bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geometry of gene regulatory dynamics
Authors: Rand David A. , Raju Archishman , Sáez Meritxell , Corson Francis , Siggia Eric D. 
Published: September 2021

Significance
Genetic screens have enumerated the genes that control the process of self-organization that converts a featureless fertilized egg into an embryo. Even the elementary steps may involve 10 genes, so models that attempt to represent each gene contain a plethora of unmeasured parameters. Mathematics has largely categorized the types of solutions that can arise from the equations governing gene networks. These representations are well suited to modern time-lapse imaging, where a limited number of genetic markers are followed in time. Models with minimal parameters that focus on the nonlinear regime from inception to pattern maturation simplify data fitting and provide an intuitive and transparent representation for the dynamics of development.
Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on superenhancers
Authors: Bansal Kushagra , Michelson Daniel A. , Ramirez Ricardo N. , Viny Aaron D. , Levine Ross L. , Benoist Christophe , Mathis Diane 
Published: September 2021

SignificanceAire controls immunological tolerance by driving promiscuous expression of a large swath of the genome in medullary thymic epithelial cells (mTECs). Its molecular mechanism remains enigmatic. To address the hypothesis that Aire impacts chromatin organization through widespread promotion of superenhancer–promoter loops, we performed genome-wide, high-resolution chromosome-conformation capture (Hi-C) experiments on ex vivo mTECs from thymi of mice expressing Aire or not. Integration of the resulting data with inventories of the genome-wide locations of Aire, subunits of the mediator and cohesin complexes, and the chromatin-domain enforcer, CCCTC-binding factor (CTCF), indeed argued for a looping model, which was further supported by biochemical and in vivo loss-of-function analyses.
A diffuse argon plume generated downstream of an atmospheric pressure plasma jet equipped with a positively biased electrode
Authors: Zhao Na , Wu Kaiyue , He Xingran , Chen Junyu , Tan Xin , Wu Jiacun , Ran Junxia , Jia Pengying , Li Xuechen 
Published: September 2021

Abstract
Compared with the diffuse mode of helium plasma jets, a filamentary mode is normally produced in the plasma plume with less expensive inert gas, such as argon, which is undesirable because intense discharge in the filamentary mode may cause damage to fragile samples. Many efforts have been attempted to realize the diffuse mode of an argon plasma jet. In this paper, the diffuse mode is realized in an atmospheric pressure argon plasma jet with increasing biased voltage (V
b) applied to a downstream plate electrode. Results show that the diffuse mode transits from the filamentary mode with the increase of V
b. Waveforms of voltage, current and integrated light emission reveal that the filament originates from a positive discharge with a needle anode, while the diffuse mode results from negative discharges with a needle cathode, which consist of a Trichel-pulse phase and a slower-varying phase. By fast photography, the positive discharge is attributed to a streamer regime, whereas the negative discharges belong to a Townsend-discharge regime. From optical emission spectroscopy, electron density, electron excitation temperature, vibrational temperature, and rotational temperature are studied as functions of V
b.
Detection of single 13C spins coupled to NV center via dynamical decoupling design
Authors: Fan Pengcheng , Yuan Heng , Xu Lixia , Zhang Jixing , Bian Guodong , Li Mingxin , Wang Zhuo 
Published: September 2021

Abstract
The adjusted Carr–Purcell–Meiboom–Gill (CPMG) sequence is mathematically simulated to obtain the 13C nuclear spin signals coupled to a negatively-charged nitrogen-vacancy (NV−) center in diamond. The pulse interval ratio and scanning frequency of the sequence were precisely adjusted to achieve the high-resolution 13C nuclear spin detection. The frequency resolution of the sequence was 5.8 times improved than that of the original CPMG sequence, and the full width at half maximum of the coherence dips were less than 1.7 kHz. The adjusted method can be extended to other dynamical decoupling sequence, and offers a promising approach to improve identification of the nuclear spins in coupled electron-nuclear spin systems.
Electron energy deposition in molecular hydrogen gas: a Monte Carlo simulation using convergent close-coupling cross sections
Authors: Horton Reese K , Scarlett Liam H , Zammit Mark C , Bray Igor , Fursa Dmitry V 
Published: September 2021

Abstract
A Monte Carlo simulation of electron energy deposition in a gas of molecular hydrogen has been conducted with the aim of producing an ab initio estimate of energy deposition parameters such as the mean energy per ion pair. A set of cross sections obtained using the molecular convergent close-coupling method were used as input. At high incident electron energies the mean energy per ion pair was calculated to be 36.3 eV, agreeing with the recommended value of 36.5 ± 0.3 eV. This represents the first fully ab initio calculation of the mean energy per ion pair using a self consistent data set.
Retrofitting urban land through integrative, subsoils-based planning of green stormwater infrastructure: a research framework
Authors: McGuire Mary Pat , Grimley David A , Phillips Andrew C , Stillwell Ashlynn S , William Reshmina , Shen Jinyu , Schneemann Margaret 
Published: September 2021

Abstract
We present a research framework that integrates native subsoil performance and surface retrofitting into coordinated green stormwater infrastructure (GSI) planning. This framework provides communities a strategy to move beyond opportunistic GSI, which can be limited to capturing marginal amounts of stormwater, toward more impactful, coordinated GSI planning that restores the lost hydrologic functioning of the pre-development landscape. We create this framework by establishing critical performance-based relationships among four variables: (1) saturated hydraulic conductivity of native subsoils (∼upper 2 m below urban compaction and fill); (2) GSI design depth for both rain gardens and permeable pavement (in increments of 6″ from 12–30″ for planted and paved GSI); (3) loading ratio, defined as the ratio of GSI retrofit area to upstream impervious surface runoff area (from 1:2 to 1:5 for planted GSI; and 1:1 and direct infiltration for paved GSI); and (4) design storms (rainfall quantity up to 5-inches over 2 h and 24 h durations). We model the four variables using GSI models (built in the US Environmental Protection Agency’s Storm Water Management Model) and reliability analysis, a risk-assessment method adapted to characterize the reliability of GSI in response to varying stormwater runoff loading. The outcome of the modeling is a set of fragility curves and design prototypes, adjustable to catchment and sub-catchment scales, to assist municipalities in early funding and investment decisions to retrofit urbanized land through GSI. We also share two piloted applications in which we use the research framework within the Chicago-Calumet region in Illinois, USA, to conduct site-specific subsoil sampling and determinations of saturated hydraulic conductivity and to develop urban-scale GSI retrofit scenarios. Our framework is transferable to other urban regions, and particularly useful where a lack of integrating native subsoil performance into GSI design hinders decision-making, coordinated GSI planning at scale, and achieving high runoff reduction targets.
Cytosolic phosphofructokinases are important for sugar homeostasis in leaves of Arabidopsis thaliana
Authors: Perby Laura Kathrine , Richter Simon , Weber Konrad , Hieber Alina Johanna , Hess Natalia , Crocoll Christoph , Mogensen Helle Kildal , Pribil Mathias , Burow Meike , Nielsen Tom Hamborg , Mustroph Angelika 
Published: September 2021

Abstract

Background and Aims
ATP-dependent phosphofructokinases (PFKs) catalyse phosphorylation of the carbon-1 position of fructose-6-phosphate, to form fructose-1,6-bisphosphate. In the cytosol, this is considered a key step in channelling carbon into glycolysis. Arabidopsis thaliana has seven genes encoding PFK isoforms, two chloroplastic and five cytosolic. This study focuses on the four major cytosolic isoforms of PFK in vegetative tissues of A. thaliana.

Methods
We isolated homozygous knockout individual mutants (pfk1, pfk3, pfk6 and pfk7) and two double mutants (pfk1/7 and pfk3/6), and characterized their growth and metabolic phenotypes.

Key Results
In contrast to single mutants and the double mutant pfk3/6 for the hypoxia-responsive isoforms, the double mutant pfk1/7 had reduced PFK activity and showed a clear visual and metabolic phenotype with reduced shoot growth, early flowering and elevated hexose levels. This mutant also has an altered ratio of short/long aliphatic glucosinolates and an altered root–shoot distribution. Surprisingly, this mutant does not show any major changes in short-term carbon flux and in levels of hexose-phosphates.

Conclusions
We conclude that the two isoforms PFK1 and PFK7 are important for sugar homeostasis in leaf metabolism and apparently in source–sink relationships in A. thaliana, while PFK3 and PFK6 only play a minor role under normal growth conditions.
Botulinum Toxin A in the Management of a Gummy Smile: A Clinical Controlled Preliminary Study
Authors: Costa Aline Bitencourt , Romansina Dinete , Ramalho Juliana , Pereira Priscilla , Tedesco Tamara Kerber , Morimoto Susana , Gonçalves Flávia , Ramalho Karen Müller 
Published: September 2021

Abstract

Background
Botulinum toxin type A (BTX-A) is recent technique for the treatment of gummy smile.

Objectives
The aim of this randomized controlled preliminary clinical trial was to evaluate the effects of BTX-A on excessive gingiva display (EGD) reduction, muscle activity, and patient satisfaction at 2, 8, 12, 16, 21, and 25 weeks.

Methods
Group 1 (G1) received 4 points of BTX-A application (2 U/point) for relaxation of the levator labii superioris alaeque nasi and levator labii superioris muscles; Group 2 (G2) received 2 points of BTX-A (2 U/point) for relaxation of only the levator labii superioris alaeque nasi muscle.

Results
A high dropout of patients from follow-up sessions occurred. Therefore, because of this data limitation, the results were considered a preliminary outcome. At 2 weeks, there was a significant difference between baseline regarding the reduction of EGD in G1 and G2, reduction in muscle activity in G1, and increased satisfaction in G1 and G2. At 2 weeks, there was no difference between the 2 groups. Statistically significant EGD reduction was maintained until 16 weeks in G2 and 25 weeks in G1. After 14 days there was a gradual recovery of muscle activity in both groups until recovery of baseline values by 25 weeks. Patients’ satisfaction with treatment lasted 21 weeks in G1 and 16 weeks in G2.

Conclusions
Increasing the number of BTX-A injection points resulted in a prolonged effect regarding EGD reduction and patient satisfaction but did not increase the intensity of the outcome. However, due to the high dropout of patients, this is a preliminary conclusion and further studies are necessary to confirm these results.

Level of Evidence: 2
Waking up from a taxonomist’s nightmare: emerging structure ofRanunculussectionBatrachium(Ranunculaceae) in central Europe based on molecular data and genome sizes
Authors: Koutecký Petr , Prančl Jan , Košnar Jiří , Koutecká Eva , Hanzlíčková Johana , Lučanová Magdalena , Nejedlá Michaela , Kaplan Zdeněk 
Published: September 2021

AbstractRanunculus section Batrachium (water crowfoot) ranks among the most taxonomically challenging aquatic plant groups due to morphological reduction, phenotypic plasticity, polyploidy and reticulate evolution. This study, for the first time in this group, linked morphology, genome size and genetic data (two non-coding regions of plastid DNA and the ITS region of nuclear ribosomal DNA). This extensive data set, including 258 central European populations, enables us to recognize widespread lineages from hybrids and to trace the evolutionary processes underlying the observed diversity. Most of the traditionally recognized species are supported. However, the presence of two morphologically cryptic but genetically well-differentiated lineages was detected within Ranunculus trichophyllus, and three separate lineages of different parentage were confirmed in the Ranunculus penicillatus complex. An allopolyploid origin was revealed in Ranunculus aquatilis, Ranunculus baudotii and in both lineages of R. trichophyllus, for which the parentage has not yet been studied, and allopolyploidy is suspected in all other polyploid taxa except for the triploid cytotype of Ranunculus fluitans, which is most likely autopolyploid. We detected putative F1 hybrids of seven different parentage combinations, including two involving Ranunculus rionii, representing the first known hybrids of this species. An additional 13 hybrid cytotypes (backcrosses or entailing additional polyploidization) were revealed; c. 20% of Ranunculus peltatus accessions seem to be influenced by introgression detectable only using sequence data. The Batrachium group is remarkable due to the coexistence of well-defined lineages with recently evolved biotypes arising due to hybridization and polyploidization.
Total and Unbound Doravirine Concentrations and Viral Suppression in CSF
Authors: Tiraboschi Juan , Scévola Sofia , Penchala Sujan Dilly , Challenger Elisabeth , Else Laura , Prieto Paula , Saumoy Maria , Imaz Arkaitz , Silva-Klug Ana , Niubó Jordi , Soriano Irene , Khoo Saye , Rigo-Bonin Raul , Podzamczer Daniel 
Published: September 2021

Abstract
We determined total and unbound concentrations of doravirine (DOR) in cerebrospinal fluid and blood plasma. Total and unbound DOR concentrations in cerebrospinal fluid exceeded the half-maximal effective concentration against wild-type virus (5.1 ng/mL) in all patients, suggesting that DOR may contribute to inhibit viral replication in this compartment.
10 EFFECT OF SUBSPECIALTIES OF GASTRO-INTESTINAL SURGERIES ON PATIENT’S OUTCOMES
Authors: Ezz Reda 
Published: September 2021

Abstract

Subspecialty policy is increasing all over the world aiming to improve the results of heavy esophageal surgeries.
Our aim is to define the impact of having surgical specialized esophageal unit on the volume of patients and the results.

Methods
We reviewed all esophageal cases managed in our esophageal specialized department (from May 2016 to May 2019 Group A) and we compared the results to previous 3 years (from May 2013 to May 2016 Group B) and to the international results. There was 394 cases in group A compared to 104 cases in group B.

Results
For Gastro esophageal reflux disease (GERD),180 operations were performed in group a (45.7%) compared to 61 cases in group B (68.7%). Forty two (10.7%) modified Heller’s cardiomyotomy (Open and laparoscopic) for achalasia were performed in group A compared to 17 cases (16.3%) in group B. Surgeries for malignant lesions were performed for 122 cases (30.9%) in group A compared to 13 cases (12.5%) in group B. Other Esophageal operations were also done for 50 cases (12.7%) in group A compared to 13 cases (12.5%) in group B. Morbidities and mortalities are reported and compared to the international results.

Conclusion
Our results in group A are comparable to Hospital mortality rates for patients in medium-volume centers (7.5%). Also we approach the International results for morbidities of benign esophageal disease (5.7–12.7%) for fundoplication.
Having a specialized esophageal unit resulted in increase of the volume of patients and improvement of the results.
113 CONCURRENT SURGICAL TREATMENT STRATEGY FOR SYNCHRONOUS ESOPHAGEAL CANCER AND HEAD AND NECK CANCER IN OUR INSTITUTION
Authors: Shimada Ayako , Tanaka Motomu , Ishii Satoru , Yamamoto Yusuke , Oosaki Masaumi , Nishijima Wataru , Oomura Kenji , Wakabayashi Go 
Published: September 2021

Abstract

Esophageal cancer patients have a high frequency to coincide with head and neck (H&N) cancer. We have corporated together with Otorhinolaryngology, H&N Surgery, and Plastic surgery department doctors for the treatment of synchronous esophageal and H&N cancer patients. The aim of this study is to analyze the treatment results and prognosis of synchronous esophageal and H&N cancer patients.

Methods
From January 2014 to December 2019, 5 patients underwent concurrent surgical resection of synchronous esophageal and H&N cancer in our institution. We retrospectively reviewed the surgical outcomes and prognosis of these patients of synchronous esophageal and H&N cancer (HNEC group) and compared the results with 27 patients who had esophagectomy with 3 regional lymph node dissection during the same period (EC group).

Results
The location of H&N cancers were pharynx/tongue; 4/1, and clinical stage was all Stage IV. The clinical stage of esophageal cancers was Stage 0/I/II/III; 1/1/2/1. All patients underwent video-assisted thoracic esophagectomy. The surgical procedures concurrently performed for the H&N cancer were pharyngolaryngectomy with free jejunum transfer for 3 patients, wide tongue and mandibular segment resection with mandibular reconstruction in 1 patient, and mandibular transection with radial forearm flap reconstruction in 1 patient. There was no significant difference in the frequency of postoperative complication between 2 groups. HNEC group tend to have shorter recurrence free survival compared to EC group (p = 0.051).

Conclusion
H&N surgery with thoracotomy is a highly invasive surgery, however, it can be safely performed with local management. The risk of recurrence is high in H&N cancer patients, therefore it is important to move onto adjuvant therapy without delay. Paraenteral nutrition may be useful in management of these patients.
131 PRACTICES IN PERIOPERATIVE NUTRITION PRECEDING OR FOLLOWING OESOPHAGECTOMY: RESULTS OF A EUROPEAN SURVEY
Authors: Van Veer Hans , Luyer Misha , Depypere Lieven , Nafteux Philippe , Coosemans Willy 
Published: September 2021

Abstract

The route and type of peri-operative feeding after oesophagectomy varies widely across centres, usually based on local experiences and standing orders. The aim of this survey on perioperative nutrition after oesophagectomy (PONOS) was to create a snapshot the way perioperative nutrition preceding or following oesophagectomy is established across reference centres in Europe, and what the reasons are for preferring one method over another.

Methods
A survey consisting of four parts was distributed to the membership of 3 European, mainly surgical oriented scientific societies between October 2019 and January 2020. The first part contained some general questions regarding demographics of the participants and type of performed surgery. In the second section, centres were asked about practices in preoperative nutrition. The third section questioned participants about their practices in postoperative nutrition; in the last part the daily practice was reflected against the current available ESPEN guidelines.

Results
Fifty-one surgeons from 49 centres in 16 countries participated. The majority had a structured nutrition team in their institution. An Enhanced Recovery Pathway was implemented in 2/3 of centres. ESPEN guidelines were followed in 50% of centers. Routine preoperative nutritional assessment was performed in 84%. Preoperative nutritional support consisted mainly of enteral and oral support; immediate postoperatively mostly a combination of oral and enteral or enteral only; at discharge mostly a combination of oral and enteral or only oral nutritional supplementation were used. Timing, definition and means of postoperative oral intake also seemed to differ widely across centres.

Conclusion
The PONOS survey confirmed our assumption that perioperative feeding after oesophagectomy exists in a wide variety across European centres performing oesophageal resections for cancer. Survey based feedback to the surgical community draws attention to this often underexposed part of the surgical pathway of a patient. As such, this might further enhance the exchange of experiences in order to try to harmonise peri-operative feeding regimen.
142 A RANDOMIZED TRIAL: THREE-FILED LYMPHADENECTOMY COMPARED WITH TWO-FIELD LYMPHADENECTOMY FOR MIDDLE AND LOWER THORACIC ESOPHAGEAL CANCER
Authors: Li Bin 
Published: September 2021

Abstract

Esophagectomy combined with radical lymphadenectomy is widely accepted, but the role of three-field lymphadenectomy (3-FLD) remains unclear.

Methods
We performed an open-label, randomized, controlled trial involving patients with resectable cancer of the middle or lower third of the esophagus. Patients were randomly assigned to undergo esophagectomy with either 3-FLD (cervical-thoracic-abdominal lymphadenectomy) or two-field lymphadenectomy (thoracic-abdominal lymphadenectomy, 2-FLD) at a 1:1 ratio. The primary endpoint was overall survival (OS). Analysis were done according to the intent-to-treat principle.

Results
Postoperative complications were similar in the two arms. More lymph nodes were resected in 3-field arm (Median, 37 vs. 24 [2-FLD], P &lt; 0.001), 43 (21.5%) patients had cervical LNM. More pN3 patients were identified in the 3-FLD arm (10.5%, 21/200 vs. 5.0%, 10/200 [2-FLD], P = 0.040). The cumulative probability of disease-free survival (DFS) was comparable between the two arms (HR, 1.021, 95%CI, 0.735–1.417, P = 0.903), as well as the OS (HR, 1.026, 95%CI, 0.694–1.515, P = 0.899). The cumulative 5-year DFS was 52% in the 3-FLD arm, as compared with 53% in the 2-FLD arm; 5-year OS rates were 64% and 62%.

Conclusion
Three-field lymphadenectomy offered more accurate nodal staging without increasing the surgical complications. Comparing with radical 2-FLD, there was no improvement in OS or DFS after 3-FLD for patients with middle and lower thoracic esophageal cancer.
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