bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progression of
ampC
amplification during
de novo
amoxicillin resistance development in
E. coli
Authors: Nong Luyuan , Jonker Martijs , de Leeuw Wim , Wortel Meike T. , ter Kuile Benno 
Published: December 2024

ABSTRACT

Beta-lactam antibiotics are the most applied antimicrobials in human and veterinarian health care. Hence, beta-lactam resistance is a major health problem. Gene amplification of AmpC beta-lactamase is a main contributor to
de novo
β-lactam resistance in
Escherichia coli
. However, the time course of amplification and the accompanying DNA mutations are unclear. Here, we study the progression of
ampC
amplification and
ampC
promoter mutations during the evolution of resistance induced by stepwise increasing amoxicillin concentrations.
AmpC
promoter mutations occurred by day 2, while the approximately eight-fold amplification occurred after more than 6 days of amoxicillin exposure. The combination of the amplification and the promoter mutations increased the
ampC
mRNA level by an average factor of 200 after 22 days. An IS
1
insertion is identified in the amplification junction after resistance induction in the wild type (WT) and the
ampC
gene complementation strain (CompA), but not in ∆
ampC
, suggesting that the amplification depends on mobile genetic element transposition. In order to elucidate the correlation between gene mutations and
ampC
amplification, the DNA mutations acquired during resistance evolution by the WT, ∆
ampC
, and CompA were analyzed. Compared to evolved ∆
ampC
, several resistance-causing mutations are absent in evolved WT, while more mutations accumulated in stress response. The amoxicillin-resistant ∆
ampC
did not show amplification of the fragment around the original
ampC
position but exhibited a large duplication or triplication at another position, suggesting the essential role of the duplicated genes in resistance development.

IMPORTANCE

Amoxicillin is the most used antimicrobial against bacterial infections. DNA fragments containing
ampC
are amplified upon prolonged and stepwise increasing exposure to amoxicillin, causing resistance. These
ampC
-containing fragments have been identified in extended-spectrum beta-lactamase plasmids, which are considered the main cause of beta-lactam resistance. In this study, we document the time course of two important factors for
ampC
transcription enhancement,
ampC
amplification and
ampC
promoter mutations, during
de novo
amoxicillin resistance evolution. We propose that the transposon IS
1
contributes to the amplification
ampC
region, that the sigma factor 70 regulates
ampC
overexpression, and that these combined form the backbone of a putative mechanism for
ampC
amplification.
Genome sequence of
Vibrio harveyi
strain TUMSAT-2019, isolated from kuruma shrimp,
Penaeus japonicus
Authors: Yuasa Hajime , Koiwai Keiichiro , Konishi Kayo , Furukawa Miho , Nozaki Reiko , Kondo Hidehiro , Hirono Ikuo 
Published: December 2024

ABSTRACT

The Gram-negative bacterium
Vibrio harveyi
is a serious shrimp pathogen. Here, we present the genome sequence of
Vibrio harveyi
TUMSAT-2019, which was isolated from a kuruma shrimp (
Penaeus japonicus
) that originated from a shrimp farm in Okinawa Prefecture. The assembly totaled 5.7 Mbp, consisting of two chromosomes with no plasmid.
mtlA,
a novel typing gene offering enhanced resolution for pandemic
Vibrio
species
Authors: Zhou Lei , Liu Danlei , Zhang Zilong , Zhu Yongqiang , Zheng Huajun 
Published: December 2024

ABSTRACT

The gene
mtlA
, encoding the mannitol transporter subunit IICBA of the phosphotransferase system, was the core gene with the greatest variability in
Vibrio parahaemolyticus
and could be used as a new typing marker in
Vibrio parahaemolyticus
. To expand its application, we performed an evolutionary analysis and found that the
mtlA
gene was present in nine phyla, 371 genera, and 1,662 species of bacteria. It is commonly found in pathogenic species of
Vibrio
, followed by
Paenibacillus
,
Mycolicibacterium
, etc. To investigate whether the
mtlA
gene could serve as a novel typing gene for whole
Vibrio
species, we compared the typing effect of the
mtlA
gene with multilocus sequence type (MLST) in 13 common pathogenic
Vibrio
species. The results revealed that the
mtlA
gene was present in all common pathogenic species, providing comparable or even higher typing resolution than MLST, especially in
Vibrio cholerae
,
Vibrio alginolyticus
,
Vibrio harveyi
, and
Vibrio anguillarum
, enabling accurate typing and traceability; however, many species lacked allelic profiles of MLST genes, making it impossible to obtain accurate STs. In summary, these findings validated the potential typing application of the
mtlA
gene in
Vibrio
species.

IMPORTANCE

Vibrio
is a collection of gram-negative bacteria characterized by possessing two chromosomes, which exhibit numerous shared biological and genomic traits. Around 13 species of
Vibrio
are known to cause infections in humans. Without appropriate medical interventions, the consequences of these infections can escalate to become life-threatening. Therefore, based on the prevalent characteristics of pathogenic
Vibrio
, it is imperative for us to classify and trace various
Vibrio
species that cause human illness and prescribe medication rationally to control the spread of diseases. In our investigation, we explored the prevalence and typing accuracy of the
mtlA
gene in
Vibrio
. Our findings revealed its ubiquitous presence across typical pathogenic
Vibrio
species, offering superior typing efficacy compared with MLST and more extensive implications.
Supplemental Material: Geochemical transition from Miocene–Pliocene to Quaternary arc volcanism in the northern Sierra Nevada, California
Authors: Stoffers Albert J. 
Published: December 2024

<div>Supplemental File S1: Map showing locations of previous K-Ar and <sup>40</sup>Ar/<sup>39</sup>Ar age determinations on volcanic rocks; Supplemental File S2: Sagehen Volcanic Center Rock unit descriptions (Fig. 3 map units); Supplemental File S3: <sup>40</sup>Ar/<sup>39</sup>Ar ages, Sagehen Field Station Area, with plateau and isochron diagrams; Supplemental File S4: Analytical techniques at Washington State University and University of Kansas Radiogenic Isotope Laboratory analytical procedures; Supplemental File S5: All samples; Supplemental File S6: Major, trace element, and radiogenic isotope data for Mesozoic Sierra Nevada granitoids of the North Sierra segment; and Supplemental File S7: Estimates of analytical precision from repeat analyses of internal and international rock standards. </div>
Beta-cell, but not autonomic nervous system, function is related to MAFLD in early stages of glucose intolerance
Authors: Dimova Rumyana , Chakarova Nevena , Serdarova Mina , Marinova Cvetelina , Popov Dimitar , Del Prato Stefano , Tankova Tsvetalina 
Published: December 2024

IntroductionPrevious studies have suggested an association between beta-cell and autonomic function and metabolic-associated fatty liver disease (MAFLD). We explored the association between controlled attenuated parameter (CAP) and insulin secretion and action, as well as sympathetic and parasympathetic activity in normal (NGT) and impaired (IGT) glucose tolerance.Research design and methodsTwenty-five NGT (age 44.8±9.6 years; body mass index (BMI) 32.3±6.9 kg/m2) and 27 IGT (47.6±11.8 years; 31.0±6.5 kg/m2) subjects underwent a 75 g oral glucose tolerance test (OGTT) and a mixed meal tolerance test (MMTT) for assessment of glucose and insulin secretion. Parameters of beta-cell function and insulin sensitivity were calculated. Body composition was assessed by bioimpedance analysis (Inbody720). Autonomic function was assessed by ANX V.3.0 monitoring system. CAP was determined by Fibroscan (Echosense) and presence of MAFLD was defined as CAP >233 dB/m.ResultsA CAP >233 dB/m was found in 72% of subjects with NGT and 67% of subjects with IGT. Subjects with MAFLD, irrespective of glucose tolerance, had higher BMI and waist circumference, lower insulin secretion and action, and lower parasympathetic activity. On a matrix analysis, after adjustment for age and BMI, CAP was positively related to systolic blood pressure (SBP); insulin action was negatively related to parasympathetic activity. Regression analysis showed that AUC-insulin MMTT remained independently related to MAFLD: OR 24.4 (95% CI 2.17 to 274.77; p=0.010). A “cut-off” value of 15,620 uIU/mL-1*180 min-1provided a 75% sensitivity and 75% specificity for CAP >233 dB/m.ConclusionsOur results do not support a role for parasympathetic activity in MAFLD. Rather, they show that stimulated hyperinsulinemia may be associated with greater risk of MAFLD irrespective of glucose tolerance in a high-risk population without diabetes.
Retrospective derivation of a causal pathway for diabetic ketoacidosis in adult patients with type 2 diabetes mellitus
Authors: Kline Jeffrey A , Wesner Nicholas A , Sharif Amina T , Griffey Richard T , Levy Phillip D , Welch Robert D , Grunberger George 
Published: December 2024

BackgroundType 2 ketone-prone diabetes mellitus (T2KPDM) is thought to occur in men of African descent, with obesity who experienced prolonged hyperglycemia; the role of medication non-adherence as a contributing cause remains unstudied.Research design and methodsThis was a retrospective study of unique adults (>18 years) who sought emergency care one of four hospitals in the greater Detroit area. Patients were identified on the basis of a laboratory order for a ß-hydroxybutyrate concentration. Two research coordinators abstracted 119 data fields. Patients were divided into four phenotypes: (1) no prior DM, (2) type 2 DM without prior ketosis, (3) type 2 with prior ketosis and (4) type 1 DM. A ß-hydroxybutyrate >20 mg/dL defined diabetic ketoacidosis (DKA). A directed acyclic graph was constructed to diagram a causal pathway.ResultsOf 450 patients, 326 were non-type I and 37% of these had DKA. Concentrations of ß-hydroxybutyrate, glucose, bicarbonate were not different between non-type1 versus type 1 DM patients. Admission rates to the ICU and hospital lengths of stay were similar between the four phenotypes with DKA. We found no association with sex, race or body mass index. Unadjusted odds for DKA were significant for non-adherence (odds=1.74, 95% CI 1.08 to 2.21) arrival by Emergency Medical Services (odds=0.54, 95% CI 0.33 to 0.86) and private or Medicare insurance (odds=6.80, 95% CI 4.00 to 11.60). The median HbA1C was statistically higher in patients with DKA (median 11.3%) versus those without DKA (median 9.5%, Mann-Whitney U p<0.001) and was also higher in patients with a history of non-adherence. In multivariable analysis, non-adherence was found to be a mediator of DKA with T2KPDM.Conclusionsin Detroit, MI, prior ketosis and private or Medicare health insurance were significantly associated with new or recurrent DKA in T2KPDM. Medication non-adherence had a mediating role.
Enabling precise predictions for left-right symmetry at colliders
Authors: Kriewald Jonathan , Nemevšek Miha , Nesti Fabrizio 
Published: December 2024

Abstract
We investigate the structure of the minimal left-right symmetric model that enables precise predictions in the gauge, scalar and neutrino sector. We revisit the complete set of mass spectra and mixings for the charged and neutral gauge bosons, would-be-Goldstones and gauge fixing, together with the ghost Lagrangian. In the scalar sector, we analytically re-derive all the massive states with mixings and devise a non-trivial physical input scheme, expressing the model couplings in terms of masses and mixing angles. Fermion couplings are also determined in closed form, including the Dirac mixing in the neutrino sector, evaluated explicitly using the Cayley–Hamilton theorem. These analytic developments are implemented in a comprehensive FeynRules model file. We calculate the one loop QCD corrections and provide a complete UFO file for NLO studies, demonstrated on relevant hadron-collider benchmarks. We provide various restricted variants of the model file with different gauges, massless states, neutrino hierarchies and parity violating

$$g_L \ne g_R$$

g
L

≠

g
R

gauge couplings.
Astrophysical insights into magnetic Penrose process around parameterized Konoplya–Rezzolla–Zhidenko black hole
Authors: Xamidov Tursunali , Shaymatov Sanjar , Sheoran Pankaj , Ahmedov Bobomurat 
Published: December 2024

Abstract
In this study, we investigate the parameterized Konoplya–Rezzolla–Zhidenko (KRZ) black hole (BH) spacetime in the presence of an external asymptotically uniform magnetic field. We first examine the innermost stable circular orbit (ISCO) radii for both neutral and charged test particles, demonstrating that the deformation parameters,

$$\delta _1$$

δ
1

and

$$\delta _2$$

δ
2

, reduce the ISCO values. Subsequently, we assess the energy efficiency of the magnetic Penrose process (MPP) for an axially symmetric parameterized BH, analyzing the effects of the deformation parameters and the magnetic field on the energy extraction process. Our findings indicate that the rotational deformation parameter

$$\delta _2$$

δ
2

is crucial for the efficiency of energy extraction from the BH. The synergy between the rotational deformation parameter and the magnetic field significantly boosts the energy extraction efficiency, with values exceeding

$$100\%$$

100
%

. Interestingly, for extremal BHs with negative

$$\delta _2$$

δ
2

values, the energy efficiency increases, in contrast to Kerr BHs where the MPP effect diminishes. Additionally, we explore the astrophysical implications of the MPP by deriving the maximum energy of a proton escaping from the KRZ parameterized BH due to the beta decay of a free neutron near the horizon. Our results show that negative

$$\delta _2$$

δ
2

values require stronger magnetic fields to achieve equivalent energy levels for high-energy protons, providing deeper insights into high-energy astrophysical phenomena around the parameterized BH.
Possible signal of an exotic $$I=1$$, $$J=2$$ state in the $$B \rightarrow D^{*-}D^+K^+$$ reaction
Authors: Lyu Wen-Tao , Duan Man-Yu , Xiao Chu-Wen , Wang En , Oset Eulogio 
Published: December 2024

Abstract
We study the

$$B^+ \rightarrow D^{*-}D^+K^+$$

B
+

→

D

∗
-

D
+

K
+

reaction, showing that a peak in the

$$D^+K^+$$

D
+

K
+

mass distribution around

$$2834 \text { MeV}$$

2834

MeV

reported by LHCb could be associated with a theoretical exotic state with that mass, a width of

$$19 \text { MeV}$$

19

MeV

and

$$J^P=2^+$$

J
P

=

2
+

, stemming from the interaction of the

$$D^{*+}K^{*+}$$

D

∗
+

K

∗
+

and

$$D^{*+}_s \rho ^+$$

D
s

∗
+

ρ
+

channels, which is a partner of the

$$0^+$$

0
+

$$T_{c{\bar{s}}}(2900)$$

T

c

s

¯

(
2900
)

. We show that the data is compatible with this assumption, but also see that the mass distribution itself cannot discriminate between the spins

$$J=0$$

J
=
0

, 1, 2 of the state. Then we evaluate the momenta of the angular mass distribution and show that they are very different for each of the spin assumptions, and that the momenta coming from interference terms have larger strength at the resonant energy than the peaks seen in the angular integrated mass distribution. We make a call for the experimental determination of these magnitudes, which has already been used by the LHCb in related decay reactions.
Memento Filter: A Fast, Dynamic, and Robust Range Filter
Authors: Eslami Navid , Dayan Niv 
Published: December 2024

Range filters are probabilistic data structures that answer approximate range emptiness queries. They aid in avoiding processing empty range queries and have use cases in many application domains such as key-value stores and social web analytics. However, current range filters do not support dynamically changing and growing datasets. Moreover, several of these designs also exhibit impractically high false positive rates under correlated workloads, which are common in practice. These impediments restrict the applicability of range filters across a wide range of use cases.
We introduce Memento filter, the first range filter to simultaneously offer dynamicity, fast operations, and a robust false positive rate for any workload. Memento filter partitions the key universe and clusters its keys according to this partitioning. For each cluster, it stores a fingerprint and a list of key suffixes contiguously. The encoding of these lists makes them amenable to existing dynamic filter structures. Due to the one-to-one mapping from keys to suffixes, Memento filter supports inserts and deletes and can even expand to accommodate a growing dataset.
We implement Memento filter on top of a Rank-and-Select Quotient filter and InfiniFilter and demonstrate that it achieves a competitive false positive rate and performance with the state of the art while also providing dynamicity. Due to its dynamicity, Memento filter is the first range filter applicable to B-Trees. We showcase this by integrating Memento filter into WiredTiger, a B-Tree-based key-value store, significantly boosting its performance for mixed workloads.
Holographic Storage for the Cloud: advances and challenges
Authors: Cheriere Nathanaël , Chu Jiaqi , Brennan Grace , Cameron Pashmina , Da Costa Pedro , Gladrow Jannes , Ilunga Guilherme , Kelly Douglas , Lewis Sarah , Lim Joowon , Maltese Giorgio , Mason Tony , O'Shea Greg , Ponnapalli Soujanya , Rudow Michael , Sanders Alan , Stavrinos Theano , Wu Xingbo , Yang Mengyang , Narayanan Dushyanth , Thomsen Benn , Rowstron Antony 
Published: December 2024

Holographic Storage is an old idea that has always promised high density and fast random access, but has never been commercially competitive with Hard Disk Drives (HDDs) and Solid State Devices (SSDs). In Project HSD at Microsoft Research we asked the question: “Does holographic storage finally make sense for cloud storage?” This article describes our journey toward answering this question.
We achieved 1.8× higher density than the previous state-of-the-art, using commodity components available today and leveraging machine learning to compensate for the noise and distortions introduced by commodity components. This uncovered two new challenges which are the focus of this article: achieving high end-to-end energy efficiency without sacrificing capacity, and spatial multiplexing without mechanical movement.
Improving end-to-end energy efficiency requires joint optimization across low-level media parameters and higher-level system parameters that govern background maintenance operations such as read refresh and garbage collection. We developed new physics models of the media; analytic and simulation models of the media access and background media maintenance; and workload-driven optimization to find optimal parameter combinations. These techniques resulted in a 14× improvement over the previous approach for typical workloads without sacrificing capacity. We also designed the first scalable and mechanical movement free spatial multiplexing system for holographic storage.
Despite these advances, we conclude that currently, holographic storage is still far from the combination of density, capacity scaling, and energy efficiency needed to compete with the incumbent technologies. We need fundamental advances in the physical media that improve energy efficiency by another 1–2 orders of magnitude without reducing data density. Further advances in optics are also required to achieve spatial multiplexing that is simultaneously scalable, low-loss, and high-density.
Clinical Characteristics and Prognostic Factors of COVID‐19 Patients Admitted to the National Treatment Center in The Gambia
Authors: Bittaye Sheikh Omar , Jagne Abubacarr , Iddrisu Abdul-Karim , Njie Ramou , Jaiteh Lamin ES , Nyan Ousman , Jobe Ya Fatou BM , Joof Sidat , Joof Sohna , Danso Morrikebba , Bah Ebrima , Cham Musa , Roberts Charles , Bittaye Mustapha 
Published: December 2024

Background and Aims: Information regarding the clinical features and outcomes of severely ill COVID‐19 patients in low‐resource settings is limited. The objective of this study was to evaluate the clinical characteristics, comorbidities, and prognostic factors associated with mortality and COVID‐19 severity among COVID‐19 patients admitted to the national COVID‐19 treatment center in The Gambia.Methods: We conducted a retrospective cross‐sectional study on 930 confirmed COVID‐19 patients admitted to The Gambia’s national COVID‐19 treatment center from March 17, 2020, to March 13, 2023. We assessed the association between patients’ characteristics using the t‐test and the chi‐square test. Prognostic factors of mortality and COVID‐19 severity were investigated using a multivariable logistic regression model. Statistical analyses were performed using the STATA/SE 12.1 statistics/data analysis.Results: Patients with COVID‐19 who had a saturation of peripheral oxygen (SPO2) level below 90 (severe COVID‐19) faced a fivefold higher risk of death (adjusted odds ratio [aOR] = 5.15; 95% confidence interval [CI] = 1.08, 24.58; p = 0.040). Additionally, individuals aged 60 years and older had an approximately threefold higher risk of experiencing severe COVID‐19 (aOR = 3.43; 95% CI = 2.30, 5.13; p  < 0.001), while those with comorbidities showed a 60% higher risk of severe disease (aOR = 1.60; 95% CI = 1.07, 2.38; p = 0.021).Conclusion: These findings underscore the importance of early detection and management strategies targeting older patients and those with underlying health conditions to mitigate the impact of COVID‐19 and improve patient outcomes. Future efforts should prioritize tailored interventions and supportive care for these high‐risk populations.
A Long Way From Home: A Rare Case of Cutaneous Metastasis to the Scalp of Hepatocellular Carcinoma
Authors: Eggiman Evan , Dodia Paarth , Dewey Jesse , Munoz-Bishop Melissa , Overton Matthew 
Published: December 2024

Introduction: Cutaneous metastases of hepatocellular carcinoma (HCC) are uncommon but important to recognize for timely diagnosis and management.Case Presentation(s): We present a case of a 70‐year‐old man with a history of HCC who developed a painless nodule on the scalp. Histopathological examination and immunohistochemistry confirmed the nodule as cutaneous metastasis of HCC. The patient had previously undergone transarterial chemoembolization and surgery for HCC, with no evidence of disease for a period before presenting with the cutaneous lesion.Conclusion: Cutaneous metastasis of HCC is rare but signifies advanced disease. This case underscores the importance of considering cutaneous manifestations in patients with a history of HCC and highlights the need for routine follow‐up and early intervention to improve patient outcomes.