bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and assembly of DNA molecules using multi-objective optimization
Authors: Gaeta Angelo , Zulkower Valentin , Stracquadanio Giovanni 
Published: October 2021

Abstract
Rapid engineering of biological systems is currently hindered by limited integration of manufacturing constraints into the design process, ultimately reducing the yield of many synthetic biology workflows. Here we tackle DNA engineering as a multi-objective optimization problem aiming at finding the best tradeoff between design requirements and manufacturing constraints. We developed a new open-source algorithm for DNA engineering, called Multi-Objective Optimisation algorithm for DNA Design and Assembly, available as a Python and Anaconda package, as well as a Docker image. Experimental results show that our method provides near-optimal constructs and scales linearly with design complexity, effectively paving the way to rational engineering of DNA molecules from genes to genomes.
The effect of elevated CO2 on aboveground and belowground carbon allocation and eco-physiology of four species of angiosperm and gymnosperm forest trees
Authors: Dror Dar , Klein Tamir 
Published: October 2021

Abstract
Although atmospheric CO2 concentration ([CO2]) continues to rise, the question of how tree carbon (C) allocation is affected by this change remains. Studies show that C assimilation increases under elevated CO2 (eCO2). Yet, no detailed study has determined the fate of the surplus C, i.e., its compartment and physiological process allocation, nor in multiple species together. In this project, we grew 2-year-old saplings of four key Mediterranean tree species (the conifers Cupressus sempervirens L. and Pinus halepensis Mill., and the broadleaf Quercus calliprinos Webb. and Ceratonia siliqua L.) to [CO2] levels of 400 or 700 p.p.m. for 6 months. We measured the allocation of C to below and aboveground growth, respiration, root exudation, storage and leaf litter. In addition, we monitored intrinsic water-use efficiency (WUE), soil moisture, soil chemistry and nutrient uptake. Net assimilation, WUE and soil nitrogen uptake significantly increased at eCO2 across the four species. Broadleaf species showed soil water savings, which were absent in conifers. All other effects were species-specific: Cupressus had higher leaf respiration, Pinus had lower starch in branches and transiently higher exudation rate and Quercus had higher root respiration. Elevated CO2 did not affect growth or litter production. Our results are pivotal to understanding the sensitivity of tree C allocation to the change in [CO2] when water is abundant. Species-specific responses should be regarded cautiously when predicting future changes in forest function in a higher CO2 world.
Validation of a Cost-effective Cast Saw Simulation-based Educational Module to Improve Cast Removal Safety
Authors: Liles Jeffrey , Wieschhaus Kyle , Wieschhaus Keaton , Adams William , Cappello Teresa , Evans Douglas 
Published: October 2021

Background:
Inexperience in cast removal in the pediatric population can lead to a range of cast saw–related injuries. The purpose of this study is to validate a simple simulation-based wax model that is both reproducible and economical while providing a valuable tool that can be used to grade cast saw use performance in trainees.

Methods:
Cylindrical wax models were used as an analog for a pediatric upper extremity. The wax models were casted in a proscribed reproducible fashion for consistency. Two groups, the first consisting of 15 experienced cast saw users and the second consisting of 15 inexperienced individuals, completed 4 sequential longitudinal cuts in the casted wax models. After removal of the cast material, marks left by the cast saw in the wax were counted and measured. Indentation length, maximum depth, and maximum width were measured on each wax model. The total length of the cast saw indentations per cast saw user was also calculated.

Results:
For the inexperienced cast saw users, the average total length of the cast saw indentations was 526.56 mm, average maximum depth was 1.91 mm, and average maximum width was 3.24 mm. For experienced cast saw users, the average total length of the cast saw indentations was 156.57 mm with an average maximum depth of 1.06 mm and average maximum width of 2.19 mm. Receiver operating characteristic curves of the total number of errors, total error length, maximum error depth, and maximum error width show effective discrimination of experienced from inexperienced trainees.

Conclusions:
This study provides valid evidence supporting a cost-effective, time-efficient, and easily reproducible educational simulation module that can objectively measure cast saw the performance in trainees. This model demonstrates construct validity and can distinguish novice from experienced cast saw users. It is sensitive enough to identify mistakes even in the most experienced cast saw users, creating a platform that can provide performance-based feedback to cast saw users of all experience levels.

Level of Evidence:
Level III—diagnostic test.
Reoperations After Decompression With or Without Fusion for L3-4 Spinal Stenosis With Degenerative Spondylolisthesis
Authors: Joelson Anders , Nerelius Fredrik , Holy Marek , Sigmundsson Freyr G. 
Published: October 2021

Study Design:
Register study with prospectively collected data.

Objective:
The aim was to investigate reoperation rates at the index level and the adjacent levels after surgery for lumbar L3-4 spinal stenosis with concomitant degenerative spondylolisthesis (DS).

Summary of Background Data:
There are different opinions on how to surgically address lumbar spinal stenosis with DS. The potential benefit of fusion surgery should be weighed against the risks of future reoperations because of adjacent segment degeneration. Data on the reoperation rate at adjacent segments after single level L3-4 fusion surgery are limited.

Materials and Methods:
A total of 372 patients, who underwent surgery for lumbar L3-4 spinal stenosis with DS (slip >3 mm) between 2007 and 2012, were followed between 2007 and 2017 to identify reoperations at the index level and adjacent levels. The reoperation rate for decompression and fusion was compared with the reoperation rate for decompression only. Patient-reported outcome measures before and 1 year after surgery were evaluated.

Results:
The reoperation rate at the index level (L3-4) was 3.5% for decompression and fusion and 5.6% for decompression only. At the cranial adjacent level (L2-3), the corresponding numbers were 6.6% and 4.2%, respectively, and the caudal adjacent level (L4-5), the corresponding numbers were 3.1% and 4.9%, respectively. The effect sizes of change were larger for decompression and fusion compared with decompression only. The effect sizes of change were similar for leg pain and back pain.

Conclusions:
We could not identify any differences in reoperation rates at the cranial or caudal adjacent segment after decompression and fusion compared with decompression only for L3-4 spinal stenosis with DS. The improvement in back pain is similar to the improvement in leg pain after surgery for L3-4 spinal stenosis with DS.
Case Report: Polyneuropathy Pituitary Apoplexy with Normal Perimetry and Initially Normal Neuroimaging
Authors: Sowka Joseph W. , Wu Tsung-Hao 
Published: October 2021

SIGNIFICANCE
Pituitary apoplexy is a syndrome with a varied appearance, which carries a significant risk of morbidity and mortality. It is important to recognize the potential numerous symptoms and clinical findings, urgently investigate with the proper neuroimaging tests, and coordinate care with the appropriate specialists without delay.

PURPOSE
This study aimed to describe a patient with worsening headache and ophthalmoparesis attributable to pituitary apoplexy who initially had reportedly a normal neuroimaging result and were diagnosed with migraine.

CASE REPORT
A 39-year-old Hispanic man with a history of migraine developed a new and worsening headache. He presented to a hospital emergency department where he underwent a non–contrast-enhanced computed tomography and MRI, whose results were subsequently interpreted as normal. His headache was attributed to migraine, and he was medicated as such and discharged. Three days later, he developed horizontal and vertical diplopia and sought a second opinion. His visual acuity and visual fields were normal. He manifested a right pupil–sparing, external partial cranial nerve III palsy and concurrent right sixth nerve palsy. He also complained of worsening headache and lethargy. He was immediately referred for contrast-enhanced MRI and magnetic resonance angiography with suspicion of pituitary apoplexy. Subsequent imaging revealed a hemorrhagic pituitary macroadenoma consistent with pituitary apoplexy that was expanding laterally into the right cavernous sinus. He underwent immediate neurosurgical surgical repair.

CONCLUSIONS
New or worsening headache with signs and symptoms of hypopituitarism should immediately be investigated for pituitary apoplexy. Other possible findings include involvement of cranial nerves III through VI because of cavernous sinus involvement and visual deficits if the optic chiasm or intracranial portion of the optic nerve is involved. However, growth may be lateral, and no visual deficits may be found, as in this case. Multiple concurrent cranial neuropathies should increase suspicion for cavernous sinus involvement.
HIV Disease Dynamics and Markers of Inflammation and CNS Injury During Primary HIV Infection and Their Relationship to Cognitive Performance
Authors: Longino August A. , Paul Robert , Wang Yixin , Lama Javier R. , Brandes Peter , Ruiz Eduardo , Correa Cecilia , Keating Sheila , Spudich Serena S. , Pilcher Christopher , Vecchio Alyssa , Pasalar Siavash , Bender Ignacio Rachel A. , Valdez Rogelio , Dasgupta Sayan , Robertson Kevin , Duerr Ann 
Published: October 2021

Introduction:
Early systemic and central nervous system viral replication and inflammation may affect brain integrity in people with HIV, leading to chronic cognitive symptoms not fully reversed by antiretroviral therapy (ART). This study examined associations between cognitive performance and markers of CNS injury associated with acute HIV infection and ART.

Methods:
HIV-infected MSM and transgender women (average age: 27 years and education: 13 years) enrolled within 100 days from the estimated date of detectable infection (EDDI). A cognitive performance (NP) protocol was administered at enrollment (before ART initiation) and every 24 weeks until week 192. An overall index of cognitive performance (NPZ) was created using local normative data. Blood (n = 87) and cerebrospinal fluid (CSF; n = 29) biomarkers of inflammation and neuronal injury were examined before ART initiation. Regression analyses assessed relationships between time since EDDI, pre-ART biomarkers, and NPZ.

Results:
Adjusting for multiple comparisons, shorter time since EDDI was associated with higher pre-ART VL and multiple biomarkers in plasma and CSF. NPZ scores were within the normative range at baseline (NPZ = 0.52) and at each follow-up visit, with a modest increase through week 192. Plasma or CSF biomarkers were not correlated with NP scores at baseline or after ART.

Conclusions:
Biomarkers of CNS inflammation, immune activation, and neuronal injury peak early and then decline during acute HIV infection, confirming and extending results of other studies. Neither plasma nor CSF biomarkers during acute infection corresponded to NP scores before or after sustained ART in this cohort with few psychosocial risk factors for cognitive impairment.
Anthropometric Study of Human Ear: A Baseline Data for Ear Reconstruction
Authors: Prasetyo Arif Tri , Putri Indri Lakhsmi 
Published: October 2021

Background:
Creation of an auricular framework plays the main role on first stage of microtia reconstruction. The size of framework is determined based on the size of the contralateral healthy ear and customized with Nagata theory. The height of rib that added behind the previous framework is the same with the projection of the normal ear. But the height of rib needed and framework in bilateral cases is unknown. A population based auricular framework pattern and projection are urgently needed.

Objectives:
This study aimed at determining the mean values of normal anthropometric measurement of external ear and projection of human ear in males and females and their comparison on either sides and in either sex.

Materials and Methods:
Measurements are taken from 524 subjects (96 men and 428 women) aged 17 to 35 years using a Vernier caliper. The parameters measured were total ear height, ear width, lobular height, lobular width, upper pole, middle upper pole, middle pole, lower middle pole, lower pole, each subject's right and left ears.

Results:
Comparisons between gender were performed by independent t test and paired t test for comparison between right and the left ear. All dimensions were significantly different between male and female (P
< 0.05) except the right lobular height (P
> 0.05). There was no significant difference both side among groups (P
< 0.05) except total ear height on female group (P
> 0.05). All projection dimensions were significantly different between male and female. There was no significant difference of auricular projection of right and left auricular on the male (P
< 0.05) groups except the projection of lower pole. There were significant between auricular projection of right and left ears on the female groups (P
> 0.05).

Conclusions:
These findings suggest that the normal anthropometric study will have implication in the ear reconstruction especially on bilateral cases as a baseline for reconstruction.
Infratemporal Fossa Chondroblastoma
Authors: Dimitrijević Milovan V. , Sopta Jelena P. , Todorović Nikola R. , Simić Ljubica 
Published: October 2021

Introduction:
Chondroblastoma is a rare, benign mesenchymal tumor that can behave local aggressive. It most often occurs in the area of the epiphyses of long tubular bones, whereas the appearance in the region of the head and neck is rare, only few reports were published in literature. The incidence of chondroblastoma of the craniofacial region is about 6.4%.

Clinical Report:
A 46-year-old patient was hospitalized due to growth and pain in the area of the left half of the face, and a tumor of the left infratemporal fossa was diagnosed by computed tomography. The patient was operated with a preauricular surgical approach, parotidectomy, and complete tumor removal was performed. Pathohistological examination revealed chondroblastoma.

Conclusions:
Chondroblastoma of the craniofacial region is very rare pathohistological finding, characterized by slow and asymptomatic growth until it reaches the appropriate dimensions, the clinical symptomatology depends on the localization of the tumor. Computed tomography diagnostics provides important information about the location, size of the tumor, invasion of surrounding structures, and significantly contributes to the decision on the appropriate surgical approach. Diagnostic dilemma solving only final pathohistological verification.
Assessing Operative Skill in the Competency-based Education Era
Authors: Toale Conor , Morris Marie , Kavanagh Dara O. 
Published: October 2021

Introduction:
Decisions regarding the operative competence of surgical residents in the United Kingdom and Ireland are informed by operative workplace-based assessments (WBAs) and operative number targets for index procedures. This review seeks to outline the validity evidence of these assessment methods.

Methods:
A review of the MEDLINE (Pubmed), EMBASE and Cochrane Library databases was undertaken in accordance with the Joanna Briggs Institute Protocol for Scoping Reviews (2020). Articles were included if they provided evidence of the validity of procedure-based assessments, direct observation of procedural skills, or indicative operative number targets. The educational impact of each article was evaluated using a modified Kirkpatrick model.

Results:
Twenty-eight articles outlining validity evidence of WBAs and operative number targets were synthesised by narrative review. Five studies documented users’ views on current assessment methods (Kirkpatrick level 1). Two articles recorded changes in attitudes towards current operative assessments (level 2a). Ten studies documented the ability of current assessments to record improvements in operative competence (level 2b). Ten studies measured a change in behaviour as a result of the introduction of these assessments (level 3). One article studied the ability of operative assessments to predict clinical outcomes (level 4b).

Conclusions:
Operative WBAs are reliable. Scores achieved correlate with both time spent in training and recorded operative experience. Trainers and residents have concerns regarding the subjectivity of these assessments and the opportunistic nature in which they are used. Operative number targets are not criterion-referenced, lack validity evidence, and may be set too low to ensure operative competence.
The Diagnostic Accuracy of Abdominal Computed Tomography in Diagnosing Internal Herniation Following Roux-en-Y Gastric Bypass Surgery
Authors: Nawas May Al , Oor Jelmer E. , Goense Lucas , Hosman Stephanie F. M. , van der Hoeven Erik J. R. J. , Wijffels Niels A. T. , Riele Wouter W. te , Takkenberg Marijn , Wiezer Marinus J. , Derksen Wouter J. M. 
Published: October 2021

Objective:
To analyze the diagnostic accuracy of abdominal computed tomography (CT) in diagnosing internal herniation (IH) following Rouxen-Y gastric bypass (RYGB) surgery.

Summary of Background Data:
IH is one of the most important and challenging complications following RYGB. Therefore, early and adequate diagnosis of IH is necessary. Currently, exploratory surgery is considered the gold standard in diagnosing IH. Although CT scans are frequently being used, the true diagnostic accuracy in diagnosing IH remains unclear.

Methods:
PubMed, Embase, and Cochrane databases were systematically searched for relevant articles describing the diagnostic accuracy of abdominal CT in diagnosing IH after RYGB. Data were extracted, recalculated, and pooled to report on the overall diagnostic accuracy of CT in diagnosing IH, and the diagnostic accuracy of specific radiological signs.

Results:
A total of 20 studies describing 1637 patients were included. seventeen studies provided data regarding the overall diagnostic accuracy: pooled sensitivity of 82.0%, specificity of 84.8%, positive predictive value of 82.7%, and negative predictive value of 85.8% were calculated. Eleven studies reported on specific CT signs and their diagnostic accuracy. The radiological signs with the highest sensitivity were the signs of venous congestion, swirl, and mesenteric oedema (sensitivity of 78.7%, 77.8%, and 67.2%, respectively).

Conclusions:
This meta-analysis demonstrates that CT is a reliable imaging modality for the detection of IH. Therefore, abdominal CT imaging should be added to the diagnostic work-up for RYGB patients who present themselves with abdominal pain suggestive of IH to improve patient selection for explorative surgery.
Bayesian Approach to Understand the Association Between Treatment Down-staging and Survival for Patients With Pancreatic Adenocarcinoma
Authors: da Costa Wilson Luiz , Tran Cao Hop S. , Gu Xiangjun , Massarweh Nader N. 
Published: October 2021

Objective:
To evaluate the association between staging concordance, treatment sequencing, and response to neoadjuvant therapy (NAT) on the survival of patients with pancreatic ductal adenocarcinoma (PDAC).

Summary of Background Data:
NAT is increasingly utilized in the management of patients with PDAC, but it is unclear whether its benefit is contingent on tumor down-staging.

Methods:
This was a cohort study of stage I-III PDAC patients in the National Cancer Database (2006–2015) treated with upfront resection or NAT followed by surgery. We determined staging concordance using patients’ clinical and pathological staging data. For NAT patients, we used Bayesian analysis to ascertain staging concordance accounting for down-staging.

Results:
Among 16,597 patients treated at 979 hospitals, 13,982 had an upfront resection and 2,615 NAT followed by surgery. Overall survival (OS) at 5-years ranged from 26.0% (95% CI 24.9%–27.1%) among cT1-2N0 patients to 18.6% (17.9%–19.2%) among cT1-3N+ ones. Patients with cT3-4 or cN+ tumors had improved OS after NAT compared to upfront surgery (all p< 0.001), while there was no difference among patients with cT1-2N0 (P = 0.16) disease. Relative to accurately staged cT1-2-3N+ or cT4 patients treated with upfront surgery, NAT was associated with a lower risk of death [HR 0.46 (0.37–0.57) for N+; HR 0.56 (0.40–0.77) for T4 disease], even among those without tumor down-staging [HR 0.81 (0.73–0.90) for N+; HR 0.48 (0.39–0.60) for T4].

Conclusions:
NAT is associated with improved survival for PDAC, particularly for patients with more advanced disease and regardless of down-staging. Consideration should be given to recommending NAT for all PDAC patients.
Influence of Br
−
/S
2−
site-exchange on Li diffusion mechanism in Li
6
PS
5
Br: a computational study
Authors: Sadowski Marcel , Albe Karsten 
Published: October 2021

We investigate how low degrees of

Br

−

/

S

2
−

site-exchange influence the

Li

+

diffusion in the argyrodite-type solid electrolyte

Li

6

PS

5

Br

by
ab initio
molecular dynamics simulations. Based on the atomic trajectories of the defect-free material, a new mechanism for the internal

Li

+

reorganization within the

Li

+

cages around the

4
d

sites is identified. This reorganization mechanism is highly concerted and cannot be described by just one rotation axis. Simulations with

Br

−

/

S

2
−

defects reveal that

Li

+

interstitials (

L
ii
.

) are the dominant mobile charge carriers and originate from Frenkel pairs. These are formed because

B
rS
.

defects on the

4
d

sites donate one or even two

L
ii
.

to the neighbouring cages. The

L
ii
.

then carry out intercage jumps via interstitial and interstitialcy mechanisms. With that, one single

B
rS
.

defect enables

Li

+

diffusion over an extended spatial area explaining why low degrees of site-exchange are sufficient to trigger superionic conduction. The vacant sites of the Frenkel pairs, namely

V

Li

′

, are mostly immobile and bound to the

B
rS
.

defect. Because

S

Br

′

defects on

4
a

sites act as sinks for

L
ii
.

they seem to be beneficial only for the local

Li

+

transport. In their vicinity T4 tetrahedral sites start to get occupied. Because the

Li

+

transport was found to be rather confined if

S

Br

′

and

B
rS
.

defects are direct neighbours, their relative arrangement seems to be crucial for effective long-range transport.

This article is part of the Theo Murphy meeting issue ‘Understanding fast-ion conduction in solid electrolytes’.