bluuebunny/crossref_metadata_2025_split huggingface dataset:
TSWIFT: Tower Spectrometer on Wheels for Investigating Frequent Timeseries for high-throughput phenotyping of vegetation physiology
Authors: Wong Christopher Y. S. , Jones Taylor , McHugh Devin P. , Gilbert Matthew E. , Gepts Paul , Palkovic Antonia , Buckley Thomas N. , Magney Troy S. 
Published: March 2023

Abstract
Background
Remote sensing instruments enable high-throughput phenotyping of plant traits and stress resilience across scale. Spatial (handheld devices, towers, drones, airborne, and satellites) and temporal (continuous or intermittent) tradeoffs can enable or constrain plant science applications. Here, we describe the technical details of TSWIFT (Tower Spectrometer on Wheels for Investigating Frequent Timeseries), a mobile tower-based hyperspectral remote sensing system for continuous monitoring of spectral reflectance across visible-near infrared regions with the capacity to resolve solar-induced fluorescence (SIF).

Results
We demonstrate potential applications for monitoring short-term (diurnal) and long-term (seasonal) variation of vegetation for high-throughput phenotyping applications. We deployed TSWIFT in a field experiment of 300 common bean genotypes in two treatments: control (irrigated) and drought (terminal drought). We evaluated the normalized difference vegetation index (NDVI), photochemical reflectance index (PRI), and SIF, as well as the coefficient of variation (CV) across the visible-near infrared spectral range (400 to 900 nm). NDVI tracked structural variation early in the growing season, following initial plant growth and development. PRI and SIF were more dynamic, exhibiting variation diurnally and seasonally, enabling quantification of genotypic variation in physiological response to drought conditions. Beyond vegetation indices, CV of hyperspectral reflectance showed the most variability across genotypes, treatment, and time in the visible and red-edge spectral regions.

Conclusions
TSWIFT enables continuous and automated monitoring of hyperspectral reflectance for assessing variation in plant structure and function at high spatial and temporal resolutions for high-throughput phenotyping. Mobile, tower-based systems like this can provide short- and long-term datasets to assess genotypic and/or management responses to the environment, and ultimately enable the spectral prediction of resource-use efficiency, stress resilience, productivity and yield.
Melatonin and endothelial cell-loaded alginate-fibrin hydrogel promoted angiogenesis in rat cryopreserved/thawed ovaries transplanted to the heterotopic sites
Authors: Izadpanah Melika , Del Bakhshayesh Azizeh Rahmani , Bahroudi Zahra , Seghinsara Abbas Majdi , Beheshti Rahim , Mahdipour Mahdi , Zarnaghi Mahsa Rezaii , Hassanpour Parisa , Mardi Narges , Rahbarghazi Reza , Abedelahi Ali 
Published: March 2023

Abstract
Background
Ischemic niche can promote follicular atresia following the transplantation of cryopreserved/thawed ovaries to the heterotopic sites. Thus, the promotion of blood supply is an effective strategy to inhibit/reduce the ischemic damage to ovarian follicles. Here, the angiogenic potential of alginate (Alg) + fibrin (Fib) hydrogel enriched with melatonin (Mel) and CD144+ endothelial cells (ECs) was assessed on encapsulated cryopreserved/thawed ovaries following transplantation to heterotopic sites in rats.

Methods
Alg + Fib hydrogel was fabricated by combining 2% (w/v) sodium Alg, 1% (w/v) Fib, and 5 IU thrombin at a ratio of 4: 2: 1, respectively. The mixture was solidified using 1% CaCl2. Using FTIR, SEM, swelling rate, and biodegradation assay, the physicochemical properties of Alg + Fib hydrogel were evaluated. The EC viability was examined using an MTT assay. Thirty-six adult female rats (aged between 6 and 8 weeks) with a normal estrus cycle were ovariectomized and enrolled in this study. Cryopreserved/thawed ovaries were encapsulated in Alg + Fib hydrogel containing 100 µM Mel + CD144+ ECs (2 × 104 cells/ml) and transplanted into the subcutaneous region. Ovaries were removed after 14 days and the expression of Ang-1, and Ang-2 was monitored using real-time PCR assay. The number of vWF+ and α-SMA+ vessels was assessed using IHC staining. Using Masson’s trichrome staining, fibrotic changes were evaluated.

Results
FTIR data indicated successful interaction of Alg with Fib in the presence of ionic cross-linker (1% CaCl2). Data confirmed higher biodegradation and swelling rates in Alg + Fib hydrogel compared to the Alg group (p < 0.05). Increased viability was achieved in encapsulated CD144+ ECs compared to the control group (p < 0.05). IF analysis showed the biodistribution of Dil+ ECs within hydrogel two weeks after transplantation. The ratio of Ang-2/Ang-1 was statistically up-regulated in the rats that received Alg + Fib + Mel hydrogel compared to the control-matched groups (p < 0.05). Based on the data, the addition of Mel and CD144+ ECs to Alg + Fib hydrogel reduced fibrotic changes. Along with these changes, the number of vWF+ and α-SMA+ vessels was increased in the presence of Mel and CD144+ ECs.

Conclusions
Co-administration of Alg + Fib with Mel and CD144+ ECs induced angiogenesis toward encapsulated cryopreserved/thawed ovarian transplants, resulting in reduced fibrotic changes.
Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Authors: Sun Silei , Wang Daosheng , Dong Danfeng , Xu Lili , Xie Mengqi , Wang Yihui , Ni Tongtian , Jiang Weisong , Zhu Xiaojuan , Ning Ning , Sun Qian , Zhao Shuyuan , Li Mengjiao , Chen Peili , Yu Meiling , Li Jian , Chen Erzhen , Zhao Bing , Peng Yibing , Mao Enqiang 
Published: March 2023

Abstract
Background
The gut microbiome plays a pivotal role in the progression of sepsis. However, the specific mechanism of gut microbiota and its metabolites involved in the process of sepsis remains elusive, which limits its translational application.

Method
In this study, we used a combination of the microbiome and untargeted metabolomics to analyze stool samples from patients with sepsis enrolled at admission, then microbiota, metabolites, and potential signaling pathways that might play important roles in disease outcome were screened out. Finally, the above results were validated by the microbiome and transcriptomics analysis in an animal model of sepsis.

Results
Patients with sepsis showed destruction of symbiotic flora and elevated abundance of Enterococcus, which were validated in animal experiments. Additionally, patients with a high burden of Bacteroides, especially B. vulgatus, had higher Acute Physiology and Chronic Health Evaluation II scores and longer stays in the intensive care unit. The intestinal transcriptome in CLP rats illustrated that Enterococcus and Bacteroides had divergent profiles of correlation with differentially expressed genes, indicating distinctly different roles for these bacteria in sepsis. Furthermore, patients with sepsis exhibited disturbances in gut amino acid metabolism compared with healthy controls; namely, tryptophan metabolism was tightly related to an altered microbiota and the severity of sepsis.

Conclusion
Alterations in microbial and metabolic features in the gut corresponded with the progression of sepsis. Our findings may help to predict the clinical outcome of patients in the early stage of sepsis and provide a translational basis for exploring new therapies.
Changing patient preferences toward better trial recruitment: an ethical analysis
Authors: Al Pepijn , Hey Spencer , Weijer Charles , Gillies Katie , McCleary Nicola , Yee Mei-Lin , Inglis Juliette , Presseau Justin , Brehaut Jamie 
Published: March 2023

AbstractWhile randomized controlled trials are essential to health research, many of these trials fail to recruit enough participants. Approaching recruitment through the lens of behavioral science can help trialists to understand influences on the decision to participate and use them to increase recruitment. Although this approach is promising, the use of behavioral influences during recruitment is in tension with the ethical principle of respect for persons, as at least some of these influences could be used to manipulate potential participants. In this paper, we examine this tension by discussing two types of behavioral influences: one example involves physician recommendations, and the other involves framing of information to exploit cognitive biases. We argue that despite the apparent tension with ethical principles, influencing trial participants through behavior change strategies can be ethically acceptable. However, we argue that trialists have a positive obligation to analyze their recruitment strategies for behavioral influences and disclose these upfront to the research ethics committee. But we also acknowledge that since neither trialists nor ethics committees are presently well equipped to perform these analyses, additional resources and guidance are needed. We close by outlining a path toward the development of such guidance.
The maladaptive domains according to the alternative model of personality disorders (AMPD) criterion B in patients with affective disorders and temperamental triads related to these domains: two unique profiles
Authors: Komasi Saeid , Jananeh Minoo , Mahdavi Sahar , Shademan Tahereh , Vaysi Anis , Shahlaee Mehrnoosh , Mirani Atefeh , Chamandoust Zahra , Saeidi Mozhgan 
Published: March 2023

AbstractObjectivesThe study aimed to (i) compare the maladaptive domains and facets according to the Alternative Model of Personality Disorders (AMPD) Criterion B in patients with a type II bipolar disorder (BD-II) or major depressive disorder (MDD) with healthy controls (HCs), and (ii) investigating the relationship between affective temperaments and these domains and facets in the total sample.MethodsOutpatients diagnosed with current BD-II (n = 37; female 62.2%) or MDD (n = 17; female 82.4%) based on the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) criteria and community HCs (n = 177; female 62.1%) in Kermanshah from July to October 2020 included this case-control study. All participants completed the Personality Inventory for DSM-5 (PID-5), the Temperament Evaluation of Memphis, Pisa, Paris, and San Diego Autoquestionnaire (TEMPS-A), and the second version of the Beck Depression Inventory (BDI-II). Data were analyzed using analysis of variance (ANOVA), Pearson correlation, and multiple regression.ResultsThe score of patients with BD-II in all five domains and those with MDD in three domains including negative affectivity, detachment, and disinhibition are significantly higher than the HCs (p < 0.05). Depressive temperament (related to negative affectivity, detachment, and disinhibition) and cyclothymic temperament (related to antagonism and psychoticism) were the most important correlates of the maladaptive domains.ConclusionsTwo unique profiles are proposed, including three domains of negative affectivity, detachment, and disinhibition associated with the depressive temperament for MDD, and two domains of antagonism and psychoticism related to cyclothymic temperament for BD-II.
Biotic and abiotic effects of soil organic matter on the phytoavailable phosphorus in soils: a review
Authors: Jindo Keiji , Audette Yuki , Olivares Fabio Lopez , Canellas Luciano Pasqualoto , Smith D. Scott , Paul Voroney R. 
Published: March 2023

AbstractSoil organic matter (SOM) has a critical role in regulating soil phosphorus (P) dynamics and producing phytoavailable P. However, soil P dynamics are often explained mainly by the effects of soil pH, clay contents, and elemental compositions, such as calcium, iron, and aluminum. Therefore, a better understanding of the mechanisms of how SOM influences phytoavailable P in soils is required for establishing effective agricultural management for soil health and enhancement of soil fertility, especially P-use efficiency. In this review, the following abiotic and biotic mechanisms are discussed; (1) competitive sorption between SOM with P for positively charged adsorption sites of clays and metal oxides (abiotic reaction), (2) competitive complexations between SOM with P for cations (abiotic reaction), (3) competitive complexations between incorporation of P by binary complexations of SOM and bridging cations with the formation of stable P minerals (abiotic reaction), (4) enhanced activities of enzymes, which affects soil P dynamics (biotic reaction), (5) mineralization/immobilization of P during the decay of SOM (biotic reaction), and (6) solubilization of inorganic P mediated by organic acids released by microbes (biotic reaction).
Graphical Abstract
Finite element analysis on dynamic behavior of sheet pile quay wall dredged and improved seaside subsoil using cement deep mixing
Authors: Nguyen Anh-Dan , Nguyen Viet-Thanh , Kim Young-Sang 
Published: March 2023

AbstractSheet pile wall structures are commonly applied in coastal projects, particularly for the quay wall. This structural type normally is used in places where the ground has a low bearing capacity and is easily penetrable. Many sheet pile quay walls constructed in the past had low front water depth and did not satisfy the requirements of current standards. This issue could be addressed by improving the ground in front of the wall using cement deep mixing (CDM) and then excavating to increase the water depth in front of the wall. This paper numerically evaluated the dynamic behavior of the sheet pile wall after renovation. The numerical model was performed based on the finite element method (FEM) using the PLAXIS 2D program. The study focused on investigating typical parameters of the quay wall improved using the CDM, such as bending moment and displacement of sheet pile and the development of excess pore water pressure (EPWP) in the backfill. These results were compared to those of the quay wall without the CDM to elucidate the advantages of this method. In addition, the influence of some factors on the quay wall behavior, such as earthquake excitation characteristics, CDM area, and CDM strength, was also evaluated. The results demonstrated that the ground improvement using the CDM significantly decreased the bending moment and displacement of the sheet pile wall. The excitation characteristics did not affect the deformed shape of the sheet pile. With the constant CDM depth, the sheet pile displacement decreased with an increase in the improvement width until it reached a limitation. The increasing CDM strength also decreased the displacement of the wall until it raised a certain value. This demonstrated that this method was technically feasible, and it could be considered to study further by experiment before applying in practice.
Improved seismic envelope full-waveform inversion
Authors: Xiong Kai , Lumley David , Zhou Wei 
Published: March 2023

The envelope full-waveform-inversion method has the potential to greatly improve the estimation of long-wavelength components of subsurface seismic velocity, and simultaneously avoid or reduce inversion cycle skipping, by fitting the envelopes of observed and modeled seismic waveform data, rather than fitting the waveforms directly. However, some issues such as instability of the adjoint source and gradient term make it challenging to use in practice for many seismology applications. We examine the envelope inversion (EI) methods with different envelope function exponent p values from an adjoint source analysis perspective and reveal the adverse effects of the adjoint source weighting term on the data residuals, which degrade or mute important inversion gradient contributions, especially from reflected or scattered phases in the seismic data. We develop the theory and implementation for an improved EI (IEI) method by adding an upshift constant (zero-frequency direct current [DC] bias term) to the seismic waveform data before calculating the envelope functions, which can help solve the instability issue of the adjoint source of the EI with power value p = 1. Our approach is different than the common but simple addition of a “water-level” damping constant in the denominator of the data residual-weighting term, which can ignore important information contained in the data residuals. Our IEI method becomes a mixed envelope-waveform objective function, which introduces a new adjoint source weighting term that can preserve all of the information contained in the data residuals, by boosting the low-amplitude phases of the seismic waveform, while simultaneously preserving the correct envelope (energy shape) of the high-amplitude phases. We test the performance of all three methods in detail using the highly realistic SEAM4D model and data and find the advantages of our new IEI method compared with conventional EI and full-waveform inversion methods.
Re-Evaluation of Pathologic Complete Response as a Surrogate for Event-Free and Overall Survival in Human Epidermal Growth Factor Receptor 2–Positive, Early Breast Cancer Treated With Neoadjuvant Therapy Including Anti–Human Epidermal Growth Factor Receptor 2 Therapy
Authors: Squifflet Pierre , Saad Everardo D. , Loibl Sibylle , van Mackelenbergh Marion T. , Untch Michael , Rastogi Priya , Gianni Luca , Schneeweiss Andreas , Conte Pierfranco , Piccart Martine , Bonnefoi Hervé , Jackisch Christian , Nekljudova Valentina , Tang Gong , Valagussa Pinuccia , Neate Colin , Gelber Richard , Poncet Coralie , Heinzmann Dominik , Denkert Carsten , Geyer Charles E. , Cortes Javier , Guarneri Valentina , de Azambuja Evandro , Cameron David , Ismael Gustavo , Wolmark Norman , Cortazar Patricia , Buyse Marc ,   on behalf of the CTNeoBC Project
Published: March 2023

PURPOSE Pathologic complete response (pCR) has prognostic importance and is frequently used as a primary end point, but doubts remain about its validity as a surrogate for event-free survival (EFS) and overall survival (OS) in human epidermal growth factor receptor 2 (HER2)–positive, early breast cancer. METHODS We obtained individual-patient data from randomized trials of neoadjuvant anti-HER2 therapy that enrolled at least 100 patients, had data for pCR, EFS, and OS, and a median follow-up of at least 3 years. We quantified the patient-level association between pCR (defined as ypT0/Tis ypN0) and both EFS and OS using odds ratios (ORs, with ORs >1.00 indicating a benefit from achieving a pCR). We quantified the trial-level association between treatment effects on pCR and on EFS and OS using R2 (with values above 0.75 considered as indicating strong associations). RESULTS Eleven of 15 eligible trials had data for analysis (3,980 patients, with a median follow-up of 62 months). Considering all trials, we found strong patient-level associations, with ORs of 2.64 (95% CI, 2.20 to 3.07) for EFS and 3.15 (95% CI, 2.38 to 3.91) for OS; however, trial-level associations were weak, with an unadjusted R2 of 0.23 (95% CI, 0 to 0.66) for EFS and 0.02 (95% CI, 0 to 0.17) for OS. We found qualitatively similar results when grouping trials according to different clinical questions, when analyzing only patients with hormone receptor–negative disease, and when using a more stringent definition of pCR (ypT0 ypN0). CONCLUSION Although pCR may be useful for patient management, it cannot be considered as a surrogate for EFS or OS in neoadjuvant trials of HER2-positive, operable breast cancer.
Leveraging Prior Healthy Participant Pharmacokinetic Data to Evaluate the Impact of Renal and Hepatic Impairment on Ritlecitinib Pharmacokinetics
Authors: Purohit Vivek , Huh Yeamin , Wojciechowski Jessica , Plotka Anna , Salts Stephanie , Antinew Jeremias , Dimitrova Angela , Nicholas Timothy 
Published: March 2023

Abstract
Ritlecitinib is a selective, covalent, irreversible inhibitor of Janus kinase 3 (JAK3) and the tyrosine kinase expressed in hepatocellular carcinoma (TEC) family kinases. Pharmacokinetics and safety of ritlecitinib in participants with hepatic (Study 1) or renal (Study 2) impairment were to be characterized from two phase I studies. Due to a study pause caused by the COVID-19 pandemic, the study 2 healthy participant (HP) cohort was not recruited; however, the demography of the severe renal impairment cohort closely matched the study 1 HP cohort. We present results from each study and two innovative approaches to utilizing available HP data as reference data for study 2: a statistical approach using analysis of variance and an in silico simulation of an HP cohort created using a population pharmacokinetics (POPPK) model derived from several ritlecitinib studies. For study 1, the observed area under the curve for 24-h dosing interval and maximum plasma concentration for HPs and their observed geometric mean ratios (participants with moderate hepatic impairment vs HPs) were within 90% prediction intervals from the POPPK simulation-based approach, thereby validating the latter approach. When applied to study 2, both the statistical and POPPK simulation approaches demonstrated that patients with renal impairment would not require ritlecitinib dose modification. In both phase I studies, ritlecitinib was generally safe and well tolerated. These analyses represent a new methodology for generating reference HP cohorts in special population studies for drugs in development with well-characterized pharmacokinetics in HPs and adequate POPPK models.

Trial Registration
ClinicalTrials.gov NCT04037865, NCT04016077, NCT02309827, NCT02684760, and NCT02969044.

Graphical Abstract
Approach to the Patient With Prolactinoma
Authors: Auriemma Renata S , Pirchio Rosa , Pivonello Claudia , Garifalos Francesco , Colao Annamaria , Pivonello Rosario 
Published: March 2023

AbstractProlactinomas are the most common pituitary tumor histotype, with microprolactinomas being prevalent in women and macroprolactinomas in men. Hyperprolactinemia is among the most common causes of hypogonadotropic hypogonadism in both sexes, prompting medical advice for hypogonadism (infertility, oligo-amenorrhea, impotence, osteoporosis/osteopenia) in both sexes, and for signs and symptoms of mass effects (hypopituitarism, visual loss, optic chiasm compression, cranial nerve deficits, headaches) predominantly in men. Diagnostic workup involves a single prolactin measurement and pituitary imaging, but some laboratory artifacts (ie, the “hook effect” and macroprolactin) can complicate or delay the diagnosis. The treatment of choice for prolactinomas is represented by dopamine agonists, mainly cabergoline, which are able to induce disease control, restore fertility in both sexes, and definitively cure one-third of patients, thus permitting treatment discontinuation. Pregnancy and menopause may promote spontaneous prolactin decline and anticipate cabergoline discontinuation in women. Surgery and/or radiotherapy are indicated in case of resistance to cabergoline not overcome by the increase in drug dose up to the maximally tolerated or the patient's personal choice of surgery. The evidence of resistance to cabergoline in invasive and proliferative tumors may indicate biological aggressiveness, thus requiring alternative therapeutic approaches mainly based on temozolomide use as monotherapy or combined with radiotherapy. In uncontrolled patients, new medical approaches (alternative hormonal treatments, cytotoxic drugs, peptide receptor radionuclide therapy, mTOR/Akt inhibitors, tyrosine kinase inhibitors, or immunotherapy) may be offered but the experience collected to date is still very scant. This article reviews different facets of prolactinomas and discusses approaches to the condition in more common clinical situations.