bluuebunny/crossref_metadata_2025 huggingface dataset:
Steering witnesses for unknown Gaussian quantum states
Authors: Mihaescu Tatiana , Kampermann Hermann , Isar Aurelian , Bruß Dagmar
Published: November 2023

We define and fully characterize the witnesses based on second moments detecting steering in Gaussian states by means of Gaussian measurements. All such tests, which arise from linear combination of variances or second moments of canonical operators, are easily implemented in experiments. We propose also a set of linear constraints fully characterizing steering witnesses when the steered party has one bosonic mode, while in the general case the constraints restrict the set of tests detecting steering. Given an unknown quantum state we implement a semidefinite program providing the appropriate steering test with respect to the number of random measurements performed. Thus, it is a ‘repeat-until-success’ method allowing for steering detection with less measurements than in full tomography. We study the efficiency of steering detection for two-mode squeezed vacuum states, for two-mode general unknown states, and for three-mode continuous variable GHZ states. In addition, we discuss the robustness of this method to statistical errors.
Extra long phosphorescence in organic materials at cryogenic temperatures investigation
Authors: Tsipenyuk D Yu , Slobodyanin V P , Voropinov A V , Chikin F K
Published: November 2023

In this paper, investigations of extra-long phosphorescence in organic materials and optical crystals at cryogenic temperatures are presented. This study continues the cycle of our previous works devoted to the physical mechanism understanding of the long-run phosphorescence excitation. We wish to create an advanced and efficient laser for the media based on the Shpolsky matrix analogue. Another goal is to consider the possibility of building an optical processor with an extra-long phosphorescence effect. For this purpose we were examining the experimental setup of complicated organic materials: cocamidopropyl betadine C19H38N2O3, polyethylene terephthalate (C10H8O4)
n
, perfluoro (2-methyl-3-pentanone, Novec 649) CF3CF2C(O)CF(CF3)2, Kalosha benzine (benzine BR-2, Nefras С2 80/120). Different optic and piezo crystals were also investigated: gadolinium aluminum gallium garnet Gd3Ga3Al2O12:Ce, lanthanum gallium silicate La3Ga5SiO14, terbium gallium garnet Tb3Ga5O12 , La3Ga5,5Ta0,5O14.
Comparative Analysis of Physiograpic Study for Hydrology of Benowo Region, Surabaya
Authors: Indriani Rista Fitri , Anjasmara Ira Mutiara , Utama Widya , Paramita Eksi Galih Kenya , Nainggolan Rompu Alden Oskanius
Published: November 2023

This study aims to determine the physiographic characteristics according to the slope, land use, and runoff that affect water control in the Benowo area, Surabaya. From the comparison of the results of the runoff in the dry season and the rainy season there was an increase in the average runoff value from 24 % to 26 %. Although there is a difference in the value of the runoff of 2 %, this can affect the increase in water runoff above the surface of the study area. The value of the runoff in the study region will be significantly impacted by changes in land use from agriculture and water to residential or industrial areas. The runoff predicted data’s overall accuracy value for both dry and wet seasons is good, and the Cohen’s kappa value is almost a perfect consistency. The overall accuracy value is 89.7% in the wet season compared to 87.4% in the dry season. During the dry season, the Cohen’s Kappa value is 83.8%, and during the rainy season, it is 86.6%. The result of this research is a preliminary study to study the distribution of rainfall, discharge, and hydrological engineering for development in Benowo area, Surabaya.
Analysis of GNSS and IMU Sensor Data Fusion Using the Unscented Kalman Filter Method on Medical Drones in Open Air
Authors: Navisa S C , Cahyadi M N , Asfihani T
Published: November 2023

Accurate and efficient position estimation is an important element in flight missions for autonomous aerial vehicles such as Unmanned Aerial Vehicles (UAVs). UAVs rely on sensors that provide information regarding position, speed, and orientation. GPS and IMU are sensors that can provide navigation information, where each sensor has characteristics that can complement each other’s shortcomings. Research related to the integration of GPS and IMU sensors for positioning with increasingly higher accuracy has been widely applied, one of which is the Kalman Filter method. Kalman filter not only performs digital signal filtering but is also capable of smoothing and predicting recursion to obtain the most accurate estimation results. Along with the development of the modification of the Kalman Filter, the Unscented Kalman Filter (UKF) method is a solution in overcoming nonlinear systems with estimation results approaching the actual value, so that the positioning accuracy is higher and convergent. This study intends to analyze the fusion performance of GPS and IMU sensor data using the UKF method on Medical Drones in an open space in order to obtain a position with high accuracy. UKF simulations on Medical Drones were carried out using a mathematical model on a 6 DOF (Degree of Freedom) UAV. The sensor data fusion performance was tested by comparing the results of the UKF method with the EKF on the Geopointer software. The results showed that the UKF simulation gave a positional accuracy of 0.022 m to the measurement data. The UKF simulation results in a better positioning accuracy when compared to EKF processing on the Geopointer software which only achieves a position accuracy of 8.467 m. The low accuracy of the EKF processing results is due to the mismatch of the IMU parameters obtained with the actual Medical Drone parameters.
Ability of Palm Kernel Shell Adsorbent in Reducing Mercury (Hg)
Authors: Purwanti I.F. , Titah H.S. , Santoso I.B. , Qotrunnadha Z.
Published: November 2023

One method to reduce the content of heavy metal mercury in wastewater is adsorption. Several media materials have been investigated for use as adsorbents. In this study the characteristics of the palm kernel shell were analysed so that it could be used as an adsorbent. In addition, it also analysed its ability to reduce levels of mercury in wastewater. Palm kernel shells were activated using two types of activators, namely H3PO4 and NaOH and variations in adsorbent sizes of 50 mesh and 100 mesh, as well as variations in contact time for 30 and 60 minutes. Based on the results of this study, it was obtained that the characteristics of the adsorbent of palm kernel shells with the use of H3PO4 and NaOH activators met the quality based on SNI 06-330-95. The adsorption efficiency of mercury (Hg) removal can reach 99.7% with a contact time of 60 minutes and an adsorbent size of 100 mesh activated by NaOH.
Potential of Plastic Waste Leakage to Environment in Indonesian Final Disposal
Authors: Ramadan A H , Sembiring E
Published: November 2023

The majority of developing nations still utilize landfills as their primary method of disposing of municipal solid waste (MSW), and Indonesia is no exception to this technology. On the other hand, landfill contributes a significant fraction of plastic in the global environmental leakage from mismanaged landfill and open dumping site in Asian countries. Furthermore, Indonesia has a long history of landfill mismanagement and open dumping. The loss of plastic to the environment could lead to multisectoral impacts on the health, environment, and economy. In this paper, we analyze the current situation of landfill and the potential of plastic waste leakage from landfills to the environment using systematic review and metadata analysis using GIS in Indonesia. In addition, this study analyses potential plastic leakage based on the distance to the waterways, leachate treatment facility and landfill facility. Based on the analysis, only around 11% of the landfill were claimed as sanitary landfill, yet only 3% operated based on the sanitary landfill standard of Indonesia after the analysis. The controlled landfill is also implemented in Indonesia at around 52%, and open dumping is around 37% of total final disposal. Based on the GIS analysis, more than 20% of landfill in Indonesia are near the waterways, which increase the potential for plastic leakage. Policymakers can use the resulting study to identify and prioritise ways to stop the environmental leakage of plastics from landfills.
Socio-behavioral assessment of household solid waste management: The case of Barangay Calicanto, Philippines
Authors: Treyes A C , Osorio E , Tanchuling M A , Andal M D , Requejo B , Inocencio B , Panopio C
Published: November 2023

The cycle of waste generation, segregation, disposal, and recovery is highly dependent on varying human activities and their awareness towards solid waste management (SWM). This study presents the first reported socio-behavioral assessment focusing on the households in a city in the Philippines to bridge the intention-action gap of SWM stakeholders by imploring socio-behavioral change communication activities through the trials of improved practices (TIPs). Findings reveal the significant contribution of women in household waste management responsibilities, highlighting their active participation in SWM initiatives. Analysis of short-term and long-term committed and accomplished actions demonstrated the willingness of the households to adopt sustainable waste management practices. Collective action of policymakers, waste management authorities, and stakeholders should consider the dynamics within households including their financial capacities, provide education and support, develop waste management infrastructures and systems, and create conducive conditions for behavioral change.
Solid waste characterization at Tanjungan dam ecovillage, Mojokerto, Indonesia
Authors: Tarigan E , Simangunsong T L , Athaya A A , Parapaga P D P
Published: November 2023

The aims of the study are to present waste composition and improve waste management at the tourism destination of Tanjungan Dam Ecovillage, Mojokerto. The sampling and interviews were conducted for estimating the characterization and management practice of solid waste. The results showed that the tourism destination generated solid waste of around 18.82 kg/day. The generation rate of organic waste was 1.68 kg/day and 5.94 kg/day of inorganic,. Another waste generated from this destination is yard waste, which was around 11.2 kg daily. The result of the interview with the ecovillage officers presented that the awareness of waste management was still low. The solid waste management of the ecovillage was collect-transport-dispose with low rates and efficiency. Furthermore, there is no segregation of the waste, no control of inorganic waste, no regular schedule of yard waste collection, and no education for the tourists to rising their awareness about solid waste. To improve the solid waste management system and ensure the ecovillage’s sustainability, these facts had to be overcome.
Bayesian parameter estimation for characterising mobile ion vacancies in perovskite solar cells
Authors: McCallum Samuel G , Nicholls Oliver , Jensen Kjeld O , Cowley Matthew V , Lerpinière James E , Walker Alison B
Published: November 2023

To overcome the challenges associated with poor temporal stability of perovskite solar cells, methods are required that allow for fast iteration of fabrication and characterisation, such that optimal device performance and stability may be actively pursued. Currently, establishing the causes of underperformance is both complex and time-consuming, and optimisation of device fabrication is thus inherently slow. Here, we present a means of computational device characterisation of mobile halide ion parameters from room temperature current–voltage (

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) measurements only, requiring ∼2 h of computation on basic computing resources. With our approach, the physical parameters of the device may be reverse-modelled from experimental

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measurements. In a drift-diffusion (DD) model, the set of coupled DD partial differential equations cannot be inverted explicitly, so a method for inverting the DD simulation is required. We show how Bayesian Parameter Estimation coupled with a DD perovskite solar cell model can determine the extent to which device parameters affect performance measured by

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characteristics. Our method is demonstrated by investigating the extent to which device performance is influenced by mobile halide ions for a specific fabricated device. The ion vacancy density N
0 and diffusion coefficient DI
were found to be precisely characterised for both simulated and fabricated devices. This result opens up the possibility of pinpointing origins of degradation by finding which parameters most influence device

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curves as the cell degrades.
Interactions with fungi vary amongTripsacum dactyloidesgenotypes from across a precipitation gradient
Authors: Kural-Rendon Ceyda , Ford Natalie E , Wagner Maggie R
Published: November 2023

Plant-associated microbes, specifically fungal endophytes, augment the ability of many grasses to adapt to extreme environmental conditions. Tripsacum dactyloides (Eastern gamagrass) is a perennial, drought-tolerant grass native to the tallgrass prairies of the central USA. The extent to which the microbiome of T. dactyloides contributes to its drought tolerance is unknown. Ninety-seven genotypes of T. dactyloides were collected from native populations across an east–west precipitation gradient in Kansas, Oklahoma and Texas, and then grown together in a common garden for over 20 years. Root and leaf samples were visually examined for fungal density. Because fungal endophytes confer drought-tolerant capabilities to their host plants, we expected to find higher densities of fungal endophytes in plants from western, drier regions, compared to plants from eastern, wetter regions. Results confirmed a negative correlation between endophyte densities in roots and precipitation at the genotype’s original location (r = −0.21 P = 0.04). Our analyses reveal that the host genotype’s origin along the precipitation gradient predicts the absolute abundance of symbionts in the root, but not the relative abundances of particular organisms or the overall community composition. Overall, these results demonstrate that genetic variation for plant–microbe interactions can reflect historical environment, and reinforce the importance of considering plant genotype in conservation and restoration work in tallgrass prairie ecosystems.
Telescopic peristomes, hygroscopic movement and the spore release model of Regmatodon declinatus (Leskeaceae Bryophyta)
Authors: Wu Yanzhi , Wang Zhihui , Zhang Zhaohui
Published: November 2023

Moss peristome hygroscopic movement plays an important role in protecting and controlling spore release. Recent studies on the peristome’s hygroscopic movement and spore release have focussed on mosses with ‘perfect’ peristomes, such as Brachytheciaceae, whereas the hygroscopic movement type and spore release pattern of ‘specialized’ peristomes, such as Regmatodon declinatus, are poorly understood. We investigated the relationship between the peristome’s hygroscopic movement and spore release in the ‘specialized’ peristome of R. declinatus by the measurement of peristome hygroscopic movement parameters and the hygroscopic movement spore release test. It was found that: (i) Exostomes (EX) are significantly shorter than endostomes (EN), triggering the hygroscopic movement of telescopic peristomes, in which the EX rapidly elongate while closing in on the EN, and the teeth rapidly converge. (ii) Spore release was minimal when peristome movement was triggered alone. The number of spores released when exposed to wind was 124 times greater than in the absence of wind. Dry capsules released seven times more spores than wet capsules. The study reveals that the hygroscopic movement of ‘telescopic’ peristomes of R. declinatus did not contribute significantly to spore release. More spores were released when wind and hygroscopic movement acted synergistically. Dry capsules released the maximum number of spores. It was also revealed that structural damage to capsules can facilitate complete spore release. Finally, we modelled the release of R. declinatus spores from initiation to complete release, namely the coupled release model of wind-water-capsule structural damage.
Serum starvation-based method of ovarian cancer cell dormancy induction and termination in vitro
Authors: Rutecki Szymon , Leśniewska-Bocianowska Agnieszka , Chmielewska Klaudia , Matuszewska Julia , Naumowicz Eryk , Uruski Paweł , Radziemski Artur , Mikuła-Pietrasik Justyna , Tykarski Andrzej , Książek Krzysztof
Published: November 2023

Awakening and growth reinitiation by dormant cells may contribute to epithelial ovarian cancer (EOC) relapse. The links between these phenomena are loose because of the limited stock of compelling models of EOC dormancy. Here, we show a simple and convenient dormancy research protocol based on serum starvation. This study was conducted on established EOC cell lines A2780, OVCAR-3, and SKOV-3, as well as on primary EOC cells. Cell growth arrest and proliferation were monitored by assessing the Ki67 antigen, PKH26 fluorescence, and cell cycle distribution. In addition, cells were tested for ERK1/2/p38 MAPK activity ratio, apoptosis, and senescence. The study showed that 72-h serum starvation induces G0/G1 growth arrest of a significant fraction of cells, accompanied by reduced Ki67 and ERK1/2/p38 MAPK activity ratio, without signs of apoptosis or cellular senescence. Moreover, providing cells with 72 h of a medium enriched in 5% serum allows the culture to regain its proliferative potential. At the same time, we attempted to induce and terminate dormancy with Mitomycin C addition and withdrawal, which were unsuccessful. In conclusion, serum starvation is a convenient way to reliably induce dormancy in EOC cells, allowing them to be efficiently awakened for further mechanistic research in vitro.
How Simple Maths Can Inform Our Basic Understanding of Phage Therapy
Authors: Abedon Stephen T
Published: November 2023

Phage therapy is the application of bacterial viruses to control and, ideally, to eliminate problematic bacteria from patients. Usually employed are so-called strictly lytic phages, which upon adsorption of a bacterium should give rise to both bacterial death and bacterial lysis. This killing occurs with single-hit kinetics, resulting in relatively simple ways to mathematically model organismal-level, phage-bacterium interactions. Reviewed here are processes of phage therapy as viewed from these simpler mathematical perspectives, starting with phage dosing, continuing through phage adsorption of bacteria, and then considering the potential for phage numbers to be enhanced through in situ phage population growth. Overall, I suggest that a basic working knowledge of the underlying “simple maths” of phage therapy can be helpful toward making dosing decisions and predicting certain outcomes. This especially is during controlled in vitro experimentation but is relevant to thinking about in vivo applications as well.
Towards Standardization of Phage Susceptibility Testing: The Israeli Phage Therapy Center “Clinical Phage Microbiology”—A Pipeline Proposal
Authors: Yerushalmy Ortal , Braunstein Ron , Alkalay-Oren Sivan , Rimon Amit , Coppenhagn-Glazer Shunit , Onallah Hadil , Nir-Paz Ran , Hazan Ronen
Published: November 2023

Using phages as salvage therapy for nonhealing infections is gaining recognition as a viable solution for patients with such infections. The escalating issue of antibiotic resistance further emphasizes the significance of using phages in treating bacterial infections, encompassing compassionate-use scenarios and clinical trials. Given the high specificity of phages, selecting the suitable phage(s) targeting the causative bacteria becomes critical for achieving treatment success. However, in contrast to conventional antibiotics, where susceptibility-testing procedures were well established for phage therapy, there is a lack of standard frameworks for matching phages from a panel to target bacterial strains and assessing their interactions with antibiotics or other agents. This review discusses and compares published methods for clinical phage microbiology, also known as phage susceptibility testing, and proposes guidelines for establishing a standard pipeline based on our findings over the past 5 years of phage therapy at the Israeli Phage Therapy Center.
Use of Bacteriophages to Target Intracellular Pathogens
Authors: Fajardo-Lubian Alicia , Venturini Carola
Published: November 2023

Bacteriophages (phages) have shown great potential as natural antimicrobials against extracellular pathogens (eg, Escherichia coli or Klebsiella pneumoniae), but little is known about how they interact with intracellular targets (eg, Shigella spp., Salmonella spp., Mycobacterium spp.) in the mammalian host. Recent research has demonstrated that phages can enter human cells. However, for the design of successful clinical applications, further investigation is required to define their subcellular behavior and to understand the complex biological processes that underlie the interaction with their bacterial targets. In this review, we summarize the molecular evidence of phage internalization in eucaryotic cells, with specific focus on proof of phage activity against their bacterial targets within the eucaryotic host, and the current proposed strategies to overcome poor penetrance issues that may impact therapeutic use against the most clinically relevant intracellular pathogens.
Phage Therapy in Lung Transplantation: Current Status and Future Possibilities
Authors: Aslam Saima
Published: November 2023

Patients with chronic lung disease and lung transplantation have high rates of colonization and infection from multidrug-resistant (MDR) organisms. This article summarizes the current state of knowledge regarding phage therapy in the setting of lung transplantation. Phage therapy has been used in several lung transplant candidates and recipients on a compassionate use basis targeting mostly MDR gram-negative infections and atypical mycobacterial infections with demonstrated clinical safety. Phage biodistribution given intravenously or via nebulization has not been extensively studied, though preliminary data are presented. Phage interacts with both the innate and adaptive immune system; current literature demonstrates the development of serum neutralization in some cases of phage therapy, although the clinical impact seems variable. A summary of current clinical trials involving patients with chronic lung disease is presented, though none are specifically targeting lung transplant candidates or recipients. In addition to treatment of active infections, a variety of clinical scenarios may benefit from phage therapy, and well-designed clinical trials involving this vulnerable patient population are needed: pre- or peritransplantation use of phage in the setting of MDR organism colonization may lead to waitlisting of candidates currently declined by many centers, along with potential reduction of waitlist mortality rates and posttransplant infections; phage may be used for biofilm-related bronchial stent infections; and, finally, there is a possibility that phage use can affect allograft function and chronic rejection.
Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy
Authors: Grigson Susanna R , Giles Sarah K , Edwards Robert A , Papudeshi Bhavya
Published: November 2023

Bacteriophages, or phages, are viruses that infect bacteria shaping microbial communities and ecosystems. They have gained attention as potential agents against antibiotic resistance. In phage therapy, lytic phages are preferred for their bacteria killing ability, while temperate phages, which can transfer antibiotic resistance or toxin genes, are avoided. Selection relies on plaque morphology and genome sequencing. This review outlines annotating genomes, identifying critical genomic features, and assigning functional labels to protein-coding sequences. These annotations prevent the transfer of unwanted genes, such as antimicrobial resistance or toxin genes, during phage therapy. Additionally, it covers International Committee on Taxonomy of Viruses (ICTV)-an established phage nomenclature system for simplified classification and communication. Accurate phage genome annotation and nomenclature provide insights into phage–host interactions, replication strategies, and evolution, accelerating our understanding of the diversity and evolution of phages and facilitating the development of phage-based therapies.
Eager Term Rewriting For The Fracterm Calculus Of Common Meadows
Authors: Bergstra Jan A , Tucker John V
Published: November 2023

Eager equality is a novel semantics for equality in the presence of partial operations. We consider term rewriting for eager equality for arithmetic in which division is a partial operator. We use common meadows which are essentially fields that contain an absorptive element $\bot $. The idea is that term rewriting is supposed to be semantics preserving for non-$\bot $ terms only. We show soundness and adequacy results for eager term rewriting w.r.t. the class of all common meadows. However, we show that an eager term rewrite system which is complete for common meadows of rational numbers is not easy to obtain, if it exists at all.
Will supplemental cone beam computed tomography change the treatment plan of impacted maxillary canines based on 2D radiography? A prospective clinical study
Authors: Stoustrup Peter , Videbæk Anja , Wenzel Ann , Matzen Louise Hauge
Published: November 2023

Aim

To evaluate the impact of cone beam computed tomography (CBCT) on treatment planning for impacted maxillary canines; secondly, to identify CBCT factors influencing a change in the treatment plan; and thirdly, to assess 2D radiographic factors that can aid in selecting appropriate candidates for CBCT.

Material and methods

Patients with impacted maxillary canines and an overlap of a neighboring tooth in 2D radiographs and the suspicion of root resorption were referred for CBCT examination. An initial treatment plan was based on 2D radiographs, and the final treatment plan was established after the CBCT examination. Logistic regression analyses and t-tests were performed to evaluate differences in radiographic findings between the groups with and without a change in treatment plan.

Results

The study prospectively included 125 impacted canines, and 43 (34.4%) of them had a change in treatment plan after the CBCT examination. The most common change was a modification in the direction of cantilever traction (n = 28; 22.4%), while the least common was the change in decision to remove/keep the canine (n = 4; 3.2%). The size of the alpha and lateral angles had a significant impact on the decision to change the treatment plan. Other radiographic findings did not influence a change in treatment plan.

Conclusions

One-third of the canines had a change in treatment plan after supplemental CBCT examination. Canines with large alpha and lateral angles measured in the panoramic image were found to be significantly more likely to undergo changes in the initial direction of cantilever traction or changes to the canine extraction strategy following CBCT examination.
Routine stress testing in diabetic patients after percutaneous coronary intervention: the POST-PCI trial
Authors: Kim Hoyun , Kang Do-Yoon , Lee Jinho , Choi Yeonwoo , Ahn Jung-Min , Kim Seonok , Yoon Yong-Hoon , Hur Seung-Ho , Lee Cheol Hyun , Kim Won-Jang , Kang Se Hun , Park Chul Soo , Lee Bong-Ki , Suh Jung-Won , Choi Jae Woong , Kim Kee-Sik , Lee Su Nam , Park Seung-Jung , Park Duk-Woo
Published: November 2023

Background and Aims

The optimal follow-up surveillance strategy for high-risk diabetic patients with had undergone percutaneous coronary intervention (PCI) remains unknown.

Methods

The POST-PCI (Pragmatic Trial Comparing Symptom-Oriented versus Routine Stress Testing in High-Risk Patients Undergoing Percutaneous Coronary Intervention) study was a randomized trial comparing a follow-up strategy of routine functional testing at 1 year vs. standard care alone after high-risk PCI. Randomization was stratified according to diabetes status. The primary outcome was a composite of death from any cause, myocardial infarction, or hospitalization for unstable angina at 2 years.

Results

Among 1706 randomized patients, participants with diabetes (n = 660, 38.7%) had more frequent comorbidities and a higher prevalence of complex anatomical or procedural characteristics than those without diabetes (n = 1046, 61.3%). Patients with diabetes had a 52% greater risk of primary composite events [hazard ratio (HR) 1.52; 95% confidence interval (CI) 1.02–2.27; P = .039]. The 2-year incidences of the primary composite outcome were similar between strategies of routine functional testing or standard care alone in diabetic patients (7.1% vs. 7.5%; HR 0.94; 95% CI 0.53–1.66; P = .82) and non-diabetic patients (4.6% vs. 5.1%; HR 0.89; 95% CI 0.51–1.55; P = .68) (interaction term for diabetes: P = .91). The incidences of invasive coronary angiography and repeat revascularization after 1 year were higher in the routine functional-testing group than the standard-care group irrespective of diabetes status.

Conclusions

Despite being at higher risk for adverse clinical events, patients with diabetes who had undergone high-risk PCI did not derive incremental benefit from routine surveillance stress testing compared with standard care alone during follow-up.
Calling on the Third-party Privacy Control into Algorithmic Governance Framework: Linking Users’ Presumed Influence with Control Agency Theory
Authors: Huang Yangkun , Cao Xucheng
Published: November 2023

In the algorithmic society, personal privacy is exposed to ever-growing risks since the platform requires huge volumes of data for algorithm training. Globally, ordinary users, faced with the formidable platform and black-boxed algorithm, usually feel powerless against elusive privacy invasion and then have set about turning to third-party proxy institutions like the government and legislature to counterbalance the algorithmic privacy security framework. Starting from it, the present study examines what triggers users’ support for third-party proxy control, and a moderated serial mediation model has been estimated based on a Chinese cross-sectional sample (N = 661). Our research suggests that users’ algorithm awareness and their presumed algorithmic privacy risk to self and others (elders and minors) significantly predict their support, and serial mediating effects of the presumed algorithmic privacy risk can be more pronounced at the higher level of perceived effectiveness of platform policy. These findings help to identify the crucial role of algorithm awareness, which equips users to navigate risk and behave as responsible digital citizens, and also extend the influence of presumed influence model and the control agency theory in algorithmic contexts, making contributions in both theory and practice.
Effectiveness of Immunization Products Against Medically Attended Respiratory Syncytial Virus Infection: Generic Protocol for a Test-Negative Case-Control Study
Authors: van Roekel Caren , Poukka Eero , Turunen Topi , Nohynek Hanna , Presser Lance , Meijer Adam , Heikkinen Terho , Kramer Rolf , Begier Elizabeth , Teirlinck Anne C , Knol Mirjam J ,   PROMISE Investigators, Nair Harish , Campbell Harry , Bont Louis , Meijer Adam , Teirlinck Anne C , Knol Mirjam , Gideonse David , Backx Anoek , de Melker Hester , van Roekel Caren , Presser Lance , Turunen Topi , Nohynek Hanna , Poukka Eero , Saukkoriipi Annika , Paget John , van Summeren Jojanneke , Dückers Michel , Heikkinen Terho , Audenis Berta Gumí , Llavero Maica , Kragten Leyla , Kriek Lies , Faksová Kristýna , Giardini Michele , Emborg Hanne-Dorthe , Rocchi Francesca , Quiles Cintia Muñoz , Diez-Domingo Javier , Vernhes Charlotte , Demont Clarisse , Robin Aurelie , Neveu David , Marcelon Lydie , Bangert Mathieu , Kramer Rolf , Martyn Oliver , Bardone Corinne , Remy Vanessa , Chaves Sandra , Molnar Daniel , dos Santos Gael , Pirçon Jean-Yves , Rizkalla Bishoy , Turriani Elisa , Li Se , Melegh Noemie Napsugar , Joosten Philip , Moreno Victor Preckler , Shambulova Aigul , Cheret Arnaud , Quelard Delphine , Aerssens Jeroen , Weber Karin , Willame Corinne , Puggina Anna , Theis-Nyland Katherine , Nikolayeva Natalia , Kumar Veena , Beyhaghi Hadi , Shinde Vivek , Schmoele-Thoma Beate , Begier Elizabeth , Swanson Kena , Htar Tin Tin , Atwell Jessica , Aliabadi Negar , Deese Jen , Fell Deshayne , Lino Maria Maddalena , Turiga Monica-Flavia , Ahani Bahar
Published: November 2023

Monitoring the real-life effectiveness of respiratory syncytial virus (RSV) products is of major public health importance. This generic protocol for a test-negative design study aims to address currently envisioned approaches for RSV prevention (monoclonal antibodies and vaccines) to study effectiveness of these products among target groups: children, older adults, and pregnant women. The generic protocol approach was chosen to allow for flexibility in adapting the protocol to a specific setting. This protocol includes severe acute respiratory infection (SARI) and acute respiratory infection (ARI), both due to RSV, as end points. These end points can be applied to studies in hospitals, primarily targeting patients with more severe disease, but also to studies in general practitioner clinics targeting ARI.
Renal outcomes in adults with HBV, HIV and HBV/HIV coinfection after 3 years of antiviral therapy in urban Tanzania
Authors: Wu En-Ling , Christian Beatrice , Rivera Adovich S , Fabian Emanuel , Macha Irene , Aris Eric , Mpangala Shida , Ulenga Nzovu , Mugusi Ferdinand , Murphy Robert L , Hawkins Claudia A
Published: November 2023

Background

An enhanced understanding of renal outcomes in persons with chronic HBV, HIV, and HBV/HIV coinfection is needed to mitigate chronic kidney disease in regions where HBV and HIV are endemic.

Objectives

To investigate changes in estimated glomerular filtration rate (eGFR) in adults with HBV, HIV or HBV/HIV enrolled in a 3 year prospective cohort study of liver outcomes in Dar es Salaam, Tanzania and initiated on antiviral therapy.

Methods

We compared eGFR between and within groups over time using mixed-effects models.

Results

Four hundred and ninety-nine participants were included in the analysis (HBV: 164; HIV: 271; HBV/HIV: 64). Mean baseline eGFRs were 106.88, 106.03 and 107.18 mL/min/1.73 m2, respectively. From baseline to Year 3, mean eGFR declined by 4.3 mL/min/1.73 m2 (95% CI −9.3 to 0.7) and 3.7 (−7.8 to 0.5) in participants with HBV and HIV, respectively, and increased by 5.1 (−4.7 to 14.9) in those with HBV/HIV. In multivariable models, participants with HBV had lower eGFRs compared with those with HIV or HBV/HIV and, after adjusting for HBV DNA level and hepatitis B e antigen (HBeAg) status, significantly lower eGFRs than those with HBV/HIV at all follow-up visits.

Conclusions

In this Tanzanian cohort, coinfection with HBV/HIV did not appear to exacerbate renal dysfunction compared with those with either infection alone. Although overall changes in eGFR were small, persons with HBV experienced lower eGFRs throughout follow-up despite their younger age and similar baseline values. Longer-term studies are needed to evaluate continuing changes in eGFR and contributions from infection duration and other comorbidities.
Value of pneumococcal PCR in respiratory samples for exclusion of pneumococcal pneumonia
Authors: Van Goethem Sam , Van Lint Philippe , Willems Philippe , Van Herendael Bruno , Hoet Katrien
Published: November 2023

Background

Streptococcus pneumoniae is the main aetiological agent in bacterial pneumonia. Therefore pneumococcal PCR is often included in respiratory multiplex PCR panels, both commercial and in-house. But respiratory PCR results for S. pneumoniae are difficult to interpret due to frequent non-pathogenic colonization on the mucosal surface of the upper airways with pneumococci or to cross-reaction of the PCR target in non-pneumococcal streptococci. In this study we investigated the value of lytA gene pneumococcal PCR in patients presenting with pneumonia.

Objectives

To assess the utility of lytA gene detection for S. pneumoniae in a respiratory multiplex quantitative PCR (qPCR) panel for patients presenting with pneumonia.

Methods

A retrospective study was conducted for lytA gene results as target for S. pneumoniae in hospitalized patients who were diagnosed with pneumonia and for which a respiratory multiplex PCR panel was performed. Patients were classified as ‘probable’, ‘possible’ or ‘unlikely’ of having a pneumococcal pneumonia.

Results

A sensitivity of 71.4% and specificity of 89.6% were found, corresponding to a negative predictive value and positive predictive value of 97.6% and 34.2%, respectively, when considering ‘probable’ versus ‘possible/unlikely’. In the PCR-positive cases we found a statistically significant difference in semi-quantitative Ct values between the ‘probable’ and the ‘possible/unlikely’ groups.

Conclusions

We conclude that a negative qPCR for the lytA gene in a respiratory sample is highly predictive of a negative S. pneumoniae culture and is possibly sufficient to exclude S. pneumoniae as a causative agent. Respiratory pneumococcal PCR has a high negative predictive value for pneumococcal disease but the positive predictive value is low.
Alcohol degradation, learning, and memory-enhancing effect of Acetobacter pasteurianus BP2201 in Caenorhabditis elegans model
Authors: Wen Xin , Yang Huazhong , Li Zhongqi , Chu Weihua
Published: November 2023

Aims

This study aimed to investigate the probiotic effects of Acetobacter pasteurianus BP2201, isolated from brewing mass, for the treatment of alcohol-induced learning and memory ability impairments in a Caenorhabditis elegans model.

Methods and results

Acetobacter pasteurianus BP2201 was examined for probiotic properties, including acid and bile salt resistance, ethanol degradation, antioxidant efficacy, hemolytic activity, and susceptibility to antibiotics. The strain displayed robust acid and bile salt tolerance, efficient ethanol degradation, potent antioxidant activity, and susceptibility to specific antibiotics. Additionally, in the C. elegans model, administering A. pasteurianus BP2201 significantly improved alcohol-induced learning and memory impairments.

Conclusions

Acetobacter pasteurianus BP2201 proves to be a promising candidate strain for the treatment of learning and memory impairments induced by alcohol intake.
Creation of a data commons for substance misuse related health research through privacy-preserving patient record linkage between hospitals and state agencies
Authors: Afshar Majid , Oguss Madeline , Callaci Thomas A , Gruenloh Timothy , Gupta Preeti , Sun Claire , Safipour Afshar Askar , Cavanaugh Joseph , Churpek Matthew M , Nyakoe-Nyasani Edwin , Nguyen-Hilfiger Huong , Westergaard Ryan , Salisbury-Afshar Elizabeth , Gussick Megan , Patterson Brian , Manneh Claire , Mathew Jomol , Mayampurath Anoop
Published: November 2023

Objectives

Substance misuse is a complex and heterogeneous set of conditions associated with high mortality and regional/demographic variations. Existing data systems are siloed and have been ineffective in curtailing the substance misuse epidemic. Therefore, we aimed to build a novel informatics platform, the Substance Misuse Data Commons (SMDC), by integrating multiple data modalities to provide a unified record of information crucial to improving outcomes in substance misuse patients.

Materials and Methods

The SMDC was created by linking electronic health record (EHR) data from adult cases of substance (alcohol, opioid, nonopioid drug) misuse at the University of Wisconsin hospitals to socioeconomic and state agency data. To ensure private and secure data exchange, Privacy-Preserving Record Linkage (PPRL) and Honest Broker services were utilized. The overlap in mortality reporting among the EHR, state Vital Statistics, and a commercial national data source was assessed.

Results

The SMDC included data from 36 522 patients experiencing 62 594 healthcare encounters. Over half of patients were linked to the statewide ambulance database and prescription drug monitoring program. Chronic diseases accounted for most underlying causes of death, while drug-related overdoses constituted 8%. Our analysis of mortality revealed a 49.1% overlap across the 3 data sources. Nonoverlapping deaths were associated with poor socioeconomic indicators.

Discussion

Through PPRL, the SMDC enabled the longitudinal integration of multimodal data. Combining death data from local, state, and national sources enhanced mortality tracking and exposed disparities.

Conclusion

The SMDC provides a comprehensive resource for clinical providers and policymakers to inform interventions targeting substance misuse-related hospitalizations, overdoses, and death.
‘Is It Too Late Now to Say Sorry?’
Authors: Kapoor Radhika
Published: November 2023

This article explores the use of remorse as a source of leniency at international criminal tribunals. It outlines the difficulties that beset international tribunals’ attempts to develop a clear, consistent conceptualization of the idea of remorse. Using a range of perspectives, it offers ways forward in terms of both comprehending remorse, as experienced by perpetrators of international crimes, and incorporating remorse into the present international criminal legal framework. In particular, it analyses how sincere expressions of remorse within the international criminal courtroom can signal and produce transformative effects for different players operating in the terrain of international criminal justice.
Critical assessment of the recent report on the gigaparsec-scale correlation of the orientations of large quasar groups
Authors: Fujii Hirokazu
Published: November 2023

Recently, it was reported that large quasar groups (LQGs) identified from the Sloan Digital Sky Survey (SDSS) data release seven catalogue are not randomly oriented but preferentially aligned or orthogonal over scales 1–2 Gpc. To confirm this claim, I reproduced the same LQG sample and performed Sobolev tests of uniformity on the LQG orientation axes in the redshift space. Contrary to the original report based on the bimodal distribution of the LQG position angles in the sky, I found no departure from uniformity in the distribution of the LQG orientation axes. I also examined whether the LQGs are physical structures using a statistically more reliable data set constructed from the SDSS data release 16 (DR16) large-scale structure (LSS) quasar catalogue. Considering the Gaussian primordial density fluctuations and shot noise, I estimated the mass density contrasts of the LQGs from the number counts of the DR16 LSS quasars and found that most of the LQGs do not trace statistically significant high-density regions. I conclude that the LQG sample is a collection of unphysical chance associations and should not be used for any cosmological studies.
Robust cosmological inference from non-linear scales with k-th nearest neighbour statistics
Authors: Yuan Sihan , Abel Tom , Wechsler Risa H
Published: November 2023

We present the methodology for deriving accurate and reliable cosmological constraints from non-linear scales ($\lt 50\, h^{-1}$ Mpc) with k-th nearest neighbour (kNN) statistics. We detail our methods for choosing robust minimum scale cuts and validating galaxy–halo connection models. Using cross-validation, we identify the galaxy–halo model that ensures both good fits and unbiased predictions across diverse summary statistics. We demonstrate that we can model kNNs effectively down to transverse scales of $r_{\rm p}\sim 3\, h^{-1}$ Mpc and achieve precise and unbiased constraints on the matter density and clustering amplitude, leading to a 2 per cent constraint on σ8. Our simulation-based model pipeline is resilient to varied model systematics, spanning simulation codes, halo finding, and cosmology priors. We demonstrate the effectiveness of this approach through an application to the Beyond-2p mock challenge. We propose further explorations to test more complex galaxy–halo connection models and tackle potential observational systematics.
Unprecedented enantio-selective live-cell mitochondrial DNA super-resolution imaging and photo-sensitizing by the chiral ruthenium polypyridyl DNA “light-switch”
Authors: Huang Rong , Huang Chun-Hua , Chen Jing , Yan Zhu-Ying , Tang Miao , Shao Jie , Cai Kaiyong , Zhu Ben-Zhan
Published: November 2023

Mitochondrial DNA (mtDNA) is known to play a critical role in cellular functions. However, the fluorescent probe enantio-selectively targeting live-cell mtDNA is rare. We recently found that the well-known DNA ‘light-switch’ [Ru(phen)2dppz]Cl2 can image nuclear DNA in live-cells with chlorophenolic counter-anions via forming lipophilic ion-pairing complex. Interestingly, after washing with fresh-medium, [Ru(phen)2dppz]Cl2 was found to re-localize from nucleus to mitochondria via ABC transporter proteins. Intriguingly, the two enantiomers of [Ru(phen)2dppz]Cl2 were found to bind enantio-selectively with mtDNA in live-cells not only by super-resolution optical microscopy techniques (SIM, STED), but also by biochemical methods (mitochondrial membrane staining with Tomo20-dronpa). Using [Ru(phen)2dppz]Cl2 as the new mtDNA probe, we further found that each mitochondrion containing 1–8 mtDNA molecules are distributed throughout the entire mitochondrial matrix, and there are more nucleoids near nucleus. More interestingly, we found enantio-selective apoptotic cell death was induced by the two enantiomers by prolonged visible light irradiation, and in-situ self-monitoring apoptosis process can be achieved by using the unique ‘photo-triggered nuclear translocation’ property of the Ru complex. This is the first report on enantio-selective targeting and super-resolution imaging of live-cell mtDNA by a chiral Ru complex via formation and dissociation of ion-pairing complex with suitable counter-anions.
NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update
Authors: Clough Emily , Barrett Tanya , Wilhite Stephen E , Ledoux Pierre , Evangelista Carlos , Kim Irene F , Tomashevsky Maxim , Marshall Kimberly A , Phillippy Katherine H , Sherman Patti M , Lee Hyeseung , Zhang Naigong , Serova Nadezhda , Wagner Lukas , Zalunin Vadim , Kochergin Andrey , Soboleva Alexandra
Published: November 2023

The Gene Expression Omnibus (GEO) is an international public repository that archives gene expression and epigenomics data sets generated by next-generation sequencing and microarray technologies. Data are typically submitted to GEO by researchers in compliance with widespread journal and funder mandates to make generated data publicly accessible. The resource handles raw data files, processed data files and descriptive metadata for over 200 000 studies and 6.5 million samples, all of which are indexed, searchable and downloadable. Additionally, GEO offers web-based tools that facilitate analysis and visualization of differential gene expression. This article presents the current status and recent advancements in GEO, including the generation of consistently computed gene expression count matrices for thousands of RNA-seq studies, and new interactive graphical plots in GEO2R that help users identify differentially expressed genes and assess data set quality. The GEO repository is built and maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM), and is publicly accessible at https://www.ncbi.nlm.nih.gov/geo/.