bluuebunny/crossref_metadata_2025 huggingface dataset:
Two new plant records, Alangium kurzii (Cornaceae) and Ficus racemosa (Moraceae), in Bhutan and corresponding distributions
Authors: WANGCHUK Tandin , DENDUP Tshering , NAMGAY Tshewang , TSHERING Tsethup , WANGCHUK Jigme
Published: October 2024

Bhutan represents a biodiversity hotspot in the eastern Himalayan region, known for its unique environment and diverse plant species. This has made Bhutan a popular destination for plant enthusiasts from all over the world. Several new plant discoveries and records have been made in recent years, contributing valuable additions to scientific knowledge and the country’s botanical records. Here, we provide two new additional records of plants for the flora of Bhutan: Alangium kurzii Craib from the Cornaceae family and Ficus racemosa L. from the Moraceae family. With these additions, Bhutan now has three Alangium species and 25 Ficus species including the current records. We also present their uses and distributions in the country.
Fuzzy-PID and interpolation: a novel synergetic approach to process control
Authors: Jha Devashish , Ahmed Arifa , Kumar Sanatan , Roy Debanjan
Published: October 2024

This paper presents a novel approach for tuning a fuzzy-based proportional-integral-derivative (PID) controller to enhance the control performance of a chemical process control system. The proposed approach combines the advantages of fuzzy- PID and interpolation to achieve improved control performance. Properly tuned PID controllers can help maintain process stability, minimize deviations from setpoints, and ensure efficient operation in industrial systems. Fuzzy logic allows for the incorporation of expert knowledge and linguistic rules, enabling the controller to handle uncertain and imprecise process information. Fuzzy PID controllers combine fuzzy logic and conventional PID control to enhance control performance, particularly in systems with complex or nonlinear dynamic such as chemical plant. It dynamically adjusts the PID parameters—proportional gain (Kp), integral gain (Ki), and derivative gain (Kd)—based on error  e(t) and change of error Delta e(t). Interpolation plays a crucial role in this context by filling in the gaps or handling situations not explicitly covered by the fuzzy rules. Comparative studies are conducted to evaluate the performance of the fuzzy PID controller against conventional PID controllers and other advanced control techniques. It is demonstrated that the synergy between fuzzy logic and interpolation not only enhances control performance but also offers a more intuitive and adaptable solution for addressing the complexities of modern chemical process control systems.
Influence of rotation on peristaltic flow for pseudoplastic fluid: a wavy channel
Authors: Ali Hayat Adel , R. Salman Mohammed
Published: October 2024

The phenomenon of rotation serves multiple purposes in cosmic and geophysical phenomena. It offers insights into the formation of galaxies and the circulation patterns of oceans. Moreover, rotational diffusion elucidates the orientation of nanoparticles within fluid mediums. Investigating the dynamics of fluid peristalsis under the influence of rotational forces holds significant relevance in addressing challenges associated with the transportation of conductive physiological fluids such as blood, polymeric materials, and saline water. This study focused on studying the impact of rotation on the peristaltic transport of non-Newtonian pseudoplastic fluids through a wavy channel. The complexity of flow equations, including the continuity and motion equations, is mathematically formulated and transformed into dimensionless nonlinear ordinary differential equations depending on the assumption of low Reynolds number and long wavelength approximation. Perturbation technique is employed to solve the problem for the stream function and the resulted system is implemented and plotted using MATHEMATICA software along with the boundary conditions. Graphical discussion is involved to utilize the impact of the emerging parameters in the flow characteristic, encompassing the velocity profile, pressure gradient, pressure rise, and trapping phenomenon. The research revealed that rotation significantly influences the fluid flow within the channel, diminishing the regressive and inhibitory impact of the fluid parameter, consequently enhancing the fluid flow within the channel.
A comparative view to H_infinity-norm of transfer functions of linear DAEs
Authors: Gündüz Hasan , Çelik Ercan , Karabacak Mesut
Published: October 2024

In this paper, bisection and extended-balanced singular perturbation methods are used to calculate the H_infinity-norm of the transfer function of a linear DAEs system for the particular case D=0. In the beginning, the approaches' algorithms and error analysis are provided separately. Next, the methods are employed to calculate the H_infinity-norms of a numerical example pertaining to an automotive gas turbine model, and the error limits are used to check the norms in the suitable range, respectively. Ultimately, every solution is compared individually with the problem's H_infinity-norm values, which are retrieved from MATLAB.
Fatigue Scattering Analytics and Prediction of SS 316L Fabricated by Laser Powder Bed Fusion
Authors: Kousoulas Panayiotis , Guo Y. B.
Published: October 2024

Laser powder bed fusion (LPBF) is an enabling process manufacture of complex metal components. However, LPBF is prone to generate geometrical defects (e.g., porosity, lack of fusion), which causes a significant fatigue scattering. However, LPBF fatigue scattering data and analysis in the literature are not only sparse and limited to tension-compression mode but also inconsistent. This article presents a robust high-frequency fatigue testing method to construct stress-cycle curves of SS 316L to understand the scattering nature and predict the scattering pattern. A series of bending fatigue tests are performed at different stress amplitudes. Two different runout criteria are used to investigate fatigue life, fatigue limits, and scattering. The endurance limit reaches around 300 MPa for the defect size distribution at the selected process space. The defect size-based fatigue limit model is found to underestimate the endurance limit by about 30 MPa when comparing with the experimental data. Fatigue scattering is further calculated by using 95% prediction intervals, showing that low fatigue scattering is present at high stresses while a large variation of fatigue life occurs at stresses near the knee point.
Minimum-Time Control of a Linear System With Input Saturation: A Practical Approach
Authors: Sinha Alok
Published: October 2024

A simple algorithm is presented to find near-minimum-time control inputs for a controllable continuous-time linear time-invariant system with any number of states and inputs. The well-known digital deadbeat control algorithm is modified to satisfy input constraints, and the design issue is the selection of sampling period to minimize the time required to reach the desired final state. During each sampling period, the input required to place all the poles at the origin of z-plane (deadbeat control) via state feedback is computed. If the infinity norm of the deadbeat input exceeds the input constraint, the input is found by placing the poles as close to the origin as possible. A sufficient condition for the system stability is developed. Numerical examples illustrate that this algorithm can lead to true time-optimal control or near time-optimal control.
Impact of Generalized Versus Individualized Load–Velocity Equations on Velocity-Loss Magnitude in Bench-Press Exercise: Mixed-Model and Equivalence Analysis
Authors: Sánchez-Moreno Miguel , Bachero-Mena Beatriz , Sánchez-Valdepeñas Juan , Nakamura Fabio Yuzo , Pareja-Blanco Fernando
Published: October 2024

Purpose: This study analyzed the influence of 2 velocity-based training-load prescription strategies (general vs individual load–velocity equations) on the relationship between the magnitude of velocity loss (VL) and the percentage of repetitions completed in the bench-press exercise. Methods: Thirty-five subjects completed 6 sessions consisting of performing the maximum number of repetitions to failure against their 40%, 60%, and 80% of 1-repetition maximum (1RM) in the Smith machine bench-press exercise using generalized and individualized equations to adjust the training load. Results: A close relationship and acceptable error were observed between percentage of repetitions completed and the percentage of VL reached for the 3 loading magnitudes and the 2 load-prescription strategies studied (R2 from .83 to .94; standard error of the estimate from 7% to 10%). A simple main effect was observed for load and VL thresholds but not for load-prescription strategies. No significant interaction effects were revealed. The 40% and 60% 1RM showed equivalence on data sets and the most regular variation, whereas the 80% 1-repetition maximum load showed no equivalence and more irregular variation. Conclusion: These results suggest that VL is a useful variable to predict percentage of repetitions completed in the bench-press exercise, regardless of the strategy selected to adjust the relative load. However, caution should be taken when using heavy loads.
Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy
Authors: Kang Tae Gun , Lan Xin , Mi Tian , Chen Hongfeng , Alli Shanta , Lim Song-Eun , Bhatara Sheetal , Vasandan Anoop Babu , Ward Grace , Bentivegna Sofia , Jang Josh , Spatz Marianne L. , Han Jin-Hwan , Schlotmann Balthasar Clemens , Jespersen Jakob Schmidt , Derenzo Christopher , Vogel Peter , Yu Jiyang , Baylin Stephen , Jones Peter , O’Connell Casey , Grønbæk Kirsten , Youngblood Ben , Zebley Caitlin C.
Published: October 2024

Epigenetic reinforcement of T cell exhaustion is known to be a major barrier limiting T cell responses during immunotherapy. However, the core epigenetic regulators restricting antitumor immunity during prolonged antigen exposure are not clear. We investigated three commonly mutated epigenetic regulators that promote clonal hematopoiesis to determine whether they affect T cell stemness and response to checkpoint blockade immunotherapy. CD8 T cells lacking Dnmt3a, Tet2, or Asxl1 preserved a progenitor-exhausted (Tpex) population for more than 1 year during chronic antigen exposure without undergoing malignant transformation. Asxl1 controlled the self-renewal capacity of T cells and reduced CD8 T cell differentiation through H2AK119 ubiquitination and epigenetic modification of the polycomb group–repressive deubiquitinase pathway. Asxl1-deficient T cells synergized with anti–PD-L1 immunotherapy to improve tumor control in experimental models and conferred a survival advantage to mutated T cells from treated patients.
Catalytic asymmetric fragmentation of cyclopropanes
Authors: Raut Ravindra Krushnaji , Matsutani Satoshi , Shi Fuxing , Kataoka Shuta , Poje Margareta , Mitschke Benjamin , Maeda Satoshi , Tsuji Nobuya , List Benjamin
Published: October 2024

The stereoselective activation of alkanes constitutes a long-standing and grand challenge for chemistry. Although metal-containing enzymes oxidize alkanes with remarkable ease and selectivity, chemical approaches have largely been limited to transition metal–based catalytic carbon–hydrogen functionalizations. Alkanes can be protonated to form pentacoordinated carbonium ions and fragmented into smaller hydrocarbons in the presence of strong Brønsted acids. However, catalytic stereocontrol over such reactions has not previously been accomplished. We show here that strong and confined acids catalyze highly enantioselective fragmentations of a variety of cyclopropanes into the corresponding alkenes, expanding the boundaries of catalytic selective alkane activation. Computational studies suggest the involvement of the long-debated cycloproponium ions.
Long-term stability in perovskite solar cells through atomic layer deposition of tin oxide
Authors: Gao Danpeng , Li Bo , Liu Qi , Zhang Chunlei , Yu Zexin , Li Shuai , Gong Jianqiu , Qian Liangchen , Vanin Francesco , Schutt Kelly , Davis Melissa A. , Palmstrom Axel F. , Harvey Steven P. , Long Nicholas J. , Luther Joseph M. , Zeng Xiao Cheng , Zhu Zonglong
Published: October 2024

Robust contact schemes that boost stability and simplify the production process are needed for perovskite solar cells (PSCs). We codeposited perovskite and hole-selective contact while protecting the perovskite to enable deposition of SnO

x

/Ag without the use of a fullerene. The SnO

x

, prepared through atomic layer deposition, serves as a durable inorganic electron transport layer. Tailoring the oxygen vacancy defects in the SnO

x

layer led to power conversion efficiencies (PCEs) of >25%. Our devices exhibit superior stability over conventional p-i-n PSCs, successfully meeting several benchmark stability tests. They retained >95% PCE after 2000 hours of continuous operation at their maximum power point under simulated AM1.5 illumination at 65°C. Additionally, they boast a certified
T
97
lifetime exceeding 1000 hours.
Catalytic prenyl conjugate additions for synthesis of enantiomerically enriched PPAPs
Authors: Ng Shawn , Howshall Casey , Ho Thanh Nhat , Mai Binh Khanh , Zhou Yuebiao , Qin Can , Tee Kai Ze , Liu Peng , Romiti Filippo , Hoveyda Amir H.
Published: October 2024

Polycyclic polyprenylated acylphloroglucinols (PPAPs) are a class of >400 natural products with a broad spectrum of bioactivity, ranging from antidepressant and antimicrobial to anti-obesity and anticancer activity. Here, we present a scalable, regio-, site-, and enantioselective catalytic method for synthesis of cyclic β-prenyl ketones, compounds that can be used for efficient syntheses of many PPAPs in high enantiomeric purity. The transformation is prenyl conjugate addition to cyclic β-ketoesters promoted by a readily accessible chiral copper catalyst and involving an easy-to-prepare and isolable organoborate reagent. Reactions reach completion in just a few minutes at room temperature. The importance of this advance is highlighted by the enantioselective preparation of intermediates previously used to generate racemic PPAPs. We also present the enantioselective synthesis of nemorosonol (14 steps, 20% yield) and its one-step conversion to another PPAP, garcibracteatone (52% yield).
Tiny comets under the sea
Authors: Cael B. B. , Guidi Lionel
Published: October 2024

A mucus drag on sinking marine snow may have big biogeochemical implications
The third era of genomics is at risk of being dismantled across the global south
Authors: de Oliveira Tulio
Published: October 2024

The first era of genomics started with the publication of Watson and Crick’s notable work on the description of the DNA double helix in 1953. This era lasted 50 years, until the publication of the human genome in April 2003. The second era is associated with the period between the completion of the human genome and the present day. I argue that, with the discontinuity caused by the COVID-19 pandemic and the spread and increased use of genomics to every corner of the world, we are entering a new, third era of genomics that provides major opportunities to advance the health of humans, animals, and the planet. However, this can only happen if the capacity that has greatly expanded in recent years is maintained and expanded further rather than left to atrophy, particularly across the global south.
Science in a shifting policy system
Authors: Harris Theresa , Alexander Rashada
Published: October 2024

In June, the US Supreme Court overturned a 40-yearold legal principle known as the
Chevron
doctrine, which deferred to federal agencies on how regulations are interpreted in legal cases when the legislation enacted by Congress is unclear. Striking a blow against this precedent, Supreme Court Chief Justice John Roberts indicated that
Chevron
was “fundamentally misguided” and that only the nation’s courts have the prerogative to interpret the laws they administer. Judges across the United States now anticipate an onslaught of litigation seeking to overturn federal regulatory actions, and many of these lawsuits will turn on scientific evidence that guided those actions. Instead of deferring to the scientific and technical expertise of federal agencies, courts must now independently review the scientific record behind a challenged regulation for its persuasiveness, along with scientific findings produced by the litigating parties. It’s too early to fully unpack the impact of overturning
Chevron
, but the scientific community must step forward to support the crafting of clear and evidence-informed legislation, and the use of scientific evidence in the courts.
Overcoming amphotericin B resistance in
Candida auris
using the antiemetic drug rolapitant
Authors: Salama Ehab A. , Elgammal Yehia , Utturkar Sagar M. , Lanman Nadia A. , Hazbun Tony R. , Seleem Mohamed N.
Published: October 2024

The emergence of
Candida auris
poses a significant health challenge that has led to a new era of multidrug-resistant fungal infections. Invasive infections caused by
C. auris
are usually associated with remarkable morbidity and mortality. For many years, amphotericin B (AmB) remained the most efficient and the last line of treatment against most hard-to-treat fungal infections. However, strains of
C. auris
possess extraordinary resistance to most antifungal agents, including AmB. In this study, we screened ~2,600 FDA-approved drugs and clinical compounds to identify the antiemetic drug rolapitant as a promising enhancer to AmB against
C. auris
. Rolapitant exhibited potent synergistic interactions with AmB against all tested (29/29)
C. auris
isolates. In a time-kill assay, rolapitant restored the fungicidal activity of AmB within 4 h. Additionally, the synergistic relationship between rolapitant and AmB was observed against other medically crucial
Candida
,
Cryptococcus,
and
Aspergillus
species. A transcriptomic study revealed that exposure to rolapitant affects oxidation reduction processes, ion transporters, and ATP production. Rolapitant triggers an elevation in cytosolic and mitochondrial calcium levels and induces oxidative stress within fungal cells. An ATP luminescence assay confirmed that rolapitant, at sub-inhibitory concentrations, significantly interfered with ATP production in
C. auris
. Moreover, rolapitant enhanced the
in vivo
activity of AmB in a mouse model of disseminated
C. auris
infection, as the combination reduced the fungal burden in murine kidneys by ~1 log (~90%) colony forming units. Our findings warrant further investigation of using rolapitant to overcome AmB resistance in
C. auris
and other fungal species.
Overexpression of β-lactamase genes (
bla
KPC,
bla
SHV
) and novel CirA deficiencies contribute to decreased cefiderocol susceptibility in carbapenem-resistant
Klebsiella pneumoniae
before its approval in China
Authors: Hong Hanxu , Fan Linping , Shi Wenbo , Zhu Yuchen , Liu Peng , Wei DanDan , Liu Yang
Published: October 2024

Cefiderocol (FDC) is an effective antibiotic that is used to treat severe infections caused by carbapenem-resistant
Klebsiella pneumoniae
(CRKP). The mechanisms underlying FDC resistance and molecular epidemiology in China remain unclear. We collected 477 non-duplicate CRKP clinical isolates in central China and characterized their susceptibility to FDC, virulence genes, and sequence typing. The overall FDC susceptibility rate of CRKP was 99.2% in central China, which was higher than that in North America and Europe (96.1%), with MIC
50/90
values of 1/2 mg/L. The decrease in FDC susceptibility in central China was concentrated in the ST11 CRKP-carrying virulence plasmids. Whole-genome sequencing (WGS) and quantitative reverse transcription PCR (qRT-PCR) experiments showed that serine β-lactamases, especially highly expressed KPC and SHV, substantially decreased FDC susceptibility in four FDC non-susceptible isolates (two resistant and two intermediate isolates). Notably, different CirA deficiencies, p.E450GfsTer16 and p.E133Ter, were found in both of the resistant isolates. In contrast, global WGS data indicate that the resistance mechanisms in North America and Europe were primarily associated with NDM and KPC variants, predominantly found in ST307 and ST147. Overall, FDC exhibits excellent activity against CRKP in central China, with resistance mechanisms primarily related to high KPC and SHV expression, along with deficiencies in CirA, frequently observed in ST11. This is remarkably different from the situation in North America and Europe and will directly impact the choice of clinical interventions. Additionally, the surveillance of FDC resistance in China is imperative.
Identification of a novel NADPH generation reaction in the pentose phosphate pathway in
Escherichia coli
using mBFP
Authors: Ueno Koichiro , Sawada Shogo , Ishibashi Mai , Kanda Yoshiki , Shimizu Hiroshi , Toya Yoshihiro
Published: October 2024

NADPH is a redox cofactor that drives the anabolic reactions. Although major NADPH generation reactions have been identified in
Escherichia coli
, some minor reactions have not been identified. In the present study, we explored novel NADPH generation reactions by monitoring the fluorescence dynamics after the addition of carbon sources to starved cells, using a metagenome-derived blue fluorescent protein (mBFP) as an intracellular NADPH reporter. Perturbation analyses were performed on a glucose-6-phosphate isomerase (PGI) deletion strain and its parental strain. Interestingly, mBFP fluorescence increased not only in the parental strain but also in the ΔPGI strain after the addition of xylose. Because the ΔPGI strain cannot metabolize xylose through the oxidative pentose phosphate pathway, this suggests that an unexpected NADPH generation reaction contributes to an increase in fluorescence. To unravel this mystery, we deleted the NADPH generation enzymes including transhydrogenase, isocitrate dehydrogenase, NADP
+
-dependent malic enzyme, glucose-6-phosphate dehydrogenase (G6PDH), and 6-phosphogluconate dehydrogenase (6PGDH) in the ΔPGI strain, and revealed that G6PDH and 6PGDH contribute to an increase in fluorescence under xylose conditions.
In vitro
assays using purified enzymes showed that G6PDH can produce NADPH using erythrose-4-phosphate (E4P) as a substitute for glucose-6-phosphate. Because the
Km
(0.65 mM) for E4P was much higher than the reported intracellular E4P concentrations in
E. coli
, little E4P must be metabolized through this bypass in the parental strain. However, the flux would increase when E4P accumulates in the cells owing to genetic modifications. This finding provides a metabolic engineering strategy for generating NADPH to produce useful compounds using xylose as a carbon source.

IMPORTANCE

Because NADPH is consumed during the synthesis of various useful compounds, enhancing NADPH regeneration is highly desirable in metabolic engineering. In this study, we explored novel NADPH generation reactions in
Escherichia coli
using a fluorescent NADPH reporter and found that glucose-6-phosphate dehydrogenase can produce NADPH using erythrose-4-phosphate as a substrate under xylose conditions. Xylose is an abundant sugar in nature and is an attractive carbon source for bioproduction. Therefore, this finding contributes to novel pathway engineering strategies using a xylose carbon source in
E. coli
to produce useful compounds that consume NADPH for their synthesis.
Lipophilic bisphosphonates reduced cyst burden and ameliorated hyperactivity of mice chronically infected with
Toxoplasma gondii
Authors: Sleda Melissa A. , Pitafi Zaid F. , Song WenZhan , Oldfield Eric , Moreno Silvia N. J.
Published: October 2024

The current treatments for toxoplasmosis are only active against fast-growing tachyzoites, present in acute infections, with little effect on slow-growing bradyzoites within tissue cysts, present in latent chronic infections. The mitochondrion of
Toxoplasma gondii
is essential for its survival, and one of the major anti-parasitic drugs, atovaquone, inhibits the mitochondrial electron transport chain at the coenzyme Q:cytochrome c oxidoreductase site. Coenzyme Q (also known as ubiquinone [UQ]) consists of a quinone head and a lipophilic, isoprenoid tail that anchors UQ to membranes. The synthesis of the isoprenoid unit is essential for cell growth and is inhibited by lipophilic bisphosphonates, which inhibit the parasite growth. In this work, we investigated the effect of lipophilic bisphosphonates on the chronic stages of
T. gondii
. We discovered that three lipophilic bisphosphonates (BPH-1218, BPH-1236, and BPH-1238), effective for the acute infection, were also effective in controlling the development of chronic stages. We showed effectiveness by testing them against
in vitro
cysts and
in vivo
derived tissue cysts and, most importantly, these compounds reduced the cyst burden in the brains of chronically infected mice. We monitored the activity of infected mice non-invasively and continuously with a novel device termed the CageDot. A decrease in activity accompanied the acute phase, but mice recovered to normal activity and showed signs of hyperactivity when the chronic infection was established. Moreover, treatment with atovaquone or BPH-1218 ameliorated the hyperactivity observed during the chronic infection.

IMPORTANCE

Treatment for toxoplasmosis is challenged by a lack of effective drugs to eradicate the chronic stages. Most of the drugs currently used are poorly distributed to the central nervous system, and they trigger allergic reactions in a large number of patients. There is a compelling need for safe and effective treatments for toxoplasmosis. Bisphosphonates (BPs) are analogs of inorganic pyrophosphate and are used for the treatment of bone disorders. BPs target the isoprenoid pathway and are effective against several experimental parasitic infections. Some lipophilic BPs can specifically inhibit the mitochondrial activity of
Toxoplasma gondii
by interfering with the mechanism by which ubiquinone is inserted into the inner mitochondrial membrane. In this work, we present the effect of three lipophilic BPs against
T. gondii
chronic stages. We also present a new strategy for the monitoring of animal activity during disease and treatment that is non-invasive and continuous.
The putative type 4 secretion system effector BspD is involved in maintaining envelope integrity of the pathogen
Brucella
Authors: Ketterer Maren , Chiquet Petra , Esposito Mara , Sedzicki Jaroslaw , Québatte Maxime , Dehio Christoph
Published: October 2024

Brucellosis is a debilitating disease caused by the Gram-negative, facultative intracellular zoonotic pathogen
Brucella.
En route to its intracellular replicative niche,
Brucella
encounters various stressful environments that may compromise envelope integrity. Here we show that the proposed type 4 secretion system (T4SS) effector BspD is a conserved protein of the Rhizobiales, which does not show signs of co-evolution with the presence of a T4SS or a certain lifestyle. We further present data indicating that BspD is critical for the envelope integrity of
Brucella abortus
in the stationary phase and in the presence of EDTA, a compound known to destabilize the outer membrane. Deletion of
bspD
resulted in abnormal bacterial morphologies, indicating its involvement in maintaining envelope integrity. Additionally, the absence of BspD led to the formation of fewer and smaller intracellular microcolonies in a macrophage infection model. From our observations, we propose that BspD of
B. abortus
is critical for preserving the integrity of the bacterial envelope, particularly under stressful conditions, which may enhance
Brucella
’s ability to survive within host cells.

IMPORTANCE

Brucellosis, caused by the intracellular pathogen
Brucella
, poses a significant health threat. Understanding how
Brucella
adapts to stressful environments is crucial. This study unveils BspD, a conserved protein within the Rhizobiales order, as a key player in maintaining
Brucella
's envelope integrity. Remarkably, BspD’s presence within the Rizobiales appears independent of the presence of a T4SS or a specific lifestyle. Deletion of
bspD
resulted in compromised envelope integrity, abnormal bacterial morphologies, and reduced intracellular microcolony formation. These findings underscore BspD’s critical role, particularly in stressful conditions like the stationary phase and EDTA exposure, and highlight its significance for the survival of
Brucella
within host cells. This elucidation deepens our understanding of
Brucella
pathogenesis and may inform future therapeutic strategies against brucellosis.
Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production
Authors: Beck Kristen L. , Haiminen Niina , Agarwal Akshay , Carrieri Anna Paola , Madgwick Matthew , Kelly Jennifer , Pylro Victor , Kawas Ban , Wiedmann Martin , Ganda Erika
Published: October 2024

The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.

IMPORTANCE

We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.
Novel motif associated with carbon catabolite repression in two major Gram-positive pathogen virulence regulatory proteins
Authors: Woo Jerry K. K. , Zimnicka Adriana M. , Federle Michael J. , Freitag Nancy E.
Published: October 2024

Carbon catabolite repression (CCR) is a widely conserved regulatory process that ensures enzymes and transporters of less-preferred carbohydrates are transcriptionally repressed in the presence of a preferred carbohydrate. This phenomenon can be regulated via a CcpA-dependent or CcpA-independent mechanism. The CcpA-independent mechanism typically requires a transcriptional regulator harboring a phosphotransferase regulatory domain (PRD) that interacts with phospho
t
ransferase
s
ystem (PTS) components. PRDs contain a conserved histidine residue that is phosphorylated by the PTS-associated HPr-His15~P protein. PRD-containing regulators often harbor additional domains that resemble PTS-associated EIIB protein domains with a conserved cysteine residue that can be phosphorylated by cognate PTS components. We noted that Mga, the PRD-containing central virulence regulator of
Streptococcus pyogenes
, has an EIIB
Gat
domain containing a cysteine that, based on the presence of a similar motif in glycerol kinase, could be a target for phosphorylation. Using site-directed mutagenesis, we constructed phospho-ablative and phospho-mimetic substitutions of this cysteine and found that these substitutions modify the CCR of the Rgg2/3 quorum-sensing system. Moreover, we provide genetic evidence that the phospho-donor of this cysteine residue is likely to be ManL, the EIIA/B subunit of the mannose PTS system. Interestingly, a structurally distinct virulence gene regulator, PrfA of
Listeria monocytogenes
, harbors a similar cysteine-containing motif, and phospho-ablative and phospho-mimetic substitutions of the cysteine-altered CCR of PrfA-dependent virulence gene expression. Collectively, our data suggest that phosphorylation of a cysteine within the shared novel motif in Mga and PrfA may be a heretofore missing link between cellular metabolism and virulence.

IMPORTANCE

In this study, we identified a novel cysteine-containing motif within the amino acid sequence of two structurally distinct transcriptional regulators of virulence in two Gram-positive pathogens that appears to link carbon metabolism with virulence gene expression. The results also highlight the potential post-translational modification of cysteine in bacterial species, a rare and understudied modification.
Characterizing the urobiome in geriatric males with chronic indwelling urinary catheters: an exploratory longitudinal study
Authors: Stewart Emma , Hochstedler-Kramer Baylie R. , Khemmani Mark , Clark Nina M. , Parada Jorge P. , Farooq Ahmer , Doshi Chirag , Wolfe Alan J. , Albarillo Fritzie S.
Published: October 2024

The impact of chronic indwelling urinary catheters (IUCs) on the composition and stability of the urinary microbiota remains unknown. The primary aim of this study was to describe the urinary microbiomes of geriatric males with chronic IUCs. A secondary aim was to explore clinical catheter-associated urinary tract infection (CAUTI) courses of the participants. Geriatric male patients with chronic IUCs were followed longitudinally. Catheterized urine, catheter tips, and both urethral and periurethral swabs were collected from participants at monthly intervals. Microbes were isolated and identified from each specimen using an enhanced culture method called expanded quantitative urine culture (EQUC) and targeted 16S rRNA gene DNA sequencing. Microbial outcomes were examined both in the absence of urinary symptoms and in the context of clinical diagnosis of CAUTI. Ten male participants (mean age 86 years) were enrolled. Urinary microbiomes differed for each participant. However, within each individual, microbiomes were similar over time and across niches (bladder, catheter, urethra, and periurethra). Within-niche microbiomes differed across individuals, and this was observed over time. The most abundant bacteria isolated from all niches were known uropathogens. Six of 10 individuals met diagnostic criteria for CAUTI at least once during the 12-month observation period, but no evidence of this or antibiotic treatment/response was discernable in our monthly samples. The microbiomes of each participant were unique and remained similar over time and across niches. Longitudinal EQUC or 16S rRNA gene sequencing data could be useful to clinicians when diagnosing or treating possible CAUTI.

IMPORTANCE

Catheter-associated urinary tract infections (CAUTIs) are serious but preventable nosocomial infections. The most common risk factor for developing CAUTI is prolonged use of indwelling urinary catheters (IUCs). This study provides the first longitudinal description of the urinary microbiomes of geriatric males with chronic IUCs, in the absence of urinary signs and symptoms, as a first step toward enhancing our knowledge of the impact of chronic IUCs on the composition and stability of the urinary microbiota. This is an understudied area, particularly for males.
Template plasmids optimized for deletion of multiple genes in yeast
Saccharomyces cerevisiae
Authors: Feng Yi-He , Song Jing-Zhen , Zhu Jing , Xie Zhiping
Published: October 2024

For
Saccharomyces cerevisiae
, gene knockout is routinely performed by transformation with a linear DNA cassette consisting of a selection marker gene flanked by upstream and downstream sequences homologous to a target gene. Over the years, several plasmid sets containing a variety of selection marker genes have been developed. Targeting fidelity under this strategy was high when performing the first gene knockout in a strain. However, we found that targeting fidelity decreased substantially when performing subsequent gene knockouts. The majority of the transformants were “incorrect,” in which the new selection marker gene replaced a pre-existing selection marker gene instead of its intended target. This was caused by the presence of shared regions in the knockout DNA cassettes. To minimize shared regions among knockout cassettes, we developed a set of template plasmids, in which each selection marker open reading frame is flanked by a unique promoter/terminator combination. Our SJZ series templates cover eight selection markers, namely,
URA3
(
C. a
.),
TRP1
(
K.l
.),
his5
(
S.p
.),
LEU2
(
K.l
.),
nat
,
hph
,
kan
, and
amdS
. When using our templates, targeting fidelity in subsequent gene knockouts was restored to as high as that of the first knockout, with essentially all the transformants being correct. Our templates can therefore bring efficiency improvements in future research projects involving multi-gene knockouts.

IMPORTANCE

When knocking out multiple genes in yeast, recombination among selection markers produces a large portion of false-positive transformants. We developed a new set of templates designed to minimize shared regions among selection markers. The use of this new template set resulted in essentially all transformants being correct knockouts.
Method to apply temporal graph analysis on electronic patient record data to explore healthcare professional–patient interaction intensity: a cohort study
Authors: Booth John , Eriksson Maria H , Marks Stephen D , Bryant William A , Denaxas Spiros , Pope Rebecca , Sebire Neil J
Published: October 2024

Aim

Interactions between patients and healthcare professionals (HCP) during hospital admissions are complex and difficult to interrogate using traditional analysis of electronic patient record (EPR) data. The objective of this study was to determine the feasibility of applying temporal network analytics to EPR data, focusing on HCP–patient interactions over time.

Method

Network (graph) analysis was applied to routinely collected structured data from an EPR for HCP interactions with individual patients during admissions for patients undergoing renal transplantation between May 2019 and June 2023. Networks were constructed per day of admission within a session, defined by whether the patient was in the intensive care unit (ICU) or standard hospital ward. Connections between HCP were defined using a 60 min period. Reports were generated visualising daily interaction network structures, across individual admissions.

Results

2300 individual networks were constructed from 127 hospital admissions for renal transplantation. The number of nodes or HCP per network varied from 2 to 45, and network metrics provided detail regarding variation in the density and transitivity, changes in structure with different diameters and radii, and variations in centralisation. Each network analysis metric has a contribution to play in describing the dynamics of a daily HCP network and the composite findings provide insights that cannot be determined with standard approaches.

Conclusions

Network analysis provides a novel approach to investigate and visualise patterns of HCP–patient interactions which allow for a deeper understanding of the complex nature of hospital patient care and could have numerous practical operational applications.
Paradoxical intention as a treatment for insomnia disorder: study protocol for a mixed-methods pilot trial
Authors: Salim Osame , Jansson-Fröjmark Markus , Sandlund Christina , Norell Annika
Published: October 2024

Introduction

Paradoxical intention (PI) is an insomnia treatment developed in the 1970s, which instructs patients to gently attempt to remain awake while in bed at night with the lights off. Previous research indicates PI’s potential in improving insomnia, although no study has been conducted in the last few decades during which the insomnia diagnostic criteria have changed. Additionally, there are knowledge gaps regarding outcomes related to wake after sleep onset, the treatment mechanisms as well as the acceptability and feasibility of the treatment. This study therefore aims to address these gaps by assessing the potential mechanisms, preliminary efficacy, and patient experience and acceptability of PI.

Methods and analysis

We aim to include 40 adult participants with insomnia, aged 18 and above, from the Swedish general population. In this uncontrolled pilot study using a mixed-methods approach, both qualitative and quantitative data will be collected. The trial will be conducted on a self-help online platform, accessible from participants’ homes, with weekly phone call support by therapists. Process and outcome measures will be assessed weekly across a 4-week intervention period and at a 3-month follow-up. A subset of participants will be asked to participate in qualitative semistructured interviews regarding the treatment.

Ethics and dissemination

Ethical approval for this project has been granted by the Swedish Ethical Review Authority (Dnr: 2023-06594-01). All participants will sign informed consent forms on a web service application prior to enrolment. From this mixed-methods study, we anticipate insights into the preliminary efficacy and mechanisms of paradoxical intention for treating insomnia, enriched by patient experience data. Results will be disseminated through peer-reviewed publications. The findings will inform adaptations to the treatment protocol and serve as groundwork for a possible larger scale randomised controlled trial.

Trial registration number

NCT06259682.
Longitudinal frailty assessment in the prediction of survival among patients with advanced chronic kidney disease: a prospective observational single-centre cohort study
Authors: Kennard Alice , Richardson Alice , Rainsford Suzanne , Hamilton Kelly , Glasgow Nicholas , Pumpa Kate , Douglas Angela , Talaulikar Girish Scricant
Published: October 2024

Objectives

This study aims to describe the prevalence, characteristics and longitudinal changes in frailty among outpatient chronic kidney disease (CKD) and haemodialysis (HD) populations and their impact on survival.

Design

Prospective observational cohort study.

Setting

Single-centre ambulatory tertiary care setting, metropolitan Australian teaching hospital.

Participants

Adult patients with advanced CKD (defined as estimated glomerular filtration rate <20 mL/min) or undergoing maintenance HD. Consent model was informed opt-out consent.

Interventions

Fried frailty assessment at baseline, 6 months and 12 months of longitudinal follow-up.

Primary outcomes

All-cause mortality and kidney transplantation events.

Results

Frailty was identified in 36.3% of the 256 participants, while an additional 46.5% exhibited prefrailty. Frailty was equally common among CKD and HD cohorts. Frailty outperformed age, comorbidity and laboratory parameters in predicting mortality risk with HR 2.83 (95% CI 1.44 to 5.56, p<0.001). Frailty also substantially reduced access to transplantation. While most participants exhibited static Fried phenotype over longitudinal assessment, improvements in frailty were observed as frequently as frailty progression. Female gender and symptom burden predicted frailty progression.

Conclusions

Frailty is highly prevalent and closely aligned with survival outcomes. Frailty among patients attending routine outpatient care may demonstrate responsiveness to intervention with subsequent improvements in mortality and other patient-level outcomes.
Transient Ischaemic attack Emergency Referral (TIER): randomised feasibility trial results
Authors: Watkins Alan , Jones Jenna Katherine , Ali Khalid , Dewar Richard , Edwards Adrian , Evans Bridie Angela , Evans Lyn , Ford Gary A , Hampton Chelsey , John Roger , Jones Charlene , Moore Chris , Obiako Michael , Porter Alison , Pryce Alan , Quinn Tom , Seagrove Anne C , Snooks Helen , Whitman Shirley , Rees Nigel
Published: October 2024

Background

Early assessment of patients with suspected transient ischaemic attack (TIA) is crucial to provision of effective care, including initiation of preventive therapies and identification of stroke mimics. Many patients with TIA present to emergency medical services (EMS) but may not require hospitalisation. Paramedics could identify and refer patients with low-risk TIA, without conveyance to the ED. Safety and effectiveness of this model is unknown.

Aim

To assess the feasibility of undertaking a fully powered randomised controlled trial (RCT) to evaluate clinical and cost-effectiveness of paramedic referral of patients who call EMS with low-risk TIA to TIA clinic, avoiding transfer to ED.

Methods

The Transient Ischaemic attack Emergency Referral (TIER) intervention was developed through a survey of UK ambulance services, a scoping review of evidence of prehospital care of TIA and convening a specialist clinical panel to agree its final form. Paramedics in South Wales, UK, were randomly allocated to trial intervention (TIA clinic referral) or control (usual care) arms, with patients’ allocation determined by that of attending paramedics.

Predetermined progression criteria considered: proportion of patients referred to TIA clinic, data retrieval, patient satisfaction and potential cost-effectiveness.

Results

From December 2016 to September 2017, eighty-nine paramedics recruited 53 patients (36 intervention; 17 control); 48 patients (31 intervention; 17 control) consented to follow-up via routine data. Three intervention patients, of seven deemed eligible, were referred to TIA clinic by paramedics. Contraindications recorded for the other intervention arm patients were: Face/Arms/Speech/Time positive (n=13); ABCD2 score >3 (n=5); already anticoagulated (n=2); crescendo TIA (n=1); other (n=8). Routinely collected electronic health records, used to report further healthcare contacts, were obtained for all consenting patients. Patient-reported satisfaction with care was higher in the intervention arm (mean 4.8/5) than the control arm (mean 4.2/5). Health economic analysis suggests an intervention arm quality-adjusted life-year loss of 0.0094 (95% CI −0.0371, 0.0183), p=0.475.

Conclusion

The TIER feasibility study did not meet its progression criteria, largely due to low patient identification and referral rates. A fully powered RCT in this setting is not recommended.

Trial registration number

ISRCTN85516498.