bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primal-dual for classification with rejection (PD-CR): a novel method for classification and feature selection—an application in metabolomics studies
Authors: Chardin David , Humbert Olivier , Bailleux Caroline , Burel-Vandenbos Fanny , Rigau Valerie , Pourcher Thierry , Barlaud Michel 
Published: December 2021

AbstractBackgroundSupervised classification methods have been used for many years for feature selection in metabolomics and other omics studies. We developed a novel primal-dual based classification method (PD-CR) that can perform classification with rejection and feature selection on high dimensional datasets. PD-CR projects data onto a low dimension space and performs classification by minimizing an appropriate quadratic cost. It simultaneously optimizes the selected features and the prediction accuracy with a new tailored, constrained primal-dual method. The primal-dual framework is general enough to encompass various robust losses and to allow for convergence analysis. Here, we compare PD-CR to three commonly used methods: partial least squares discriminant analysis (PLS-DA), random forests and support vector machines (SVM). We analyzed two metabolomics datasets: one urinary metabolomics dataset concerning lung cancer patients and healthy controls; and a metabolomics dataset obtained from frozen glial tumor samples with mutated isocitrate dehydrogenase (IDH) or wild-type IDH.ResultsPD-CR was more accurate than PLS-DA, Random Forests and SVM for classification using the 2 metabolomics datasets. It also selected biologically relevant metabolites. PD-CR has the advantage of providing a confidence score for each prediction, which can be used to perform classification with rejection. This substantially reduces the False Discovery Rate.ConclusionPD-CR is an accurate method for classification of metabolomics datasets which can outperform PLS-DA, Random Forests and SVM while selecting biologically relevant features. Furthermore the confidence score provided with PD-CR can be used to perform classification with rejection and reduce the false discovery rate.
AttCRISPR: a spacetime interpretable model for prediction of sgRNA on-target activity
Authors: Xiao Li-Ming , Wan Yun-Qi , Jiang Zhen-Ran 
Published: December 2021

Abstract
Background
More and more Cas9 variants with higher specificity are developed to avoid the off-target effect, which brings a significant volume of experimental data. Conventional machine learning performs poorly on these datasets, while the methods based on deep learning often lack interpretability, which makes researchers have to trade-off accuracy and interpretability. It is necessary to develop a method that can not only match deep learning-based methods in performance but also with good interpretability that can be comparable to conventional machine learning methods.

Results
To overcome these problems, we propose an intrinsically interpretable method called AttCRISPR based on deep learning to predict the on-target activity. The advantage of AttCRISPR lies in using the ensemble learning strategy to stack available encoding-based methods and embedding-based methods with strong interpretability. Comparison with the state-of-the-art methods using WT-SpCas9, eSpCas9(1.1), SpCas9-HF1 datasets, AttCRISPR can achieve an average Spearman value of 0.872, 0.867, 0.867, respectively on several public datasets, which is superior to these methods. Furthermore, benefits from two attention modules—one spatial and one temporal, AttCRISPR has good interpretability. Through these modules, we can understand the decisions made by AttCRISPR at both global and local levels without other post hoc explanations techniques.

Conclusion
With the trained models, we reveal the preference for each position-dependent nucleotide on the sgRNA (short guide RNA) sequence in each dataset at a global level. And at a local level, we prove that the interpretability of AttCRISPR can be used to guide the researchers to design sgRNA with higher activity.
The physiological and psychological effects of cognitive behavior therapy on patients with inflammatory bowel disease before COVID-19: a systematic review
Authors: Chen Jie , Chen Xuejie , Sun Yuhao , Xie Ying , Wang Xiaoyan , Li Ran , Hesketh Therese 
Published: December 2021

Abstract
Objective
Cognitive behavioral therapy (CBT) is now included in the treatment of patients with inflammatory bowel disease (IBD) in many settings. However, different clinical trials report different outcomes without consensus. This study aims to evaluate the impact of CBT on the mental state, quality of life and disease activity of patients with IBD.

Design
Systematic review.

Methods
This systematic review searched eligible studies from 1946 to December 8, 2019, in MEDLINE, EMBASE, CINAHL, Cochrane library, ClinicalTrials.gov, PsycINFO, Web of Science for eligible randomized controlled trials (RCT).

Results
Among the initial identified 1807 references, 11 studies met inclusion criteria. CBT was shown to improve patient's quality of life and reduce the level of depression and anxiety post-intervention but was not sustained. Evidence is not enough for the effect of CBT on disease activity, or C-reactive protein level.

Conclusions
CBT has shown short-term positive psychological effects on IBD patients, but there is insufficient evidence for sustained physical and psychological improvements of IBD patients.
PROSPERO registration: CRD42019152330.
Long-term effects of alcohol consumption on cognitive function in seniors: a cohort study in China
Authors: Han Lizhen , Jia Jinzhu 
Published: December 2021

Abstract
Background
In the context of increasing global aging, the long-term effects of alcohol consumption on cognitive function in older adults were analyzed in order to provide rationalized health recommendations to the elderly population.

Methods
The study used the Chinese Longitudinal Healthy Longevity Survey (CLHLS) dataset, from which 5354 Chinese seniors aged 65–112 years were selected as the subjects, spanning the years 1998–2018. Data on alcohol, diet, activity, and cognition were collected by questionnaire and cognitive levels were judged by the Mini-Mental State Examination scale (also referenced to the Functional Assessment Staging Test). Data cleaning and preprocessing was implemented by R software. The dynamic Cox model was applied for model construction and data analysis.

Results
The results of the dynamic Cox model suggested that seniors who drank alcohol were at higher risk of cognitive decline compared to those who never drank (HR = 1.291, 95%CI: 1.175–1.419). The risk was similarly exacerbated by perennial drinking habits (i.e., longer drinking years, HR = 1.008, 95%CI: 1.004–1.013). Compared to non-alcoholic beverages, liquor (≥ 38°), liquor (< 38°), wine and rice wine all showed negative effects. Whereas, the risk of cognitive decline was relatively lower in seniors who consumed liquors (< 38°) and rice wine compared to the high-level liquor (HR: 0.672 (0.508, 0.887) and 0.732 (0.559, 0.957), respectively).

Conclusions
Alcohol consumption has a negative and long-term effects on cognitive function in seniors. For the elderly, we suggested that alcohol intake should be avoided as much as possible.
Changes in the use of diabetes drugs among community-dwelling people with Alzheimer’s disease
Authors: López-Rubio Carlos , Koponen Marjaana , Lampela Pasi , Taipale Heidi , Tanskanen Antti , Bell J. Simon , Tolppanen Anna-Maija , Hartikainen Sirpa 
Published: December 2021

Abstract
Background
Type 2 diabetes is common in persons with Alzheimer’s disease (AD). Management of diabetes in persons with AD is challenging due to changing goals of care and susceptibility to adverse drug events including hypoglycemia. The aim of this study was to investigate the prevalence of diabetes drug use from 5 years before to 5 years after the time of AD diagnosis among persons with and without AD.

Methods
This was a nationwide register-based study of persons with and without AD and diabetes in Finland. We analyzed data from the Medication Use and Alzheimer’s disease (MEDALZ) study that included 70,718 community-dwelling people diagnosed with AD from 2005 to 2011. The study population included 8418 persons with AD and 6666 matched persons without AD who were diagnosed with diabetes 5 years before AD diagnosis (index date). We defined the prevalence of diabetes drug use in three-month evaluation periods from 5 years before until 5 years after the index date.

Results
Nearly all people with diabetes (94% in both cohorts) used one or more diabetes drugs on the index date. The most prevalent drug metformin was used by 60.9% of people with AD and 59.1% of people without AD. The next most prevalent drugs were sulfonylureas and insulin. The prevalence of diabetes drug use was similar in people with and without AD but began to decline 1 year after AD diagnosis in the AD cohort compared to non-AD cohort.

Conclusions
The decline in diabetes drug use after AD diagnosis may be attributed to clinicians and patients seeking to avoid serious adverse drug events including hypoglycemia. In addition, the findings may reflect personalized glycemic control and unintentional weight loss in persons with AD reducing the need for diabetes drugs.
Evolution and prediction of mismatch between observed and perceived upper limb function after stroke: a prospective, longitudinal, observational cohort study
Authors: Essers Bea , Van Gils Annick , Lafosse Christophe , Michielsen Marc , Beyens Hilde , Schillebeeckx Fabienne , Veerbeek Janne M. , Luft Andreas R. , Kos Daphne , Verheyden Geert 
Published: December 2021

AbstractBackgroundA previously shown ‘mismatch’ group of patients with good observed upper limb (UL) motor function but low perceived UL activity at six months post stroke tends to use the affected UL less in daily life than would be expected based on clinical tests, and this mismatch may also be present at 12 months. We aimed to confirm this group in another cohort, to investigate the evolution of this group from six to 12 months, and to determine factors on admission to inpatient rehabilitation and at 6 months that can discriminate between mismatch and good match groups at 12 months.MethodsPersons after stroke were recruited on rehabilitation admission and re-assessed at six and 12 months. Observed UL function was measured with the upper extremity subscale of the Fugl-Meyer Assessment (FMA-UE) and perceived UL activity by the hand subscale of the Stroke Impact Scale 3.0 (SIS-Hand). We defined mismatch as good observed UL function (FMA-UE > 50/66) but low perceived activity (SIS-Hand≤75/100). Potential discriminators at admission and 6 months (demographic characteristics, stroke characteristics, UL somatosensory function, cognitive deficits, mental function and activity) were statistically compared for match and mismatch groups at 12 months.ResultsWe included 60 participants (female: 42%) with mean (SD) age of 65 (12) years. We confirmed a mismatch group of 11 (18%) patients at 6 months, which increased to 14 (23%) patients at 12 months. In the mismatch group compared to the good match group at 12 months, patients had a higher stroke severity and more somatosensory impairments on admission and at 6 months.ConclusionsWe confirmed a group of patients with good observed UL function but low perceived activity both at six and at 12 months post stroke. Assessment of stroke severity and somatosensory impairments on admission into rehabilitation could determine mismatch at 12 months and might warrant intervention. However, large differences in clinical outcomes between patients in the mismatch group indicate the importance of tailoring training to the individual needs.
The ideal approach for treatment of cT1N+ and cT2Nany esophageal cancer.: a NCDB analysis
Authors: Huang Binhao , Chan Ernest G. , Pennathur Arjun , Luketich James D. , Zhang Jie 
Published: December 2021

Abstract
Background
Neoadjuvant therapy followed by surgery is recommended for locally advanced esophageal cancer. With the inaccuracies of clinical staging particularly for cT1N+ and cT2Nany tumors, some have proposed consideration of surgery followed by adjuvant treatment. Our objective is to evaluate the efficacy of neoadjuvant therapy vs surgery followed by adjuvant therapy, and to identify the ideal sequence of treatment in patients with cT1N+ and cT2Nany tumors.

Methods
We performed an analysis utilizing the National Cancer Database (2006-2015) identifying all patients with cT1N+ and cT2Nany esophageal cancer undergoing esophagectomy. The treatment was stratified as: neoadjuvant therapy (NT), adjuvant therapy (AT) and combination therapy of neoadjuvant and adjuvant (CT) groups and outcomes were analyzed.

Results
We identified 2795 patients with 81.9% (n=2289) receiving NT, 10.2% (n=285) AT, and 7.9% (n=221) CT. There were no significant differences noted in survival among AT, NT, and CT group in cT1N+(P=0.376), cT2N-(P=0.436), cT2N+(P=0.261) esophageal cancer by multivariate analysis using Cox regression model. This relationship held true in both squamous cell carcinoma and adenocarcinoma.

Conclusion
In clinical T1N+, T2Nany patients, there was no evident superiority of NT over AT. Surgery followed by adjuvant therapy can be considered to be an alternative option in these patients. Further prospective studies are needed to validate these findings.
Evaluation of depth perception and association of severity in Glaucoma patients and suspects
Authors: Adhikari Pragati Gautam , Thapa Madhu , Dahal Manisha 
Published: December 2021

Abstract
Background
To evaluate depth perception in Primary open angle glaucoma (POAG), glaucoma suspects compared to controls and to determine the association between depth perception and severity of glaucoma.

Methods
This was a hospital based, comparative, cross-sectional study. The ethical clearance was taken from institutional review committee of Institute of Medicine [Reference no.399 (6–11) E2 077-078]. Agematched, equal number of participants in each group (N=20) were evaluated with both Titmus and Frisby stereoacuity tests to measure depth perception as stereopsis threshold in seconds of arc. The participants were selected using the purposive sampling technique.

Results
There was no differences in age, sex, or best corrected visual acuity, intraocular pressure, central corneal thickness (CCT), found among the three groups (POAG, Glaucoma Suspects and Control) respectively. However, there was significant difference in cup disc ratio (CDR) between the groups. Equal number of male and female were there in each group, while in POAG group male to female ratio was 3:2. The mean stereoacuity threshold in control group was 53.5±23.23 seconds of arc with Titmus test and 38.75±18.83 seconds of arc with Frisby stereoacuity test. The difference in threshold was significant between control and glaucoma suspect with Titmus (t=1.991, p=0.05) and with Frisby (t=2.114, p=0.04). The difference was also significant in POAG group by Titmus (t=3.135, p=0.0033) and by Frisby (t=3.014, p=0.004). More so, with increasing severity of glaucoma, the mean threshold of stereopsis increased as seen with both Titmus and Frisby Tests (ANOVA, p < 0.001)

Conclusion
Primary open angle glaucoma patients and glaucoma suspects, showed significant reduction in depth perception. Decreased stereoacuity was associated with greater glaucomatous visual field loss.
Spiroplasma species as a rare cause of congenital cataract and uveitis: a case series
Authors: Farassat Navid , Reich Michael , Serr Annerose , Küchlin Sebastian , Erwemi Marwa , Auw-Hädrich Claudia , Krastel Hermann , Lagrèze Wolf Alexander 
Published: December 2021

Abstract
Background
To date, only four cases of ocular spiroplasma infection have been reported in the entire ophthalmic literature. We add two more cases to raise awareness of this sight-threatening congenital disease that manifests as cataract with ocular inflammation.

Case presentation
Both infants were referred for cataracts associated with ocular inflammation. Case 1, a 3-week-old neonate presented with unilateral cataract, ocular inflammation and elevated intraocular pressure. Case 2 was a 3-month-old infant with bilateral cataract and panuveitis. Lensectomies with or without vitrectomy and subsequent analyses of the specimens were performed. Transmission electron microscopy and multiplex polymerase chain reaction or 16 s rRNA gene polymerase chain reaction revealed spiroplasma species.

Conclusions
Spiroplasma as a very rare cause for congenital cataract might be underdiagnosed. We recommend performing polymerase chain reaction to probe for spiroplasma species in congenital cataracts with an inflammatory component.
Visual acuity and anatomical changes following vitrectomy for epiretinal membrane foveoschisis: a case series
Authors: Photcharapongsakul Chaiyaphot , Chokesuwattanaskul Susama , Choovuthayakorn Janejit , Chaikitmongkol Voraporn , Kunavisarut Paradee , Watanachai Nawat , Patikulsila Direk 
Published: December 2021

Abstract
Purpose
To evaluate the visual outcome and macular anatomic structures on spectral-domain optical coherence tomography (SD-OCT) of patients with epiretinal membrane (ERM) foveoschisis who underwent vitrectomy.

Methods
A retrospective cohort, interventional, case series.

Participants
Fourteen patients (14 eyes) with central vision loss from an ERM foveoschisis underwent vitrectomy at Chiang Mai University Hospital from 2017 to 2018 and had a follow-up period of 12 months.

Interventions
The 23G vitrectomy with ERM and internal limiting membrane (ILM) peeling was performed by a single surgeon.

Main outcomes
Best-corrected visual acuity (BCVA) and anatomic appearance on SD-OCT were assessed at the time of preoperative evaluations and post-operative follow-ups at 1, 3, 6, and 12 months.

Results
Fourteen patients with a mean (SD) age of 67.9 (7.9) years and a mean (SD) visual acuity (VA) of 0.6 (0.1) LogMAR units were included in this study. Significant VA improvements were observed at the 3-month (0.43 (0.14) LogMAR unit), 6-month (0.45 (0.16) LogMAR unit) and 12-month (0.37 (0.21) LogMAR unit) post-operative visits compared to baseline, all with P-values < 0.001. At month 12, there were vision improvements of ≥3 lines in 8 (57.2%) patients, vision improvements of 1 or 2 lines in 2 (14.3%) patients, vision remained at the same line of pre-operation in 3 (21.4%) patients, and vision decreased by 1 line in 1 (7.1%) patient. Regarding the anatomical outcomes, 13 (92.9%) patients achieved anatomical foveal restoration, while one had persistent intraretinal schisis at the 12-month follow-up. The median time to achieve a foveal restoration was 3 months. No significant visual impairments were observed post-operatively.

Conclusion
In patients with central vision loss from ERM foveoschisis, vitrectomy with ILM stripping tended to improve both visual and anatomical outcomes.
A rare case of fetus in fetu in the sacrococcygeal region: CT and MRI findings
Authors: Lu Tao , Ma Junmei , Yang Xudan 
Published: December 2021

Abstract
Background
Fetus in fetu is a rare condition in which a malformed fetus is found in the body of a living twin. The retroperitoneum is the most common location of this condition. However, the sacrococcygeal region is a rare site of the disease. The presence of vertebral bodies and limbs differentiates FIF from teratoma. Imaging modalities are important for diagnosing FIF.

Case presentation
A 12-months old boy was hospitalized because of a mass in the sacrococcygeal region. CT showed a large, complex mass with bony structure resembling sacrococcygeal bone, hip bone and the femur in the sacrococcygeal region of the boy. The blood supply of the mass was from the aorta of the host. MRI revealed the mass was connected with the dilated sacral canal of the host, which resulted in tethered cord. A preoperative diagnosis of FIF was made and surgery was performed to remove the mass. Surgical removal and subsequent pathological examination revealed the anencephalic fetus had limb buds and a sacrum but no axial skeleton, which supported the diagnosis of FIF. Conclusions CT and MRI played important roles in diagnosing FIF based on the location of the lesion.
Trend on dental caries status and its risk indicators in children aged 12 years in China: a multilevel analysis based on the repeated national cross-sectional surveys in 2005 and 2015
Authors: Li Fei , Wu Si-Cheng , Zhang Zhi-Yuan , Lo Edward Chin Man , Gu Wen-Jia , Tao Dan-Ying , Wang Xing , Tai Bao-Jun , Hu De-Yu , Lin Huan-Cai , Wang Bo , Si Yan , Wang Chun-Xiao , Zheng Shu-Guo , Liu Xue-Nan , Rong Wen-Sheng , Wang Wei-Jian , Feng Xi-Ping , Lu Hai-Xia 
Published: December 2021

Abstract
Background
This study aimed to explore the trend and risk indicators for dental caries of children aged 12 years in China based on national oral health survey data in 2005 and 2015.

Methods
Research data were from the two latest national oral health surveys conducted in mainland China, including 30 and 31 provinces, autonomous regions, and municipalities in 2005 and 2015, respectively. Children aged 12 years were clinically examined for dental caries and dental fluorosis according to the World Health Organization criteria. Sociodemographic characteristics and oral health-related behaviours were collected using questionnaires. Multilevel zero-inflated negative binomial regression model was used to investigate the association between dental caries severity and dental fluorosis, sociodemographic characteristics, and oral health-related behaviours.

Results
The final analyses included 12,350 and 27,818 children surveyed in 2005 and 2015, respectively. The standardized prevalence of dental caries increased from 27.05% (95% confidence interval [CI], 24.25-28.85) in 2005 to 37.92% (95% CI, 34.94-40.90) in 2015, and the respective standardized mean decayed, missing, filled teeth (DMFT) index scores increased from 0.50 (standard deviation [SD], 1.04) to 0.83 (SD, 1.45) (P < 0.001). Fujian province had the highest increase in dental caries, followed by Liaoning, Heilongjiang, Hainan, and Yunnan. Results revealed that children who were girls, more frequently experienced dental pain, and had more recent dental visits, had significantly higher DMFT scores after adjusting for the survey year and other variables (all P < 0.05).

Conclusions
Dental caries of 12-year-old children in China deteriorated from 2005 to 2015, particularly in the northeast and southwest regions. Dental caries was associated with sex, dental pain, and dental service utilization.