bluuebunny/crossref_metadata_2025 huggingface dataset:
Inpatient Standards of Care and the Suicidal Patient Part II: An Integration with Clinical Risk Management
Authors: Silverman Morton M. , Berman Alan L. , Bongar Bruce , Litman Robert E. , Maris Ronald W.
Published: October 2023

The authors elaborate on the standards of care for the assessment, management, and treatment of hospitalized suicidal patients. The authors attempt to synthesize the concepts of the minimal standard of care with clinical risk management and clinical judgment. They point out the areas of overlap and where optimum care diverges from legal standards of care. Case examples are provided to illustrate major areas of concern. Alleged failures of omission and commission are discussed. Tables are provided that differentiate duties and responsibilities between and among clinicians, hospital staff, and hospital administration.
Increasing illness severity of skilled nursing facility patients over time: Implications for readmission penalties
Authors: Siskind David , Dhansew Tarayn , Burns Amira , Burns Edith
Published: October 2023

Background

Current financial penalties for rehospitalization of skilled nursing facilities (SNFs) patients are based in part on the studies by Ouslander et al., 2011, and Mor et al., 2010, demonstrating that many SNF hospitalizations were avoidable. With increasing age, complex illness severity, and use of SNFs for subacute rehabilitation, readmission metrics and financial penalties based on previous data may be due for reevaluation.

Methods

Retrospective electronic medical record (EMR) review of 21,591 admissions and discharges between 2010 and 2019 inclusive. Data extracted included demographics, LACE, Charlson comorbidity index (CCI), and simplified HOSPITAL score parameters. The scores were calculated for the study years from the extracted data. Patients readmitted to the hospital within 30 days were identified.

Results

Mean yearly score of all three indices rose steadily: LACE score 10.76–12.04 (0.43 estimated annual increase, 95% CI [0.39, 0.46]), CCI 4.26–5.05 (0.31 estimated annual increase, 95% CI [0.27, 0.34]), and simplified HOSPITAL score 3.46–4.03 (0.21 estimated annual increase, 95% CI [0.18, 0.24]). The estimated probability of readmission across observed CCI scores ranged from 15.4% to 15.9%, 95% CI bounds (10.8%, 22.7%). The estimated probability of readmission across observed LACE scores ranged from 4.7% to 36.3%, 95% CI bounds (3.4%, 54.7%). The estimated probability of readmission across observed HOSPITAL scores ranged from 5.8% to 54.1%, 95% CI bounds (6.2%, 66.0%).

Conclusions and Implications

The study confirms anecdotal experience that the illness acuity of patients admitted to SNFs increased progressively over time and was associated with an increased risk of 30‐day readmissions to the hospital. Our study suggests that the use of clinically validated readmission risk assessment tools instead of the Skilled Nursing Facility Value‐Based Purchasing Program (SNF VBP) current risk adjustors may be a more accurate reflection of the current illness severity of a facility's patient population at the time of payment adjustment.
Comparative study on the Ru ware, Ru‐type ware of Qingliangsi kiln and celadon of Zhanggongxiang kiln
Authors: Tao Shiqian , Li Qiang , Yao Heliang , Liu Song , Li Qinghui
Published: October 2023

Thirty‐three porcelain shards (28 Ru ware and 5 Ru‐type ware) unearthed from Qinglingsi kiln and 31 celadon fragments from Zhanggongxiang kiln were studied systematically for tracing their correlation and difference in glaze and body characteristics through a variety of characterisation methods. Samples without HF corrosion were applied to achieve the microstructure and composition details by SEM and TEM. Results exhibited that there were certain similarities between Ru ware, Ru‐type ware and Zhanggongxiang kiln celadon in glaze colour and thickness, body features, fracture structure; however, they showed obvious differences in body thickness, chemical composition of glaze and body, phase constituents and microstructure of glaze. Plentiful needle‐like diopside were widely distributed in Zhanggongxiang kiln celadon glazes, while this type of crystals was only existed in few Ru and Ru‐type ware glazes with small content. Besides, a large amount of residual quartz was present over the Ru ware glazes, which could have relation to the incorporation of agate. The liquid‐liquid phase separation structure (Ca‐rich droplets and Si‐rich matrix) was generated within the interspaces of anorthite clusters or around the brims of anorthite needles or columns. The occurrence of phase separation was generally accompanied by Al2O3 consumption, but suppressed in the areas far from anorthite due to the rise of Al2O3 content, indicating that Al2O3 was the most sensitive constituent for this glaze behaviour. The distinguished size, shape and distribution of phase‐separated droplets or interconnected structures were closely associated with the scale and crowding level of anorthite crystallisation.
Does BRAF mutation status and related clinicopathological factors affect the recurrence rate of ameloblastoma? A systematic review, meta‐analysis and metaregression
Authors: Singh Ashutosh Kumar , Alagarsamy Ragavi , Chaulagain Rajib , Singh Abanish , Sapkota Dipak , Thavaraj Selvam , Singh Rabindra P.
Published: October 2023

Objectives

This review aims to analyse the recurrence rate in BRAFv600e+ and BRAFv600e− ameloblastomas and explore its association with clinicopathological variables.

Methods

A comprehensive search was conducted using databases including PubMed, Embase, Cochrane Central Register of Controlled Trials, Clinicaltrials.gov, Google Scholar and grey literature, without any limitation on start date or language up to 20 June 2023. A random effect meta‐analysis was conducted and Metaregression analyses were performed based on available clinicopathological factors.

Results

Fifteen studies met the criteria for meta‐analysis of outcomes. There was no significant difference in overall recurrence rates between the two groups (risk difference = 0.001, p‐value = 0.987). Increasing male:female ratio in the BRAFv600e+ group was associated with a lower reported recurrence, suggesting a higher recurrence rate in females. The odds of having mandibular lesion were four times higher in BRAFv600e+ cases compared to BRAFv600e− cases (confidence interval: 2.121–7.870, p < 0.001, I2 = 28.37%).

Conclusion

Within the BRAFv600e+ group, females showed a higher reported recurrence rate. This specific clinical group may benefit from BRAFv600e mutation investigation and potential upscaled surgical treatment and additional BRAF inhibitor therapy, which needs validation in future studies.
COVID‐19 vaccine effectiveness in children by age groups. A population‐based study in Galicia, Spain
Authors: Mallah Narmeen , Pardo‐Seco Jacobo , Ares‐Gómez Sonia , López‐Pérez Luis‐Ricardo , González‐Pérez Juan‐Manuel , Rosón Benigno , Otero‐Barrós María‐Teresa , Durán‐Parrondo Carmen , Nartallo‐Penas Victoria , Mirás‐Carballal Susana , Rodríguez‐Tenreiro‐Sánchez Carmen , Rivero‐Calle Irene , Gómez‐Carballa Alberto , Salas Antonio , Martinón‐Torres Federico
Published: October 2023

Background

Studies on vaccine effectiveness (VE) against COVID‐19 in the pediatric population are outgoing. We aimed to quantify VE against SARS‐CoV‐2 in two pediatric age groups, 5–11 and 12–17‐year‐old, while considering vaccine type, SARS‐CoV‐2 variant, and duration of protection.

Methods

A population‐based test‐negative control study was undertaken in Galicia, Spain. Children 5–11‐year‐old received the Comirnaty® (Pfizer, US) vaccine, while those aged 12–17‐year‐old received the Comirnaty® (Pfizer, US) or SpikeVax® (ModernaTX, Inc) vaccine. Participants were categorized into unvaccinated (0 doses or one dose with <14 days since vaccination), partially vaccinated (only one dose with ≥14 days, or two doses with <14 days after the second dose administration), and fully vaccinated (two doses with ≥14 days after the second injection). Adjusted odds ratios (OR) and their 95% confidence intervals (CI) were estimated using multiple logistic regression models. VE was calculated as (1‐OR) * 100. Stratified and sensitivity analyses were performed.

Results

In the fully vaccinated 5–11‐year‐old children, VE against the Omicron variant was 44.1% (95% CI: 38.2%–49.4%). In the fully vaccinated 12–17‐year‐old individuals, VE was 83.4% (95% CI: 81.2%–85.3%) against Delta and 74.8% (95% CI: 58.5%–84.9%) against Omicron. Comirnaty® and SpikeVax® vaccines showed a similar magnitude of VE against Delta [Comirnaty® VE: 81.9% (95% CI: 79.3%–84.1%) and SpikeVax® VE: 85.3% (95% CI: 81.9%–88.1%)]. Comirnaty® (Pfizer, US; VE: 79.7%; 95% CI: 50.7%–92.4%) showed a slightly higher magnitude of protection against Omicron than SpikeVax® (ModernaTX, Inc), yet with an overlapping CI (VE: 74.3%; 95% CI: 56.6%–84.9%). VE was maintained in all age subgroups in both pediatric populations, but it declined over time.

Conclusions

In Galicia, mRNA VE was moderate against SARS‐CoV‐2 infections in the 5–11‐year‐old populations, but high in older children. VE declined over time, suggesting a potential need for booster dose schedules.
Knowing what it's like
Authors: Lee Andrew Y.
Published: October 2023

David Lewis—famously—never tasted vegemite. Did he have any knowledge of what it's like to taste vegemite? Most say ‘no’; I say ‘yes’. I argue that knowledge of what it's like varies along a spectrum from more exact to more approximate, and that phenomenal concepts vary along a spectrum in how precisely they characterize what it's like to undergo their target experiences. This degreed picture contrasts with the standard all‐or‐nothing picture, where phenomenal concepts and phenomenal knowledge lack any such degreed structure. I motivate the degreed picture by appeal to (1) limits in epistemic abilities such as recognition, imagination, and inference, and (2) the semantics of ‘knows what it's like’ expressions. I argue that approximate phenomenal knowledge cannot be explained merely via determinable or vague phenomenal concepts. I develop a framework for systematizing approximate knowledge of phenomenal character. And I explain how my view challenges some standard assumptions about the acquisition conditions, requirements for mastery, and referential mechanisms of phenomenal concepts.
Grounding physicalism and the knowledge argument
Authors: Moran Alex
Published: October 2023

Standard responses to the knowledge argument grant that Mary could know all of the physical facts even while trapped inside her black‐and‐white room. What they deny is that upon leaving her black‐and‐white room and experiencing red for the first time, Mary learns a genuinely new fact. This paper develops an alternate response in a grounding physicalist framework, on which Mary does not know all of the physical facts while trapped inside the room. The main thesis is that Mary does not know certain phenomenal facts while trapped inside the room, whereby these facts classify as physical due to being wholly and fully metaphysically grounded in the underlying fundamental facts which are themselves entirely physical.
The corticomuscular response to experimental pain via blood flow occlusion when applied to the ipsilateral and contralateral leg during an isometric force task
Authors: Zambolin F. , Duro Ocana P. , Goulding R. , Sanderson A. , Venturelli M. , Wood G. , McPhee J. , Parr J. V. V.
Published: October 2023

Blood flow occlusion (BFO) has been previously used to investigate physiological responses to muscle ischemia, showing increased perceptual effort (RPE) and pain along with impaired neuromuscular performance. However, at present, it is unclear how BFO alters corticomuscular activities when either applied to the exercising or nonexercising musculature. The present study therefore set out to assess the corticomuscular response to these distinct BFO paradigms during an isometric contraction precision task. In a repeated measures design, fifteen participants (age = 27.00 ± 5.77) completed 15 isometric contractions across three experimental conditions; no occlusion (CNTRL), occlusion of the contralateral (i.e., nonexercising) limb (CON‐OCC), and occlusion of the ipsilateral (i.e., exercising) limb (IPS‐OCC). Measures of force, electroencephalographic (EEG), and electromyographic (EMG) were recorded during contractions. We observed that IPS‐OCC broadly impaired force steadiness, elevated EMG of the vastus lateralis, and heightened RPE and pain. IPSI‐OCC also significantly decreased corticomuscular coherence during the early phase of contraction and decreased EEG alpha activity across the sensorimotor and temporoparietal regions during the middle and late phases of contraction compared with CNTRL. By contrast, CON‐OCC increased perceived levels of pain (but not RPE) and decreased EEG alpha activity across the prefrontal cortex during the middle and late phases of contraction, with no changes observed for EMG and force steadiness. Together, these findings highlight distinctive psychophysiological responses to experimental pain via BFO showing altered cortical activities (CON‐OCC) and altered cortical, corticomuscular, and neuromuscular activities (IPS‐OCC) when applied to the lower limbs during an isometric force precision task.
Delayed seeding and nutrient amendment seed enhancement technology: potential to improve sagebrush establishment?
Authors: Donovan Christopher , Eshleman Magdalena , Riginos Corinna
Published: October 2023

The sagebrush steppe provides vital habitat across the western United States, but its range is declining. Wyoming big sagebrush (Artemesia tridentata Nutt. spp. wyomingensis Beetle & Young) is difficult to establish on restoration and reclamation sites, with low seedling survival due to drought, competition, and limited available nutrients. Incorporating seeds into seed enhancement technologies (SET) has potential to overcome barriers to establishment. Here, we tested the effects of a high phosphorus nutrient amendment using three application techniques (dust over bare seed, dispersed seed pellets, and clustered seed pellets) versus bare seed on sagebrush establishment on 5‐, 1‐, and 0‐year‐old mine reclamation sites. Regardless of seed technology, emergence was highest in the year 5 site, but survival was lowest, likely due to competition from established plants. Survival and growth were highest in the year 0 site, but emergence was lowest, likely due to poor soil stability. The year 1 site, where soil was stable and competition was low, produced the greatest number of surviving seedlings. Across all times since reclamation, pellets reduced emergence compared to dust and bare seed treatments. There was no clear evidence of any benefit of the SETs. These results highlight the challenges of delivering nutrient amendments in SETs and unresolved questions about the effectiveness of the amendment tested here. Seeding sagebrush 1 year after reclamation may be an additional way to improve restoration and reclamation success for this foundation species.
The impact of an antibody investigation algorithm emphasizing specificity on reducing potential false‐positive warm autoantibody detection at a Canadian tertiary care centre
Authors: Hutspardol Sakara , Boyd Lyz Frances , Zamar David , Sham Lawrence , Kalar Debbie , Mi Jian , Marcon Krista , Shih Andrew W.
Published: October 2023

Background and Objectives

To reduce potential false‐positive warm autoantibody (WAA) by solid‐phase red cell adherence assay (SPRCA), our centre implemented a new antibody investigation algorithm (AIA) by classifying cases with panreactive SPRCA but negative saline‐indirect antiglobulin test as ‘antibody of undetermined significance’ (AUS) after excluding clinically significant antibodies. We assessed the effects of the new AIA and subsequent alloantibody formation in patients with AUS.

Materials and Methods

Samples from patients with positive SPRCA screens between 1 September 2017 and 31 August 2021 were selected for the study. Frequencies of antibodies classified by the old and new AIAs were compared using Fisher's exact test. Patient demographics, transfusion history and antibody formation in cases of AUS were collected.

Results

A significant reduction in potential WAA frequencies from 127/1167 (11%) to 53/854 (6%) was observed (p < 0.001) when compared between the old and new AIAs among 2021 positive SPRCA antibody screens. While no patients with AUS later transitioned to potential WAA using the new AIA, four patients developed alloantibodies, including anti‐E, anti‐C, both anti‐C and anti‐E, and anti‐Wra.

Conclusion

A significant reduction in the frequencies of potential false‐positive WAA detection at our centre was observed after implementing the new AIA, leading to less resource and phenotypically matched red blood cell (RBC) use. Some patients still developed subsequent RBC alloimmunization, so clinically relevant alloantibodies should be carefully excluded before determining AUS, taking forming or evanescent antibodies into consideration.
Ca2+ influx modulation of temporal and spatial patterns of inositol trisphosphate‐mediated Ca2+ liberation in Xenopus oocytes.
Authors: Yao Y , Parker I
Published: October 2023

Inositol 1,4,5‐trisphosphate (InsP3) functions as a second messenger by liberating intracellular Ca2+ and by promoting influx of extracellular Ca2+. We examined the effects of Ca2+ influx on the temporal and spatial patterns of intracellular Ca2+ liberation in Xenopus oocytes by fluorescence imaging of cytosolic free Ca2+ together with voltage clamp recording of Ca(2+)‐activated Cl‐ currents. Oocytes were injected with a poorly metabolized InsP3 analogue (3‐F‐InsP3; see Introduction) to induce sustained activation of InsP3 signalling, and Ca2+ influx was controlled by applying voltage steps to change the driving force for Ca2+ entry. Positive‐ and negative‐going potential steps (corresponding, respectively, to decreases and increases in Ca2+ influx) evoked damped oscillatory Cl‐ currents, accompanied by cyclical changes in cytosolic free Ca2+. The source of this Ca2+ was intracellular, since oscillations persisted when Ca2+ entry was suppressed by removing extracellular Ca2+ or by polarization close to the Ca2+ equilibrium potential. Fluorescence recordings from localized (ca 5 microns) spots on the oocyte showed repetitive Ca2+ spikes. Their frequency increased at more negative potentials, but they became smaller and superimposed on a sustained ‘pedestal’ of Ca2+. Spike periods ranged from about 50 s at +20 mV to 4s at potentials between ‐60 and ‐120 mV. Ca2+ spike frequency decreased after removing extracellular Ca2+, but the spike amplitude was not reduced and low frequency spikes continued for at least 30 min in the absence of extracellular Ca2+. Membrane current oscillations decayed in amplitude following voltage steps, while locally recorded Ca2+ spikes did not. This probably arose because Ca2+ release was initially synchronous across the cell, leading to large Ca(2+)‐activated Cl‐ currents, but the currents then diminished as different areas of the cell began to release Ca2+ asynchronously. Fluorescence imaging revealed that Ca2+ liberation in 3‐F‐InsP3‐loaded oocytes occurred as transient localized puffs and as propagating waves. Polarization to more negative potentials increased the frequency of puffs and the number of sites at which they were seen, and enhanced their ability to initiate waves. The frequency and velocity of Ca2+ waves increased at more negative potentials. When the potential was returned to more positive levels, repetitive Ca2+ spikes at first occurred synchronously across the recording area, but this synchronization was gradually lost and Ca2+ waves began at several foci. We conclude that influx of extracellular Ca2+ regulates the temporal and spatial patterns of Ca2+ liberation from InsP3‐sensitive intracellular stores, probably as a result of dual excitatory and inhibitory actions of cytosolic Ca2+ on the InsP3 receptor.(ABSTRACT TRUNCATED AT 400 WORDS)
Baroreceptor and somatic sensory regulation of kidney function in two‐kidney, one‐clip Goldblatt hypertensive rats.
Authors: Davis G , Johns E J
Published: October 2023

The aim of this investigation was to characterize the renal haemodynamic and tubular responses to somatic afferent nerve stimulation following the removal of afferent nerve input from the atria or the carotid sinuses in chloralose‐urethane‐anaesthetized Sprague‐Dawley rats and two‐kidney, one‐clip Goldblatt hypertensive rats. Bilateral stimulation of the brachial nerve plexi at 15 V, 1.3 Hz for 0.2 ms resulted in an increase in systemic blood pressure in each group of 10‐40%, while renal perfusion pressure was maintained at a constant level. There were significantly larger falls in left renal blood flow and combined left and right glomerular filtration rate in all groups following selective denervation of either the cardiopulmonary or the carotid sinus baroreceptors, respectively. Brachial nerve stimulation decreased urine flow rate and absolute and fractional sodium excretion from both kidneys in Sprague‐Dawley intact animals by 53, 65 and 59%; in vagotomized animals by 68, 77 and 63%; and in carotid sinus denervated animals by 86, 90 and 48%, respectively. The renal response in the Goldblatt group were similar to the normotensive group, but the main contribution of the total response was from the untouched left kidney. The inhibitory influence of the vagus and carotid sinuses on the renal sympathetic nerve‐mediated sodium and water resorption appeared to be enhanced in the Goldblatt hypertensive rats when compared with the normotensive rats. The renal functional responses to somatic afferent nerve stimulation appeared to be well preserved in the renovascular hypertensive rats, although there were important differences in the contributions to the responses from the left and right kidneys. Furthermore, the baroreceptors exerted a greater influence on basal renal function in the hypertensive rats.
ADOLESCENCIA Y DERECHO AL ESPACIO PÚBLICO. EL CASO DEL BARRIO DE CARABANCHEL Y EL BARRIO DE SALAMANCA EN MADRID
Authors: Levesque Bonnín Aina
Published: October 2023

En este trabajo se pretende esclarecer algunas cuestiones relacionadas con el espacio público y el derecho a la ciudad del siglo XXI y responder a la pregunta «¿Cuál es la influencia del paisaje urbano en las relaciones sociales entre los jóvenes y los adolescentes?» y tiene por objetivo general el de conocer la influencia que tiene el paisaje urbano sobre las relaciones sociales que se establecen en el espacio público. Se han elegido dos barrios alejados social y geográficamente. Los espacios seleccionados son una plaza sin nombre cercana al Palacio de Vista Alegre, en un barrio periférico madrileño, Carabanchel y la plaza de Colón, situada en el lujoso barrio de Salamanca. Los sujetos de estudio son los y las adolescentes. La metodología propuesta en este trabajo es la etnografía y la búsqueda bibliográfica, estableciendo un diálogo teórico y práctico entre ambas. De esta forma se pretende responder a la pregunta planteada: ¿Qué? uso hacen los y las adolescentes del espacio público? A parte de resolver esta cuestión, se pretende conocer y seguir trabajando para construir espacios para el uso y el disfrute de los y las adolescentes. Esta investigación esta? abierta a cualquier modificación y abre el campo a seguir investigando sobre posibles cuestiones y a reformular nuevas preguntas.
A lucky covariance estimator based on cumulative coherence
Authors: Brooker D. J. , Edelmann G. F.
Published: October 2023

The performance of adaptive acoustic localization methodologies depends on the quality of the covariance matrix being inverted. This paper demonstrates a technique to improve covariance estimation using the principles of lucky signal processing and the cumulative coherence. Lucky processing, popularized in astro-photography, is a technique that increases signal quality by selectively keeping only a small fraction from a pool of potential snapshots. Cumulative coherence, a measure of how well a set of vectors is described by its subsets, provides the measure of “data quality” that enables the lucky processing. This approach was applied to covariance estimation on an acoustic array by taking a fixed duration sample of data and creating a dense set of snapshots with higher than usual overlap. From these densely sampled snapshots, the “luckiest” ones were found using cumulative coherence, and the covariance was averaged as normal. Using data from the SWellEX-96 experiment, this new estimator was compared with standard practice. It was found that the lucky covariance estimate was successful at adaptive matched field processing and produced a less ambiguous processor output than the conventional estimator. The lucky covariance estimate had a higher estimated signal-to-noise ratio, especially when the source was at longer ranges from the array.
Fumagillin inhibits growth of the enteric protozoan parasite
Entamoeba histolytica
by covalently binding to and selectively inhibiting methionine aminopeptidase 2
Authors: Watanabe Natsuki , Saito-Nakano Yumiko , Kurisawa Naoaki , Otomo Keisuke , Suenaga Kiyotake , Nakano Kentaro , Nozaki Tomoyoshi
Published: October 2023

Amebiasis is an important cause of morbidity and mortality worldwide, and caused by infection with the protozoan parasite
Entamoeba histolytica
. Metronidazole is currently the first-line drug despite adverse effects and concerns on the emergence of drug resistance. Fumagillin, a fungal metabolite from
Aspergillus fumigatus,
and its structurally related natural and synthetic compounds have been previously explored as potential anti-angiogenesis inhibitors for cancers, anti-microbial, and anti-obese compounds. Although fumagillin was used for human amebiasis in clinical trials in 1950s, the mode of action of fumagillin remains elusive until now. In this report, we showed that fumagillin covalently binds to methionine aminopeptidase 2 (MetAP2) and non-covalently but abundantly binds to patatin family phospholipase A (PLA). Susceptibility against fumagillin of the amebic strains in which expression of
E. histolytica MetAP2
(
EhMetAP2
) gene was silenced increased compared to control strain. Conversely, overexpression of EhMetAP2 mutants that harbors amino acid substitutions responsible for resistance to ovalicin, a fumagillin analog, in human MetAP2, also resulted in decrease in fumagillin susceptibility. In contrast, neither gene silencing nor overexpression of
E. histolytica
PLA (EhPLA) affected fumagillin susceptibility. These data suggest that EhPLA is not essential and not the target of fumagillin for its amebicidal activity. Taken together, our data have demonstrated that EhMetAP2 is the primary target for amebicidal activity of fumagillin, and EhMetAP2 represents a rational explorable target for the development of alternative therapeutic agents against amebiasis.
Emergence of ciprofloxacin- and penicillin-resistant
Neisseria meningitidis
isolates in Japan between 2003 and 2020 and its genetic features
Authors: Takahashi Hideyuki , Morita Masatomo , Kamiya Hajime , Fukusumi Munehisa , Yasuda Mitsuru , Sunagawa Masatomi , Nakamura-Miwa Haruna , Ohama Yuki , Shimuta Ken , Ohnishi Makoto , Saito Ryoichi , Akeda Yukihiro
Published: October 2023

Although we previously reported that some meningococcal isolates in Japan were resistant to penicillin (PCG) and ciprofloxacin (CIP), the antibiotic susceptibilities of
Neisseria meningitidis
isolates obtained in Japan remained unclear. In the present study, 290
N
.
meningitidis
isolates in Japan between 2003 and 2020 were examined for the sensitivities to eight antibiotics (azithromycin, ceftriaxone, ciprofloxacin, chloramphenicol, meropenem, minocycline, penicillin, and rifampicin). All isolates were susceptible to chloramphenicol, ceftriaxone, meropenem, minocycline, and rifampicin while two were resistant to azithromycin. Penicillin- and ciprofloxacin-resistant and -intermediate isolates (PCG
R
, CIP
R
, PCG
I
and CIP
I
, respectively) were also identified. Based on our previous findings from whole genome sequence analysis, approximately 40% of PCG
I
were associated with ST-11026 and cc2057 meningococci, both of which were unique to Japan. Moreover, the majority of ST-11026 meningococci were CIP
R
or CIP
I
. Sensitivities to PCG and CIP were closely associated with genetic features, which indicated that, at least for Japanese meningococcal isolates, PCG
R/I
or CIP
I/R
would be less likely to be horizontally conferred from other neisserial genomes by transferring of the genes responsible (
penA
and
gyrA
genes, respectively), but rather that ancestral
N. meningitidis
strains conferring PCG
R/I
or CIP
I/R
phenotypes clonally disseminated in Japan.
intI
1 gene abundance from septic tanks in Thailand using validated
intI
1 primers
Authors: Okonkwo Valentine , Cholet Fabien , Ijaz Umer Z. , Koottatep Thammarat , Pussayanavin Tatchai , Polpraset Chongrak , Sloan William T. , Connelly Stephanie , Smith Cindy J.
Published: October 2023

Antimicrobial resistance (AMR) poses a serious global health threat, and wastewater treatment (WWT), including septic tanks, is a source of AMR. In Thailand, antibiotics are unregulated, and septic tanks are commonly used. Yet, their impact on the spread or mitigation of AMR is unknown. We monitored household and healthcare conventional septic tanks (CST) and household solar septic tanks (SST) in Thailand using the class 1 integron-integrase (
intI
1) gene abundance as a proxy for AMR. A systematic review of the literature found 65
intI
1 primers. We evaluated the coverage and specificity of each, including a new MGB TaqMan primer-probe, against clinical and environmental
intI
1,
intI
1-like, and non-
intI
1 databases. The three best primers were selected, laboratory validated for DNA and mRNA quantification, and used to quantify septic tank
intI
1 gene abundance. No primer set could distinguish between
intI
1 and
intI
1-like sequences. While primer choice did not affect gene abundance of the same sample (
P
-value > 0.05), sometimes when comparing the same samples quantified by different primers, statistical differences were observed for one but not the other primer set. This may lead to different interpretations of AMR risk. Irrespective of primers or reactor type
intI
1 gene abundance was greatest in influent > effluent > sludge.
intI
1 gene abundance was lowest in the effluent of the SST-household < CST-household < CST-healthcare. 31% to 42% of
intI
1 was removed by the CST-household tank, indicating while septic tanks remove some
intI
1 they remain a source to the surrounding environment. Toward the goal of achieving standardization across studies, we recommend the F3-R3 primer for
intI
1 quantification.

IMPORTANCE

Antimicrobial resistance is a global crisis, and wastewater treatment, including septic tanks, remains an important source of antimicrobial resistance (AMR) genes. The role of septic tanks in disseminating class 1 integron, and by extension AMR genes, in Thailand, where antibiotic use is unregulated remains understudied. We aimed to monitor gene abundance as a proxy to infer potential AMR from septic tanks in Thailand. We evaluated published
intI
1 primers due to the lack of consensus on optimal Q-PCR primers and the absence of standardization. Our findings confirmed septic tanks are a source of class 1 integron to the environment. We highlighted the significance of
intI
1 primer choice, in the context of interpretation of risk associated with AMR spread from septic tanks. We recommend the validated set (F3-R3) for optimal
intI
1 quantification toward the goal of achieving standardization across studies.
Multiple TonB homologs are important for carbohydrate utilization by
Bacteroides thetaiotaomicron
Authors: Pollet Rebecca M. , Foley Matthew H. , Kumar Supriya Suresh , Elmore Amanda , Jabara Nisrine T. , Venkatesh Sameeksha , Vasconcelos Pereira Gabriel , Martens Eric C. , Koropatkin Nicole M.
Published: October 2023

The human gut microbiota is able to degrade otherwise undigestible polysaccharides, largely through the activity of
Bacteroides
. Uptake of polysaccharides into
Bacteroides
is controlled by TonB-dependent transporters (TBDTs), whose transport is energized by an inner membrane complex composed of the proteins TonB, ExbB, and ExbD.
Bacteroides thetaiotaomicron
(
B. theta
) encodes 11 TonB homologs that are predicted to be able to contact TBDTs to facilitate transport. However, it is not clear which TonBs are important for polysaccharide uptake. Using strains in which each of the 11 predicted
tonB
genes are deleted, we show that TonB4 (BT2059) is important but not essential for proper growth on starch. In the absence of TonB4, we observed an increase in the abundance of TonB6 (BT2762) in the membrane of
B. theta
, suggesting functional redundancy of these TonB proteins. The growth of the single deletion strains on pectic galactan, chondroitin sulfate, arabinan, and levan suggests a similar functional redundancy of the TonB proteins. A search for highly homologous proteins across other
Bacteroides
species and recent work in
Bacteroides fragilis
suggests that TonB4 is widely conserved and may play a common role in polysaccharide uptake. However, proteins similar to TonB6 are found only in
B. theta
and closely related species, suggesting that the functional redundancy of TonB4 and TonB6 may be limited across
Bacteroides
. This study extends our understanding of the protein network required for polysaccharide utilization in
B. theta
and highlights differences in TonB complexes across
Bacteroides
species.

IMPORTANCE

The human gut microbiota, including
Bacteroides
, is required for the degradation of otherwise undigestible polysaccharides. The gut microbiota uses polysaccharides as an energy source, and fermentation products such as short-chain fatty acids are beneficial to the human host. This use of polysaccharides is dependent on the proper pairing of a TonB protein with polysaccharide-specific TonB-dependent transporters; however, the formation of these protein complexes is poorly understood. In this study, we examine the role of 11 predicted TonB homologs in polysaccharide uptake. We show that two proteins, TonB4 and TonB6, may be functionally redundant. This may allow for the development of drugs targeting
Bacteroides
species containing only a TonB4 homolog with limited impact on species encoding the redundant TonB6.
Whole-genome sequence of the
Halobacillus naozhouensis
type strain KACC 21980
Authors: Choi Hyorim , Kim Seunghwan , Kim Yiseul , Heo Jun
Published: October 2023

We present the whole-genome sequence of
Halobacillus naozhouensis
Korean Agricultural Culture Collection (KACC) 21980
T
, isolated from China by Chen et al.. The genome of
Halobacillus naozhouensis
KACC 21980
T
comprises a circular chromosome (4.2 Mb) and one plasmid (17 kb). It includes a total of 4,168 predicted coding genes.
Implementation factors influencing the sustained provision of tele-audiology services: insights from a combined methodology of scoping review and qualitative semistructured interviews
Authors: Ramkumar Vidya , Shankar Varsha , Kumar Shuba
Published: October 2023

Objectives

The objectives of the current study were to (a) identify long-term tele-audiology services reported to be implemented beyond the research phase and determine whether they are sustained, (b) map the implementation process to Standards for Reporting Implementation Studies guidelines and (c) map the factors that influenced its sustainability to the Implementation Outcomes Framework (IOF) to understand the gaps from an implementation research perspective.

Study design, setting and participants

This cross-sectional study included a scoping review of articles describing long-term tele-audiology services from around the world to determine the factors influencing the implementation. Six electronic databases (PubMed, Cochrane Library, Web of Science, Scopus, Google Scholar and ProQuest) were searched for literature published between 2010 and 2023. This was followed by semistructured interviews (SSIs), which were guided by the IOF. Six project implementers were interviewed to obtain an in-depth understanding of factors that influenced sustainability of these tele-audiology services. Thematic analysis of the interview transcripts was carried out using a hybrid inductive-deductive approach.

Results

Data were extracted from 32 tele-audiology studies included in the review, which were then mapped to 21 projects. The findings of the scoping review reveal that tele-audiology services were predominantly provided using synchronous telepractice methods. The ‘professional-facilitator-patient’ model was most commonly used. None of the studies reported the use of implementation research and/or outcome frameworks. Factors that influenced sustainability of tele-audiology services were identified from the combined results of the scoping review and the SSIs. These factors could be mapped to implementation outcomes of acceptability, adoption, feasibility, implementation cost and sustainability.

Conclusion

Implementation research and/or outcome framework should be used to guide the implementation processes, its evaluation and measurement of outcomes systematically in tele-audiology service delivery. When such frameworks are used, gaps in information regarding the context influencing implementation, reporting of fidelity and adaptability measures can be addressed.
Effect of long-term Tai Chi training on Parkinson’s disease: a 3.5-year follow-up cohort study
Authors: Li Gen , Huang Pei , Cui Shishuang , He Yachao , Tan Yuyan , Chen Shengdi
Published: October 2023

Background

Tai Chi has shown beneficial effects on the motor and non-motor symptoms of Parkinson’s disease (PD), but no study has reported the effect of long-term Tai Chi training.

Objective

To examine whether long-term Tai Chi training can maintain improvement in patients with PD.

Methods

Cohorts of patients with PD with Tai Chi training (n=143) and patients with PD without exercise as a control group (n=187) were built from January 2016. All subjects were assessed at baseline and in November 2019, October 2020 and June 2021. A logarithmic linear model was used to analyse rating scales for motor and non-motor symptoms. The need to increase antiparkinsonian therapies was presented as a Kaplan–Meier plot and as a box plot. The bootstrap method was used to resample for statistical estimation.

Results

Tai Chi training reduced the annual changes in the deterioration of the Unified Parkinson’s Disease Rating Scale and delayed the need for increasing antiparkinsonian therapies. The annual increase in the levodopa equivalent daily dosage was significantly lower in the Tai Chi group. Moreover, patients benefited from Tai Chi training in motor symptoms, non-motor symptoms and complications.

Conclusion

Tai Chi training has a long-term beneficial effect on PD, with an improvement in motor and non-motor symptoms and reduced complications.

Trial registration number

NCT05447975.
Crop yields under no-till in Canada: implications for soil organic carbon change
Authors: VandenBygaart A.J. , Liang B.C.
Published: October 2023

Crop yields directly affect carbon (C) inputs into soils. Tillage management can influence crop performance, and as such should be considered when quantifying soil organic carbon (SOC) change, and thus net greenhouse gas emissions from croplands for national greenhouse gas inventory reporting. We conducted a meta-analysis of the effects of no-tillage (NT) and conventional tillage (CT) on crop yields for multiple crop species, soil types, and climatic regions of Canada. Yield response to NT varied between western and eastern Canada. Regardless of crop type, experiment duration, soil texture, and residue management, experiments in eastern Canada showed an average of 6% lower yields ( p ≤ 0.005) under NT compared to CT. In western Canada, crop type had an important effect on yields between NT and CT with wheat, canola, and legumes exhibiting 10% ( p ≤ 0.001), 7% ( p ≤ 0.05), and 9% ( p ≤ 0.05) higher yields on average under NT compared to CT, respectively. In western Canada, higher yields would be reflected in a similar scale of higher C inputs to NT systems. A recent meta-analysis of the effects of tillage management on SOC in Canada showed an 8% higher storage of SOC under NT systems compared to CT, a difference limited to western Canadian soils. Incorporating the effect of tillage on C inputs will lead to improvements in the accuracy of the effects of tillage management on SOC change in Canadian cropland. The activity data can be improved by applying weightings to the yield data by site-specific assessment of tillage practices across Canada.
Neural network reconstruction of cosmology using the Pantheon compilation
Authors: Dialektopoulos Konstantinos F. , Mukherjee Purba , Said Jackson Levi , Mifsud Jurgen
Published: October 2023

In this work, we reconstruct the Hubble diagram using various data sets, including correlated ones, in artificial neural networks (ANN). Using ReFANN, that was built for data sets with independent uncertainties, we expand it to include non-Guassian data points, as well as data sets with covariance matrices among others. Furthermore, we compare our results with the existing ones derived from Gaussian processes and we also perform null tests in order to test the validity of the concordance model of cosmology.
Theoretical interpretation of the $$\Xi (1620)$$ and $$\Xi (1690)$$ resonances seen in $$\Xi _c^+ \rightarrow \Xi ^- \pi ^+ \pi ^+$$ decay
Authors: Li Hai-Peng , Zhang Gong-Jie , Liang Wei-Hong , Oset E.
Published: October 2023

We study the Belle reaction $$\Xi _c^+ \rightarrow \Xi ^- \pi ^+ \pi ^+$$

Ξ
c
+

→

Ξ
-

π
+

π
+

looking at the mass distribution of $$\pi ^+ \Xi $$

π
+

Ξ

, where clear signals for the $$\Xi (1620)$$

Ξ
(
1620
)

and $$\Xi (1690)$$

Ξ
(
1690
)

resonances are seen. These two resonances are generated dynamically from the interaction in coupled channels of $$\pi \Xi , {\bar{K}} \Lambda , {\bar{K}} \Sigma $$

π
Ξ
,

K

¯

Λ
,

K

¯

Σ

and $$\eta \Xi $$

η
Ξ

within the chiral unitary approach. Yet, the weak decay process at the quark level, together with the hadronization to produce pairs of mesons, does not produce the $$\pi \pi \Xi $$

π
π
Ξ

final state. In order to produce this state one must make transitions from the $${\bar{K}} \Lambda , {\bar{K}} \Sigma $$

K

¯

Λ
,

K

¯

Σ

and $$\eta \Xi $$

η
Ξ

components to $$\pi \Xi $$

π
Ξ

, and this interaction is what produces the resonances. So, the reaction offers a good test for the molecular picture of these resonances. Adding the contribution of the $$\Xi ^*(1530)$$

Ξ
∗

(
1530
)

and some background we are able to get a good reproduction of the mass distribution showing the signatures of the two resonances as found in the experiment.
Supplementary Figure S8 from Ewing Sarcoma Single-cell Transcriptome Analysis Reveals Functionally Impaired Antigen-presenting Cells
Authors: Visser Lindy L. , Bleijs Margit , Margaritis Thanasis , van de Wetering Marc , Holstege Frank C. P. , Clevers Hans
Published: October 2023

Comparison myeloid cells originating from Ewing sarcoma and neuroblastoma tissue samples
Supplementary Figure S2 from Ewing Sarcoma Single-cell Transcriptome Analysis Reveals Functionally Impaired Antigen-presenting Cells
Authors: Visser Lindy L. , Bleijs Margit , Margaritis Thanasis , van de Wetering Marc , Holstege Frank C. P. , Clevers Hans
Published: October 2023

The single-cell architecture of Ewing sarcoma - part 1
Targeted Degradation of XIAP is Sufficient and Specific to Induce Apoptosis in MYCN-overexpressing High-risk Neuroblastoma
Authors: Choo Zhang'E , Koh Xiaoying , Wong Megan Rui En , Ashokan Ruth Minothini , Ali Ahamed Nurul Suhana Binte , Kang CongBao , Kuick Chik Hong , Chang Kenneth Tou En , Larisch Sarit , Loh Amos Hong Pheng , Chen Zhi Xiong
Published: October 2023

XIAP, the most potent mammalian inhibitor of apoptosis protein (IAP), critically restricts developmental culling of sympathetic neuronal progenitors, and is correspondingly overexpressed in most MYCN-amplified neuroblastoma tumors. Because apoptosis-related protein in the TGFβ signaling pathway (ARTS) is the only XIAP antagonist that directly binds and degrades XIAP, we evaluated the preclinical effectiveness and tolerability of XIAP antagonism as a novel targeting strategy for neuroblastoma. We found that antagonism of XIAP, but not other IAPs, triggered apoptotic death in neuroblastoma cells. XIAP silencing induced apoptosis while overexpression conferred protection from drug-induced apoptosis. From a screen of IAP inhibitors, first-in-class ARTS mimetic A4 was most effective against high-risk and high XIAP-expressing neuroblastoma cells, and least toxic toward normal liver- and bone marrow–derived cells, compared with pan-IAP antagonists. On target engagement assays and nuclear magnetic resonance spectroscopy, A4 was observed to degrade rather than inhibit XIAP, catalyzing rapid degradation of XIAP through the ubiquitin-proteasome pathway. In MYCN-amplified neuroblastoma patient-derived xenografts, A4 significantly prolonged survival as a single agent, and demonstrated synergism with standard-of-care agents to reduce their effective required doses 3- to 6-fold. Engagement and degradation of XIAP by ARTS mimetics is a novel targeting strategy for neuroblastoma that may be especially effective against MYCN-amplified disease with intrinsically high XIAP expression. First-in-class ARTS mimetic A4 demonstrates preclinical efficacy and warrants further development and study.

Significance:

XIAP degradation is sufficient to kill MYCN-amplified neuroblastoma which overexpresses and relies on XIAP as a brake against cell death, without affecting normal cells.
4. Scientific Hoaxes and the Predatory Paradox: Past, Present, and Future
Authors: Koerber Amy , Starkey Jesse C. , Ardon-Dryer Karin , Cummins R. Glenn , Eko Lyombe , Kee Kerk F.
Published: October 2023

In Chapter 4, ‘Scientific Hoaxes and the Predatory Paradox: Past, Present, and Future,’ Amy Koerber examines scientific hoax articles with a focus on the weaknesses and flaws that such hoaxes can expose in the larger information ecosystem of scholarly publishing. The chapter thus reveals that scientific hoaxes further complicate any neat distinction between journals that are predatory and those that are not. Hoaxes have, in some cases, exposed specific journals as predatory. But in other cases, they have had effects beyond those that the author anticipated, exposing major weaknesses or fraudulent practices not only at journals or publishers suspected to be predatory but also at the most prestigious and well-respected journals. More importantly, publishing hoaxes have unintentionally exposed weaknesses in the mechanisms that we have long relied on to ensure research quality. For example, hoaxes have exposed flaws in even the best journals’ peer review systems, and when hoax articles continue to get cited in subsequent literature—sometimes even after retraction—they lead us to question our habit of relying on citation counts as a measure of research quality. Partly in response to hoaxes, industries have emerged around the desire to pin down the legitimacy of a particular author or publication in an environment that makes it increasingly easy for fakes to be mistaken as the real thing. For example, we now have ORCID identifiers to help us establish the identity of authors and Digital Object Identifiers (DOI) to help us pinpoint the location and verify the identity of published texts. These identifiers are becoming commonplace in academic lingo, but it is easy to overlook the fact that each of these markers emerged as a commercial development with its own complexities, nuances, and shortcomings. As we argue, these innovations reflect our desire to pin down something that is certain and real in a landscape where it is increasingly easy for fakes to circulate as the real thing.