. Bird et al., Sci. Rep. 9, 8220 (2019), 10.1038/s41598-019-42946-9]. Our results also highlight the need to revisit these questions in the Mediterranean and test their validity with new technologies, field methods, and data. By applying stochastic models to the Mediterranean region, we can place Cyprus and large islands in general as attractive and favorable destinations for paleolithic peoples.


Assuntos
Arqueologia , Humanos , Chipre , Arqueologia/métodos , História Antiga , Migração Humana/história , Demografia/métodos
4.
Proc Natl Acad Sci U S A ; 121(1): e2311280120, 2024 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-38147645

RESUMO

The dominant paradigm is that large tracts of Southeast Asia's lowland rainforests were replaced with a "savanna corridor" during the cooler, more seasonal climates of the Last Glacial Maximum (LGM) (23,000 to 19,000 y ago). This interpretation has implications for understanding the resilience of Asia's tropical forests to projected climate change, implying a vulnerability to "savannization". A savanna corridor is also an important foundation for archaeological interpretations of how humans moved through and settled insular Southeast Asia and Australia. Yet an up-to-date, multiproxy, and empirical examination of the palaeoecological evidence for this corridor is lacking. We conducted qualitative and statistical analyses of 59 palaeoecological records across Southeast Asia to test the evidence for LGM savannization and clarify the relationships between methods, biogeography, and ecological change in the region from the start of Late Glacial Period (119,000 y ago) to the present. The pollen records typically show montane forest persistence during the LGM, while δ13C biomarker proxies indicate the expansion of C4-rich grasslands. We reconcile this discrepancy by hypothesizing the expansion of montane forest in the uplands and replacement of rainforest with seasonally dry tropical forest in the lowlands. We also find that smooth forest transitions between 34,000 and 2,000 y ago point to the capacity of Southeast Asia's ecosystems both to resist and recover from climate stressors, suggesting resilience to savannization. Finally, the timing of ecological change observed in our combined datasets indicates an 'early' onset of the LGM in Southeast Asia from ~30,000 y ago.


Assuntos
Ecossistema , Florestas , Humanos , Floresta Úmida , Mudança Climática , Sudeste Asiático
5.
PLoS Genet ; 19(1): e1010045, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36706133

RESUMO

The Arp2/3 complex is an actin nucleator with well-characterized activities in cell morphogenesis and movement, but its roles in nuclear processes are relatively understudied. We investigated how the Arp2/3 complex affects genomic integrity and cell cycle progression using mouse fibroblasts containing an inducible knockout (iKO) of the ArpC2 subunit. We show that permanent Arp2/3 complex ablation results in DNA damage, the formation of cytosolic micronuclei, and cellular senescence. Micronuclei arise in ArpC2 iKO cells due to chromatin segregation defects during mitosis and premature mitotic exits. Such phenotypes are explained by the presence of damaged DNA fragments that fail to attach to the mitotic spindle, abnormalities in actin assembly during metaphase, and asymmetric microtubule architecture during anaphase. In the nuclei of Arp2/3-depleted cells, the tumor suppressor p53 is activated and the cell cycle inhibitor Cdkn1a/p21 mediates a G1 arrest. In the cytosol, micronuclei are recognized by the DNA sensor cGAS, which is important for stimulating a STING- and IRF3-associated interferon response. These studies establish functional requirements for the mammalian Arp2/3 complex in mitotic spindle organization and genome stability. They also expand our understanding of the mechanisms leading to senescence and suggest that cytoskeletal dysfunction is an underlying factor in biological aging.


Assuntos
Complexo 2-3 de Proteínas Relacionadas à Actina , Actinas , Animais , Camundongos , Complexo 2-3 de Proteínas Relacionadas à Actina/genética , Complexo 2-3 de Proteínas Relacionadas à Actina/metabolismo , Actinas/metabolismo , Senescência Celular/genética , DNA/metabolismo , Instabilidade Genômica/genética , Mitose/genética
6.
Mol Psychiatry ; 29(5): 1228-1240, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38317012

RESUMO

Transcranial magnetic stimulation (TMS) is increasingly used as a noninvasive technique for neuromodulation in research and clinical applications, yet its mechanisms are not well understood. Here, we present the neurophysiological effects of TMS using intracranial electrocorticography (iEEG) in neurosurgical patients. We first evaluated safety in a gel-based phantom. We then performed TMS-iEEG in 22 neurosurgical participants with no adverse events. We next evaluated intracranial responses to single pulses of TMS to the dorsolateral prefrontal cortex (dlPFC) (N = 10, 1414 electrodes). We demonstrate that TMS is capable of inducing evoked potentials both locally within the dlPFC and in downstream regions functionally connected to the dlPFC, including the anterior cingulate and insular cortex. These downstream effects were not observed when stimulating other distant brain regions. Intracranial dlPFC electrical stimulation had similar timing and downstream effects as TMS. These findings support the safety and promise of TMS-iEEG in humans to examine local and network-level effects of TMS with higher spatiotemporal resolution than currently available methods.


Assuntos
Eletrocorticografia , Estimulação Magnética Transcraniana , Humanos , Estimulação Magnética Transcraniana/métodos , Eletrocorticografia/métodos , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Encéfalo/fisiologia , Encéfalo/fisiopatologia , Córtex Pré-Frontal Dorsolateral/fisiologia , Mapeamento Encefálico/métodos , Potenciais Evocados/fisiologia , Adulto Jovem , Estimulação Elétrica/métodos
8.
Cereb Cortex ; 34(4)2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38596882

RESUMO

We currently lack a reliable method to probe cortical excitability noninvasively from the human dorsolateral prefrontal cortex (dlPFC). We recently found that the strength of early and local dlPFC transcranial magnetic stimulation (TMS)-evoked potentials (EL-TEPs) varied widely across dlPFC subregions. Despite these differences in response amplitude, reliability at each target is unknown. Here we quantified within-session reliability of dlPFC EL-TEPs after TMS to six left dlPFC subregions in 15 healthy subjects. We evaluated reliability (concordance correlation coefficient [CCC]) across targets, time windows, quantification methods, regions of interest, sensor- vs. source-space, and number of trials. On average, the medial target was most reliable (CCC = 0.78) and the most anterior target was least reliable (CCC = 0.24). However, all targets except the most anterior were reliable (CCC > 0.7) using at least one combination of the analytical parameters tested. Longer (20 to 60 ms) and later (30 to 60 ms) windows increased reliability compared to earlier and shorter windows. Reliable EL-TEPs (CCC up to 0.86) were observed using only 25 TMS trials at a medial dlPFC target. Overall, medial dlPFC targeting, wider windows, and peak-to-peak quantification improved reliability. With careful selection of target and analytic parameters, highly reliable EL-TEPs can be extracted from the dlPFC after only a small number of trials.


Assuntos
Eletroencefalografia , Estimulação Magnética Transcraniana , Humanos , Estimulação Magnética Transcraniana/métodos , Eletroencefalografia/métodos , Córtex Pré-Frontal Dorsolateral , Reprodutibilidade dos Testes , Córtex Pré-Frontal/fisiologia , Potenciais Evocados/fisiologia
9.
Cancer ; 130(11): 2031-2041, 2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38294959

RESUMO

INTRODUCTION: It was hypothesized that use of proton beam therapy (PBT) in patients with locally advanced non-small cell lung cancer treated with concurrent chemoradiation and consolidative immune checkpoint inhibition is associated with fewer unplanned hospitalizations compared with intensity-modulated radiotherapy (IMRT). METHODS: Patients with locally advanced non-small cell lung cancer treated between October 2017 and December 2021 with concurrent chemoradiation with either IMRT or PBT ± consolidative immune checkpoint inhibition were retrospectively identified. Logistic regression was used to assess the association of radiation therapy technique with 90-day hospitalization and grade 3 (G3+) lymphopenia. Competing risk regression was used to compare G3+ pneumonitis, G3+ esophagitis, and G3+ cardiac events. Kaplan-Meier method was used for progression-free survival and overall survival. Inverse probability treatment weighting was applied to adjust for differences in PBT and IMRT groups. RESULTS: Of 316 patients, 117 (37%) received PBT and 199 (63%) received IMRT. The PBT group was older (p < .001) and had higher Charlson Comorbidity Index scores (p = .02). The PBT group received a lower mean heart dose (p < .0001), left anterior descending artery V15 Gy (p = .001), mean lung dose (p = .008), and effective dose to immune circulating cells (p < .001). On inverse probability treatment weighting analysis, PBT was associated with fewer unplanned hospitalizations (adjusted odds ratio, 0.55; 95% CI, 0.38-0.81; p = .002) and less G3+ lymphopenia (adjusted odds ratio, 0.55; 95% CI, 0.37-0.81; p = .003). There was no difference in other G3+ toxicities, progression-free survival, or overall survival. CONCLUSIONS: PBT is associated with fewer unplanned hospitalizations, lower effective dose to immune circulating cells and less G3+ lymphopenia compared with IMRT. Minimizing dose to lymphocytes may be warranted, but prospective data are needed.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Quimiorradioterapia , Hospitalização , Neoplasias Pulmonares , Terapia com Prótons , Radioterapia de Intensidade Modulada , Humanos , Carcinoma Pulmonar de Células não Pequenas/radioterapia , Carcinoma Pulmonar de Células não Pequenas/terapia , Carcinoma Pulmonar de Células não Pequenas/patologia , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Radioterapia de Intensidade Modulada/métodos , Radioterapia de Intensidade Modulada/efeitos adversos , Feminino , Masculino , Neoplasias Pulmonares/patologia , Neoplasias Pulmonares/terapia , Neoplasias Pulmonares/radioterapia , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/mortalidade , Idoso , Pessoa de Meia-Idade , Hospitalização/estatística & dados numéricos , Terapia com Prótons/métodos , Terapia com Prótons/efeitos adversos , Quimiorradioterapia/métodos , Quimiorradioterapia/efeitos adversos , Estudos Retrospectivos , Inibidores de Checkpoint Imunológico/uso terapêutico , Inibidores de Checkpoint Imunológico/efeitos adversos , Linfopenia/etiologia , Anticorpos Monoclonais
10.
Am J Gastroenterol ; 2024 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-38752626

RESUMO

INTRODUCTION: It is unknown whether concomitant esophageal involvement or anatomic location of eosinophilic infiltration affects the natural history of eosinophilic gastrointestinal disease (EGID). METHODS: A retrospective cohort study was performed using the University of North Carolina EGID Clinicopathologic Database. Patients were adults and children with a prior EGID diagnosis based on clinicopathologic features. Demographics, clinical characteristics, treatment information, and procedural data were extracted from medical records. Clinical course and flare history were characterized. RESULTS: Among 97 patients, 43% had EGID + esophageal involvement and 57% had EGID only. Patients with esophageal involvement had a longer diagnostic delay preceding diagnosis (36.6 vs 11.6 months, P = 0.001), more dysphagia (50% vs 18%; P = 0.001), required more chronic therapy (77% vs 52%, P = 0.016), and exhibited more progressive disease (25% vs 6%, P = 0.027). A continuous disease course was most common in eosinophilic gastritis (78%) while patients with eosinophilic gastritis + eosinophilic enteritis (29%) and eosinophilic enteritis + eosinophilic colitis (50%) had the highest proportion of progressive and relapsing disease, respectively ( P = 0.045). A continuous disease course occurred more frequently in children (71%, P = 0.03) and those with single organ involvement (65%), whereas adults had more relapsing (39%) or progressive disease (18%). DISCUSSION: EGIDs with and without esophageal involvement display many similarities, although patients with esophageal involvement more frequently had dysphagia, had progressive disease courses, and required more chronic therapy. Location of involvement and age of onset affected the natural history with higher proportions of relapsing or progressive disease seen in adults and patients with small bowel or multiorgan involvement while a continuous disease course was more common in children and patients with gastric-only involvement.

11.
Am J Gastroenterol ; 119(2): 262-269, 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-37782465

RESUMO

INTRODUCTION: Differences in eosinophilic esophagitis (EoE) presentation and outcomes by ethnicity or race remain understudied. We aimed to determine whether EoE patients of Hispanic/Latinx ethnicity or non-White race have differences in presentation at diagnosis or response to topical corticosteroid (tCS) treatment. METHODS: This retrospective cohort study included subjects of any age with a new diagnosis of EoE and documentation of ethnicity or race. For those who had treatment with tCS and follow-up endoscopy/biopsy, we assessed histologic response (<15 eosinophils/hpf), global symptom response, and endoscopic response. Hispanic EoE patients were compared with non-Hispanics at baseline and before and after treatment. The same analyses were repeated for White vs non-Whites. RESULTS: Of 1,026 EoE patients with ethnicity data, just 23 (2%) were Hispanic. Most clinical features at presentation were similar to non-Hispanic EoE patients but histologic response to tCS was numerically lower (38% vs 57%). Non-White EoE patients (13%) were younger at diagnosis and had less insurance, lower zip code-level income, shorter symptom duration, more vomiting, less dysphagia and food impaction, fewer typical endoscopic features, and less dilation. Of 475 patients with race data treated with tCS, non-Whites had a significantly lower histologic response rate (41% vs 59%; P = 0.01), and odds of histologic response remained lower after controlling for potential confounders (adjusted odds ratio 0.40, 95% confidence intervals: 0.19-0.87). DISCUSSION: Few EoE patients at our center were Hispanic, and they had similar clinical presentations as non-Hispanics. The non-White EoE group was larger, and presentation was less dysphagia-specific. Non-White patients were also less than half as likely to respond to tCS.


Assuntos
Transtornos de Deglutição , Enterite , Eosinofilia , Esofagite Eosinofílica , Gastrite , Humanos , Esofagite Eosinofílica/diagnóstico , Transtornos de Deglutição/etiologia , Estudos Retrospectivos , Minorias Étnicas e Raciais , Esteroides/uso terapêutico , Glucocorticoides/uso terapêutico
12.
Proc Biol Sci ; 291(2031): 20240967, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39288802

RESUMO

The hypothesized main drivers of megafauna extinctions in the late Quaternary have wavered between over-exploitation by humans and environmental change, with recent investigations demonstrating more nuanced synergies between these drivers depending on taxon, spatial scale, and region. However, most studies still rely on comparing archaeologically based chronologies of timing of initial human arrival into naïve ecosystems and palaeontologically inferred dates of megafauna extinctions. Conclusions arising from comparing chronologies also depend on the reliability of dated evidence, dating uncertainties, and correcting for the low probability of preservation (Signor-Lipps effect). While some models have been developed to test the susceptibility of megafauna to theoretical offtake rates, none has explicitly linked human energetic needs, prey choice, and hunting efficiency to examine the plausibility of human-driven extinctions. Using the island of Cyprus in the terminal Pleistocene as an ideal test case because of its late human settlement (~14.2-13.2 ka), small area (~11 000 km2), and low megafauna diversity (2 species), we developed stochastic models of megafauna population dynamics, with offtake dictated by human energetic requirements, prey choice, and hunting-efficiency functions to test whether the human population at the end of the Pleistocene could have caused the extinction of dwarf hippopotamus (Phanourios minor) and dwarf elephants (Palaeoloxodon cypriotes). Our models reveal not only that the estimated human population sizes (n = 3000-7000) in Late Pleistocene Cyprus could have easily driven both species to extinction within < 1000 years, the model predictions match the observed, Signor-Lipps-corrected chronological sequence of megafauna extinctions inferred from the palaeontological record (P. minor at ~12-11.1 ka, followed by P. cypriotes at ~10.3-9.1 ka).


Assuntos
Extinção Biológica , Animais , Humanos , Chipre , Caça , Fósseis , Paleontologia
13.
PLoS Comput Biol ; 19(7): e1011268, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37498846

RESUMO

Permafrost thawing and the potential 'lab leak' of ancient microorganisms generate risks of biological invasions for today's ecological communities, including threats to human health via exposure to emergent pathogens. Whether and how such 'time-travelling' invaders could establish in modern communities is unclear, and existing data are too scarce to test hypotheses. To quantify the risks of time-travelling invasions, we isolated digital virus-like pathogens from the past records of coevolved artificial life communities and studied their simulated invasion into future states of the community. We then investigated how invasions affected diversity of the free-living bacteria-like organisms (i.e., hosts) in recipient communities compared to controls where no invasion occurred (and control invasions of contemporary pathogens). Invading pathogens could often survive and continue evolving, and in a few cases (3.1%) became exceptionally dominant in the invaded community. Even so, invaders often had negligible effects on the invaded community composition; however, in a few, highly unpredictable cases (1.1%), invaders precipitated either substantial losses (up to -32%) or gains (up to +12%) in the total richness of free-living species compared to controls. Given the sheer abundance of ancient microorganisms regularly released into modern communities, such a low probability of outbreak events still presents substantial risks. Our findings therefore suggest that unpredictable threats so far confined to science fiction and conjecture could in fact be powerful drivers of ecological change.


Assuntos
Biota , Espécies Introduzidas , Humanos , Ecossistema
14.
Pain Med ; 25(3): 173-186, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38243702

RESUMO

OBJECTIVE: This study compared opioid utilization trajectories of persons initiating tramadol, short-acting hydrocodone, or short-acting oxycodone, and it characterized opioid dose trajectories and type of opioid in persistent opioid therapy subsamples. METHODS: A retrospective cohort study of adults with chronic non-cancer pain who were initiating opioid therapy was conducted with the IQVIA PharMetrics® Plus for Academics data (2008-2018). Continuous enrollment was required for 6 months before ("baseline") and 12 months after ("follow-up") the first opioid prescription ("index date"). Opioid therapy measures were assessed every 7 days over follow-up. Group-based trajectory modeling (GBTM) was used to identify trajectories for any opioid and total morphine milligram equivalent measures, and longitudinal latent class analysis was used for opioid therapy type. RESULTS: A total of 40 276 tramadol, 141 023 hydrocodone, and 45 221 oxycodone initiators were included. GBTM on any opioid therapy identified 3 latent trajectories: early discontinuers (tramadol 39.0%, hydrocodone 54.1%, oxycodone 61.4%), late discontinuers (tramadol 37.9%, hydrocodone 39.4%, oxycodone 33.3%), and persistent therapy (tramadol 6.7%, hydrocodone 6.5%, oxycodone 5.3%). An additional fourth trajectory, intermittent therapy (tramadol 16.4%), was identified for tramadol initiators. Of those on persistent therapy, 2687 individuals were on persistent therapy with tramadol, 9169 with hydrocodone, and 2377 with oxycodone. GBTM on opioid dose resulted in 6 similar trajectory groups in each persistent therapy group. Longitudinal latent class analysis on opioid therapy type identified 6 latent classes for tramadol and oxycodone and 7 classes for hydrocodone. CONCLUSION: Opioid therapy patterns meaningfully differed by the initial opioid prescribed, notably the presence of intermittent therapy among tramadol initiators and higher morphine milligram equivalents and prescribing of long-acting opioids among oxycodone initiators.


Assuntos
Dor Crônica , Tramadol , Adulto , Humanos , Analgésicos Opioides/uso terapêutico , Tramadol/uso terapêutico , Oxicodona/uso terapêutico , Hidrocodona/uso terapêutico , Seguimentos , Estudos Retrospectivos , Dor Crônica/tratamento farmacológico
15.
Nucleic Acids Res ; 50(W1): W753-W760, 2022 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-35524571

RESUMO

Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming-especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks, based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with automated continuous integration and adhering to the idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub.


Assuntos
Quimioinformática , Software , Biologia Computacional , Descoberta de Drogas
16.
J Ultrasound Med ; 43(4): 751-760, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38240323

RESUMO

OBJECTIVES: This study compared levels of discomfort among three positions for ultrasound-guided carpal tunnel injections (USCTI) to potentially facilitate and improve the procedure's tolerability in treating carpal tunnel syndrome (CTS). METHODS: Ambulatory Veterans referred for electromyography (EMG) evaluation of CTS were eligible for the study; a total of 30 participants were evaluated. Participants were asked to hold three different positions: 1) Hypersupination, 2) Airplane, and 3) total supported abduction (TSA). Participants rated their pain level, ease of performing/holding each position, exacerbation of underlying symptoms, and position preference. Results were analyzed with two-way repeated measures ANOVA. RESULTS: Hypersupination was determined to be the least preferred and most painful position to hold, demonstrating a statistically significant increase in the Numeric Rating Scale score for pain during the procedure compared with Airplane and TSA, which were not significantly different from one another. Pre-procedure neck, shoulder, elbow, and wrist pain were not significantly associated with intra-procedure pain. CONCLUSIONS: When performing USCTI, patient comfort can be optimized by avoiding Hypersupination. Utilizing the Airplane or TSA positions may provide similar access for ulnar approach injections while inducing lower levels of discomfort. Clinical space, resources, patient mobility, and laterality of procedures may further guide one's selection among the positions.


Assuntos
Síndrome do Túnel Carpal , Preferência do Paciente , Humanos , Síndrome do Túnel Carpal/diagnóstico por imagem , Síndrome do Túnel Carpal/tratamento farmacológico , Ultrassonografia , Dor , Ultrassonografia de Intervenção
17.
Proc Natl Acad Sci U S A ; 118(46)2021 11 16.
Artigo em Inglês | MEDLINE | ID: mdl-34772815

RESUMO

Signal processing is critical to a myriad of biological phenomena (natural and engineered) that involve gene regulation. Biological signal processing can be achieved by way of allosteric transcription factors. In canonical regulatory systems (e.g., the lactose repressor), an INPUT signal results in the induction of a given transcription factor and objectively switches gene expression from an OFF state to an ON state. In such biological systems, to revert the gene expression back to the OFF state requires the aggressive dilution of the input signal, which can take 1 or more d to achieve in a typical biotic system. In this study, we present a class of engineered allosteric transcription factors capable of processing two-signal INPUTS, such that a sequence of INPUTS can rapidly transition gene expression between alternating OFF and ON states. Here, we present two fundamental biological signal processing filters, BANDPASS and BANDSTOP, that are regulated by D-fucose and isopropyl-ß-D-1-thiogalactopyranoside. BANDPASS signal processing filters facilitate OFF-ON-OFF gene regulation. Whereas, BANDSTOP filters facilitate the antithetical gene regulation, ON-OFF-ON. Engineered signal processing filters can be directed to seven orthogonal promoters via adaptive modular DNA binding design. This collection of signal processing filters can be used in collaboration with our established transcriptional programming structure. Kinetic studies show that our collection of signal processing filters can switch between states of gene expression within a few minutes with minimal metabolic burden-representing a paradigm shift in general gene regulation.


Assuntos
Regulação Alostérica/genética , Processamento de Sinais Assistido por Computador/instrumentação , Fatores de Transcrição/genética , Escherichia coli/genética , Expressão Gênica/genética , Regulação da Expressão Gênica/genética , Redes Reguladoras de Genes/genética , Cinética , Regiões Promotoras Genéticas/genética , Ligação Proteica/genética , Engenharia de Proteínas/instrumentação , Engenharia de Proteínas/métodos , Biologia Sintética/métodos
18.
Proc Natl Acad Sci U S A ; 118(5)2021 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-33495346

RESUMO

Earthquake prediction, the long-sought holy grail of earthquake science, continues to confound Earth scientists. Could we make advances by crowdsourcing, drawing from the vast knowledge and creativity of the machine learning (ML) community? We used Google's ML competition platform, Kaggle, to engage the worldwide ML community with a competition to develop and improve data analysis approaches on a forecasting problem that uses laboratory earthquake data. The competitors were tasked with predicting the time remaining before the next earthquake of successive laboratory quake events, based on only a small portion of the laboratory seismic data. The more than 4,500 participating teams created and shared more than 400 computer programs in openly accessible notebooks. Complementing the now well-known features of seismic data that map to fault criticality in the laboratory, the winning teams employed unexpected strategies based on rescaling failure times as a fraction of the seismic cycle and comparing input distribution of training and testing data. In addition to yielding scientific insights into fault processes in the laboratory and their relation with the evolution of the statistical properties of the associated seismic data, the competition serves as a pedagogical tool for teaching ML in geophysics. The approach may provide a model for other competitions in geosciences or other domains of study to help engage the ML community on problems of significance.

19.
J Intellect Disabil Res ; 68(11): 1221-1252, 2024 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-39210565

RESUMO

BACKGROUND: Individuals (i.e. children/young adults) with developmental disabilities (DDs) and intellectual disabilities (IDs) often display a variety of physical and motor impairments. It is well known that participation in motor activities can positively impact the development of children's cognitive and social skills. Recently, virtual and digital technologies (e.g. video conferencing applications, virtual reality and video gaming) have been increasingly used to promote better physical/motor outcomes. The efficacy of digital technologies in improving motor outcomes for those with DD/ID varies depending on the technology and population, and the comparative effects of various technologies are unknown. The aim of our study is to conduct a systematic review to comprehensively examine the quantitative and qualitative results of current studies reporting the efficacy of digitally based motor interventions on motor outcomes in individuals with DD/ID. METHODS: Literature published from 1900 to 2024 was searched in four health sciences databases: PubMed, PsycINFO, Scopus and CINAHL. Articles that examined the effects of gross motor/physical activity training using technologies such as exergaming (i.e. exercise through video gaming such as the Wii and Xbox Kinect), virtual reality or telehealth video conferencing applications (i.e. Zoom, Webex or mobile health apps) on the standardised or game-specific gross motor performance of individuals with DD/ID diagnoses that do not typically experience significant walking challenges using experimental or quasi-experimental study designs were included. Thirty relevant articles were retrieved from a search of the databases PubMed (914), PsycINFO (1201), Scopus (1910) and CINAHL (948). RESULTS: Our quantitative synthesis of this published literature suggests strong and consistent evidence of small-to-large improvements in motor skill performance following digital movement interventions. CONCLUSIONS: Our review supports the use of digital motor interventions to support motor skill performance in individuals with DD without ID. Digital technologies can provide a more engaging option for therapists to promote motor skill development in individuals with DD or for caregivers to use as an adjunct to skilled therapy.


Assuntos
Deficiências do Desenvolvimento , Humanos , Deficiências do Desenvolvimento/reabilitação , Deficiências do Desenvolvimento/fisiopatologia , Deficiências do Desenvolvimento/terapia , Criança , Deficiência Intelectual/fisiopatologia , Deficiência Intelectual/reabilitação , Jogos de Vídeo , Adulto , Terapia por Exercício/métodos , Adulto Jovem , Adolescente , Destreza Motora/fisiologia
20.
Aging Ment Health ; : 1-7, 2024 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-38869165

RESUMO

OBJECTIVES: Longer time horizons are associated with positive health behaviors, but the associations of time horizons with disability and mortality are less understood. This study aims to test the hypothesis that longer time horizons are associated with decreased disability and mortality in older adults. METHOD: Participants were 1052 older adults (mean age = 81 ± 7 years) without dementia. Proportional hazard models adjusted for age, sex, and education were used to examine the associations of time horizons with risk of mortality and disability. RESULTS: During up to 11 years of follow up (mean = 5.7), 317 participants died. In fully adjusted models, longer time horizons were associated with reduced mortality risk (hazard rate [HR] = 0.78, 95% confidence interval [CI] = 0.68-0.89). About 36.7% of participants developed disability in instrumental activities of daily living (ADLs) and 49.3% developed disability in basic ADLs during follow up. Longer time horizons were associated with a reduced risk of disability in basic ADLs (HR = 0.89, 95% CI = 0.79-0.99) but not instrumental ADLs (HR = 0.90, 95% CI = 0.80-1.03). CONCLUSION: Longer time horizons are associated with a reduced risk of all-cause mortality and disability in basic ADLs among community-dwelling older adults, thus highlighting a potentially modifiable psychological risk factor for negative health outcomes in aging.

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