bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enabling adaptive pedestals in predictive transport simulations using neural networks
Authors: Gillgren A. , Fransson E. , Yadykin D. , Frassinetti L. , Strand P. , JET Contributors  
Published: June 2022

Abstract
We present PEdestal Neural Network (PENN) as a machine learning model for tokamak pedestal predictions. Here, the model is trained using the EUROfusion JET pedestal database to predict the electron pedestal temperature and density from a set of global engineering and plasma parameters. Results show that PENN makes accurate predictions on the test set of the database, with R
2 = 0.93 for the temperature, and R
2 = 0.91 for the density. To demonstrate the applicability of the model, PENN is employed in the European transport simulator (ETS) to provide boundary conditions for the core of the plasma. In a case example in the ETS with varied neutral beam injection (NBI) power, results show that the model is consistent with previous studies regarding NBI power dependency on the pedestal. Additionally, we show how an uncertainty estimation method can be used to interpret the reliability of the predictions. Future work includes further analysis of how pedestal models, such as PENN, or other advanced deep learning models, can be more efficiently implemented in integrating modeling frameworks, and also how similar models may be generalized with respect to other tokamaks and future device scenarios.
Microscopic density-functional approach to nonlinear elasticity theory
Authors: Haussmann Rudolf 
Published: June 2022

Abstract
Starting from a general classical model of many interacting particles we present a well defined step by step procedure to derive the continuum-mechanics equations of nonlinear elasticity theory with fluctuations which describe the macroscopic phenomena of a solid crystal. As the relevant variables we specify the coarse-grained densities of the conserved quantities and a properly defined displacement field which describes the local translations, rotations, and deformations. In order to stay within the framework of the conventional density-functional theory we first and mainly consider the isothermal case and omit the effects of heat transport and warming by friction where later we extend our theory to the general case and include these effects. We proceed in two steps. First, we apply the concept of local thermodynamic equilibrium and minimize the free energy functional under the constraints that the macroscopic relevant variables are fixed. As results we obtain the local free energy density and we derive explicit formulas for the elastic constants which are exact within the framework of density-functional theory. Second, we apply the methods of nonequilibrium statistical mechanics with projection-operator techniques. We extend the projection operators in order to include the effects of coarse-graining and the displacement field. As a result we obtain the time-evolution equations for the relevant variables with three kinds of terms on the right-hand sides: reversible, dissipative, and fluctuating terms. We find explicit formulas for the transport coefficients which are exact in the limit of continuum mechanics if the projection operators are properly defined. By construction the theory allows the diffusion of particles in terms of point defects where, however, in a normal crystal this diffusion is suppressed.
Study on a micro radiation probe with high SNR based on CdZnTe detector
Authors: Xiaoyu X. , Lian C. , Weiwei Q. , Ge J. 
Published: June 2022

Abstract
In this paper, we develop a micro radiation probe with a
CdZnTe detector. To obtain a high signal-to-noise ratio(SNR)
performance, circuit simulation and analysis were performed before
circuit design, to evaluate the signal characters and frequency
response of the electronic design. We adopted a method to evaluate
the electronic noise level of specific readout circuits design and
determined a better timing parameter of the shaping circuit. Our
results confirmed that using a proper design of charge sensitive
amplifier(CSA) circuit and the filter system on the readout circuit
improved the energy resolution of the probe. Energy spectrum
measurement using a 137Cs source showed that the energy
resolution of 662 keV γ-ray can reach 2.6%. This enables
this microprobe for multi-nuclides recognition or nuclides to
monitor in nuclear medicine applications.
Alternative stable states and hydrological regime shifts in a large intermittent river
Authors: Zipper Sam , Popescu Ilinca , Compare Kyle , Zhang Chi , Seybold Erin C 
Published: June 2022

Abstract
Non-perennial rivers and streams make up over half the global river network and are becoming more widespread. Transitions from perennial to non-perennial flow are a threshold-type change that can lead to alternative stable states in aquatic ecosystems, but it is unknown whether streamflow itself is stable in either wet (flowing) or dry (no-flow) conditions. Here, we investigated drivers and feedbacks associated with regime shifts between wet and dry conditions in an intermittent reach of the Arkansas River (USA) over the past 23 years. Multiple lines of evidence suggested that these regimes represent alternative stable states, including (a) significant jumps in discharge time series that were not accompanied by jumps in flow drivers such as precipitation and groundwater pumping; (b) a multi-modal state distribution with 92% of months experiencing no-flow conditions for <10% or >90% of days, despite unimodal distributions of precipitation and pumping; and (c) a hysteretic relationship between climate and flow state. Groundwater levels appear to be the primary control over the hydrological regime, as groundwater levels in the alluvial aquifer were higher than the stream stage during wet regimes and lower than the streambed during dry regimes. Groundwater level variation, in turn, was driven by processes occurring at both the regional scale (surface water inflows from upstream, groundwater pumping) and the reach scale (stream–aquifer exchange, diffuse recharge through the soil column). Historical regime shifts were associated with diverse pressures including network disconnection caused by upstream water use, increased flow stability potentially associated with reservoir operations, and anomalous wet and dry climate conditions. In sum, stabilizing feedbacks among upstream inflows, stream–aquifer interactions, climate, vegetation, and pumping appear to create alternative wet and dry stable states at this site. These stabilizing feedbacks suggest that widespread observed shifts from perennial to non-perennial flow will be difficult to reverse.
Alien invasiveLeucaena leucocephalasuccessfully acquires nutrients by investing in below-ground biomass compared to nativeVachellia niloticain nutrient-amended soils in South Africa
Authors: Ndabankulu Khululwa , Tsvuura Zivanai , Magadlela Anathi 
Published: June 2022

AbstractSoils in grasslands and savannas of southern Africa are acidic and nutrient-poor. Legume plants, such as Vachellia nilotica and alien invasive Leucaena leucocephala, are a major component of the vegetation there. Vachellia nilotica can establish in drought-prone environments, and is invasive in high rainfall areas. Leucaena leucocephala is an emerging invasive in South Africa and is ranked among the world’s 100 most invasive alien species. Alien plants can invade native habitats through their adaptability to low-resource soils, and thus can out-compete and displace native vegetation. We investigated the effects of phosphorus (P) deficiency and soil acidity on legume–microbe symbiosis, nitrogen (N) nutrition and carbon (C) growth costs of these two legumes in grassland soils. We used as inoculum and growth substrate soils collected from a long-term (&gt;65 years) nutrient and lime-addition trial, the Veld Fertilizer Trial (VFT), located at Ukulinga Research Farm near Pietermaritzburg in South Africa. We used soils from three VFT treatments: soils fertilized with superphosphate (336 kg ha−1) applied once per year (+P), soils fertilized with superphosphate (336 kg ha−1) applied once per year with dolomitic lime (2250 kg ha−1) applied once every 5 years (P+L) and soils with no superphosphate and no dolomitic lime applications (Control). Seeds of V. nilotica and L. leucocephala were germinated and grown independently in these soils in green house conditions and harvested after 125 days for measurement of growth, legume–microbe symbiosis, N nutrition and C growth costs. Results showed that the two legumes had different growth adaptations. Vachellia nilotica grown in control soils and +P soils nodulated with various Burkholderia spp., while L. leucocephala did not nodulate in all soil treatments. Both legumes utilized for growth both atmospheric- and soil-derived N across all treatments thereby decreasing C growth costs. Vachellia nilotica grown in +P soils accumulated the most biomass and N nutrition. Leucaena leucocephala maximized specific N assimilation rates by investing in below-ground biomass accumulation in control soils. This shows that L. leucocephala possesses traits that are successful in acquiring nutrients by investing in below-ground biomass and relying on utilization of N from both the soil and the atmosphere.
Design, synthesis, and biological activity of a synthetically accessible analog of aplysiatoxin with an (R)-(−)-carvone-based conformation-controlling unit
Authors: Suzuki Yoshiyuki , Moritoki Keiichi , Kajiwara Mizuki , Yanagita Ryo C , Kawanami Yasuhiro , Hanaki Yusuke , Irie Kazuhiro 
Published: June 2022

Abstract
Simplified analogs of aplysiatoxin (ATX) such as 10-Me-aplog-1 exhibit potent antiproliferative activity toward human cancer cell lines by activating protein kinase C (PKC). However, the synthesis of 10-Me-aplog-1 involved a 23-step longest linear sequence (LLS). Therefore, we have been working toward the development of a more synthetically accessible analog of ATX. In this study, we designed a new analog of ATX wherein a cyclic ketal moiety derived from (R)-(−)-carvone replaced the spiroketal moiety in 18-deoxy-aplog-1. The new analog's synthesis proceeded in an eight-step LLS. Although the configuration at position 3 of the cyclic ketal in the (R)-(−)-carvone-based analog was opposite to those of ATX and 18-deoxy-aplog-1, the antiproliferative activity toward human cancer cell lines of the carvone-based analog was comparable to that of 18-deoxy-aplog-1. The obtained results indicate the potential of the carvone-based analog as a basis for discovering PKC-targeting molecules requiring a decreased number of synthetic steps.
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning
Authors: Huffman Anthony , Ong Edison , Hur Junguk , D’Mello Adonis , Tettelin Hervé , He Yongqun 
Published: June 2022

AbstractRational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general, computational vaccine design includes three major stages: (i) identification and annotation of experimentally verified gold standard protective antigens through literature mining, (ii) rational vaccine design using reverse vaccinology (RV) and structural vaccinology (SV) and (iii) post-licensure vaccine success and adverse event surveillance and its usage for vaccine design. Protegen is a database of experimentally verified protective antigens, which can be used as gold standard data for rational vaccine design. RV predicts protective antigen targets primarily from genome sequence analysis. SV refines antigens through structural engineering. Recently, RV and SV approaches, with the support of various machine learning methods, have been applied to COVID-19 vaccine design. The analysis of post-licensure vaccine adverse event report data also provides valuable results in terms of vaccine safety and how vaccines should be used or paused. Ontology standardizes and incorporates heterogeneous data and knowledge in a human- and computer-interpretable manner, further supporting machine learning and vaccine design. Future directions on rational vaccine design are discussed.
Endoscopic surveillance after bariatric surgery: Results from a large, single-institution cohort
Authors: Lazaridis I , Kraljevic M , Thomas K , Gätzi D , Stöcklin P , Zingg U , Delko T 
Published: June 2022

Abstract

Objective
Sleeve gastrectomy (SG) and Roux-en-Y-gastric bypass (RYGB) are associated with long- term abnormalities, including erosive esophagitis (EE), hiatal hernia (HH), gastritis, Barrett`s esophagus and ulcers. The aim of this study is to assess the prevalence of abnormal endoscopic and histologic findings after SG and RYGB in a large cohort.

Methods
This is a retrospective analysis of 720 consecutive patients who underwent esophagogastroduodenoscopy (EGD) after primary SG or RYGB. Patients were invited for a control EGD after two years of follow-up. EGD was also performed in order to evaluate postoperative symptoms, such as nausea, vomiting or reflux. If revisional surgery was planned, an EGD was included in the prerevisional work up.

Results
304 post-SG patients (64.1% female) and 416 post-RYGB patients (85% female) were included. The mean age at the time of operation was 43.9 years (95% confidence intervals (CI) 42.5–43.3 years) for the post-SG group and 40.5 years (95% CI 39.4–41.6 years) for the post-RYGB group (p&lt;0.001). The mean preoperative body mass index (BMI) was 44.2 kg/m2 (95%CI 43.4–44.9) and 41.1 kg/m2 (95%CI 40.7–41.5) for the post-SG and the post-RYGB group respectively (p&lt;0.001). EE, gastritis and HH were more prevalent after SG than RYGB (38.8% vs 8.9%, 62.5% vs 27.6% and 28% vs 2.6% respectively, p&lt;0.001). RYGB was associated with more postoperative ulcers than SG (14.4% vs 0.7%, p&lt;0.001). The incidence of anastomotic strictures requiring anastomotic dilatation after RYGB was 4.6%. No significant difference was found in the prevalence of Barrett`s esophagus (4.3% post SG vs. 4.1 post RYGB, p=1.000) and Helicobacter pylori (3.3% post SG vs. 1.2% post RYGB, p=0.065) between the two groups.

Conclusion
SG is associated with higher rates of EE, gastritis and HH, while the prevalence of ulcers is higher post RYGB. There is a low risk of anastomotic stricture post RYGB. The incidence of Barrett`s oesophagus is low after both procedures. Routine use of EGD after bariatric surgery should be evaluated.
Long-term quality of life after gastric band removal and concomitant conversion to gastric bypass: A single center cohort study
Authors: Pfister M , Teuben M P J , Teuber H , Nocito A , Probst P , Müller M K 
Published: June 2022

Abstract

Objective
To report long-term quality of life and determine predictors for improved quality of life after gastric band removal and concomitant conversion to Roux-en-Y gastric bypass.

Methods
Clinical data of all patients who underwent conversion surgery from 2011 to 2017 were extracted from a prospectively maintained bariatric database and retrospectively analysed. During scheduled follow-up visits at 1, 6, 12, 24, 36, 48, and 60 months after surgery, physical and laboratory data as well as quality of life questionnaires were obtained. The primary outcome was change in postoperative Moorehead-Ardelt Quality of Life Questionnaire II Score (Moorehead Score). Secondary outcomes included common efficacy and safety outcomes utilized in bariatric surgery. Mixed ANOVA analysis, Chi Square test and Fisher's exact test were used.

Results
Overall, 108 patients who underwent conversion surgery were included. Mean duration of banding until conversion was 11.3 ± 4.3 years. The reason for conversion surgery was band failure in 45.4% (n=49) and band intolerance in 33.3% (n=36) of patients. In the remaining 21.3% (n=23) of cases a combination of both failure and intolerance was present. Mean follow-up time was 53 months. Postoperative mean Moorehead Score increased significantly after one (1.6 ± 0.9, p&lt;0.01) and after five years (1.6 ± 0.8, p&lt;0.01) compared to baseline values (0.7 ± 1.1). Mixed ANOVA analysis showed a significantly superior increase in Moorehead Score in males (p=0.024). No other significant predictors were identified. Neither the reason for conversion, nor preoperative parameters or long-term postoperative outcome parameters including postoperative weight loss or safety outcomes significantly affected postoperative quality of life improvement. Lasting BMI reduction (-4.6 kg/m2, p&lt;0.01) to 33.0 ± 6.7 kg/m2 and weight loss (-12.9%, p&lt;0.01) five years after conversion surgery were present. Internal hernia was the most common early postoperative complication, occurring in 14.8% (n=16) of cases.

Conclusion
Band removal with concomitant gastric bypass in patients with failed gastric banding improves long-term quality of life and may be the rescue procedure of choice in this setting.
Does the change from conventional circular to linear stapling in proximal gastric bypass surgery affect long-term quality of life?
Authors: Teixeira H , Teuben M P J , Teuber H , Hauswirth F , Probst P , Müller M K 
Published: June 2022

Abstract

Objective
The continuous desire to improve bariatric surgery outcomes, and therefore patient satisfaction, leads to a constant search for new surgical approaches. Every change in a well-established protocol needs to undergo evaluation and its benefit for patients must be demonstrated. With respect to technical changes in bariatric surgery, long-term effects on quality of life have not yet been studied. We analyzed quality of life scores and clinical outcomes at a single bariatric center transitioning from circular to a linear bypass protocol.

Methods
Between June 2012 and March 2016, 235 patients were included in this retrospective study from a prospectively collected database. Two groups were compared. Group CBP included those patients treated with a circular stapling bypass protocol (n=117). This protocol was primarily used in 2012. Between 2013 and 2015 a transition period occurred. Thereafter, the linear stapling bypass protocol (Group LBP, n=118) was primarily utilized. Quality of life (QoL) was assessed with the Moorehead-Ardelt QoL score, which was gathered preoperatively, and at 1, 2, and 5 years after surgery.

Results
Quality of life scores improved significantly after intervention in both study groups. The most prominent improvement was seen within the first year after surgery. There were no statistically significant differences between the groups. During the first two years, quality of life score improvement occurred independently of achieved weight loss, whereas a correlation between QoL-improvement and reported weight loss was identified between 24 and 60 months postoperatively (r2 0.112, p&lt;0.001). Further, complications had no impact on change in QoL scores.

Conclusion
Quality of life scores assessed by the Moorehead-Ardelt QoL questionnaire were, independent of operative technique and postoperative weight loss, significantly improved in the first two years after gastric bypass surgery. Thereafter, QoL scores showed lasting improvement in correlation with further weight loss.
Comparison of single- versus double-anastomosis duodenal switch: A single-center experience with 2-year follow-up
Authors: Iranmanesh P , Boudreau V , Gmora S , Hong D , Anvari M 
Published: June 2022

Abstract

Objective
Single-anastomosis duodenal switch (SADS) has emerged in recent years as an alternative to the standard double-anastomosis duodenal switch (DADS). The objective of this study was to compare short- and medium-term outcomes between SADS and DADS.

Methods
Data collected in the Ontario Bariatric Registry between 2010 and 2019 were used for this retrospective study to determine outcomes of patients undergoing primary laparoscopic SADS versus DADS at a Canadian tertiary hospital and bariatric center of excellence. The primary outcome was weight loss at 1 and 2 years after surgery. Short-term secondary outcomes included operative times, intra- and early postoperative complications, hospital length of stay (LOS), and 30-day readmissions. Medium-term secondary outcomes included late postoperative complications as well as nutritional deficiencies and persistent diarrhea at 1 and 2 years after surgery. Subgroup analyses were performed to compare patients undergoing one- and two-stage procedures.

Results
Data of 107 patients who underwent SADS (n = 25) or DADS (n = 82) were included in the study. Follow-up data were available for 59/107 (55.1%) patients at 1 year and 47/107 (43.9%) at 2 years after surgery. Patients in the SADS and DADS groups had similar %TBWL at 1 year (23.6 versus 26.2, P = 0.617) and 2 years (24.8 versus 30.2, P = 0.116) after surgery. Short- and medium-term outcomes were similar between groups. There was no difference between patients undergoing one- versus two-stage procedures.

Conclusion
This study showed that patients undergoing SADS and DADS had similar weight loss at 1 and 2 years. Early and late postoperative morbidity, operative times, early readmissions, and LOS were also similar between groups. Further studies with longer follow-up are required to confirm these results.
Long-term outcomes of ruptured hepatocellular carcinoma: An international multicentric propensity score-matched study
Authors: Joliat G-R , de Man R , Rijckborst V , Cimino M , Torzilli G , Choi G H , Lee H S , Goh B , Kokudo T , Shirata C , Hasegawa K , Nishioka Y , Vauthey J-N , Baimas-George M , Vrochides D , Demartines N , Halkic N , Labgaa I 
Published: June 2022

Abstract

Objective
Long-term outcomes of patients with ruptured hepatocellular carcinoma (rHCC) remain scant. This study aimed to assess disease-free survival (DFS) and overall survival (OS) after surgical resection of rHCC compared to non-ruptured HCC (nrHCC).

Methods
Patients with rHCC and nrHCC were collected from 8 centers in Europe, Asia, and North America. Resected rHCC patients were matched 1:1 to patients undergoing surgery for nrHCC using propensity score and nearest-neighbor method (matching criteria: age, tumor size, cirrhosis, Child-Pugh score, Barcelona Clinic Liver Cancer stage, resection status, grade, and microvascular invasion). Survival rates were calculated using Kaplan-Meier method.

Results
A total of 2033 patients were included: 226 rHCC patients (172 operated: 68 with upfront surgery and 104 after embolization) and 1807 nrHCC patients. Median DFS and OS of rHCC patients (all treatments confounded) were 10 months (95% CI 7–13) and 22 months (95% CI 13–31). Prognostic factors for worse OS among rHCC patients were absence of preoperative arterial embolization (HR 2.3, 95% CI 1.2–4.6, p=0.016), cirrhosis Child B/C (HR 2.4, 95% CI 1.1–5.4, p=0.040), and R1/R2 margins (HR 2, 95% CI 1–5, p=0.049). Survivals were similar between Western and Eastern rHCC patients.
After propensity score matching, 106 rHCC patients and 106 nrHCC patients displayed similar characteristics. Patients with rHCC had shorter median DFS (12 months, 95% CI 7–17 vs. 22 months, 95% CI 12–32, p=0.011), but similar median OS compared to nrHCC patients (43 months, 95% CI 21–65 vs. 63 months, 95% CI 21–105, p=0.060).

Conclusion
In this large dataset including Eastern and Western patients, rHCC was associated with shorter DFS compared to nrHCC, while OS was similar.