bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hearing characteristics of infantile-onset Pompe disease after early enzyme-replacement therapy
Authors: Hsueh Chien-Yu , Huang Chii-Yuan , Yang Chia-Feng , Chang Chia-Chen , Lin Wei-Sheng , Cheng Hsiu-Lien , Wu Shang-Liang , Cheng Yen-Fu , Niu Dau-Ming 
Published: August 2021

Abstract
Background
Studies suggest that enzyme-replacement therapy (ERT) is crucial to the survival of patients with infantile-onset Pompe disease (IOPD). Hearing impairment (HI) is one of the clinical sequelae observed in long-term survivors. However, the benefits of early ERT for hearing outcomes have not yet been reported. This study aimed to investigate the impact of early ERT on IOPD patients.

Methods
This retrospective longitudinal study recruited IOPD patients who were referred by newborn screening for confirmatory diagnosis based on our rapid diagnostic criteria and received early ERT treatment between January 1, 2010, and January 31, 2018. The hearing test battery included a tympanogram, otoacoustic emission, auditory brainstem evoked response (ABR), pure-tone audiometry or conditioned play audiometry.

Results
Nineteen patients with IOPD were identified, 6 of whom had hearing impairment (HI); 1 had conductive HI, 2 had sensorineural HI (one had bilateral mild HI and one had mild HI in a single ear) and 1 had moderate mixed-type HI. Two patients failed the newborn screening test and had mild HI in the ABR. The mean age of the initial time to ERT was 11.05 ± 4.31 days, and the HI rate was 31.6% (6/19).

Conclusion
Our study is the largest cohort to show the characteristic hearing outcomes of IOPD patients after ERT. Early ERT within 2 weeks after birth may contribute to better hearing outcomes. Clinicians should be vigilant in testing for the hearing issues associated with IOPD and should intervene early if any HI is detected.
Auditory cortex hypoperfusion: a metabolic hallmark in Beta Thalassemia
Authors: Manara Renzo , Ponticorvo Sara , Perrotta Silverio , Barillari Maria Rosaria , Costa Giuseppe , Brotto Davide , Di Concilio Rosanna , Ciancio Angela , De Michele Elisa , Carafa Pasquale Alessandro , Canna Antonietta , Russo Andrea Gerardo , Troisi Donato , Caiazza Martina , Ammendola Federica , Roberti Domenico , Santoro Claudia , Picariello Stefania , Valentino Maria Sole , Inserra Emanuela , Carfora Roberta , Cirillo Mario , Raimo Simona , Santangelo Gabriella , di Salle Francesco , Esposito Fabrizio , Tartaglione Immacolata 
Published: August 2021

Abstract
Background
Sensorineural hearing loss in beta-thalassemia is common and it is generally associated with iron chelation therapy. However, data are scarce, especially on adult populations, and a possible involvement of the central auditory areas has not been investigated yet. We performed a multicenter cross-sectional audiological and single-center 3Tesla brain perfusion MRI study enrolling 77 transfusion-dependent/non transfusion-dependent adult patients and 56 healthy controls. Pure tone audiometry, demographics, clinical/laboratory and cognitive functioning data were recorded.

Results
Half of patients (52%) presented with high-frequency hearing deficit, with overt hypoacusia (Pure Tone Average (PTA) > 25 dB) in 35%, irrespective of iron chelation or clinical phenotype. Bilateral voxel clusters of significant relative hypoperfusion were found in the auditory cortex of beta-thalassemia patients, regardless of clinical phenotype. In controls and transfusion-dependent (but not in non-transfusion-dependent) patients, the relative auditory cortex perfusion values increased linearly with age (p < 0.04). Relative auditory cortex perfusion values showed a significant U-shaped correlation with PTA values among hearing loss patients, and a linear correlation with the full scale intelligence quotient (right side p = 0.01, left side p = 0.02) with its domain related to communication skills (right side p = 0.04, left side p = 0.07) in controls but not in beta-thalassemia patients. Audiometric test results did not correlate to cognitive test scores in any subgroup.

Conclusions
In conclusion, primary auditory cortex perfusion changes are a metabolic hallmark of adult beta-thalassemia, thus suggesting complex remodeling of the hearing function, that occurs regardless of chelation therapy and before clinically manifest hearing loss. The cognitive impact of perfusion changes is intriguing but requires further investigations.
Placing women in Cytogenetics: Lore Zech and the chromosome banding technique
Authors: Söhner Felicitas , Hansson Nils 
Published: August 2021

Abstract
Background
Scholars agree that Torbjörn Caspersson’s lab at the Institute of Medical Cell Research and Genetics at the Karolinska Institute, Sweden, played a key role in the first description of the so-called Q-banding technique. It laid the foundation for a new era of cytogenetic diagnostics and had a lasting impact in several areas of biology and medicine.

Methods
Based on a mixed-method approach, essential aspects of the history of human cytogenetics are considered via primary and secondary analysis of biographical interviews as well as the qualitative evaluation of bibliometrics. Drawing on interviews with colleagues of lab member Lore Zech (1923–2013) and contemporary publications, this paper illuminates the role of and contribution by Zech: To what extent is the discovery attached to her and what does her legacy look like today?

Results
The analysis of the contemporary witness interviews with colleagues, students and junior researchers shows that Lore Zech was a committed member of Caspersson's research group. In addition, memoirs by contemporary colleagues describe her outstanding skills in microscopy. The different sources paint a multifaceted picture. In addition to the historians' patterns of interpretation, different legacies can also be found within the peer group.

Conclusions
We argue that Zech represent the type of scientist who, although her research was acknowledged with several prizes, so far has not been part of the canon of pioneers of international cytogenetics.
Personalized single-cell networks: a framework to predict the response of any gene to any drug for any patient
Authors: Harikumar Haripriya , Quinn Thomas P. , Rana Santu , Gupta Sunil , Venkatesh Svetha 
Published: August 2021

Abstract
Background
The last decade has seen a major increase in the availability of genomic data. This includes expert-curated databases that describe the biological activity of genes, as well as high-throughput assays that measure gene expression in bulk tissue and single cells. Integrating these heterogeneous data sources can generate new hypotheses about biological systems. Our primary objective is to combine population-level drug-response data with patient-level single-cell expression data to predict how any gene will respond to any drug for any patient.

Methods
We take 2 approaches to benchmarking a “dual-channel” random walk with restart (RWR) for data integration. First, we evaluate how well RWR can predict known gene functions from single-cell gene co-expression networks. Second, we evaluate how well RWR can predict known drug responses from individual cell networks. We then present two exploratory applications. In the first application, we combine the Gene Ontology database with glioblastoma single cells from 5 individual patients to identify genes whose functions differ between cancers. In the second application, we combine the LINCS drug-response database with the same glioblastoma data to identify genes that may exhibit patient-specific drug responses.

Conclusions
Our manuscript introduces two innovations to the integration of heterogeneous biological data. First, we use a “dual-channel” method to predict up-regulation and down-regulation separately. Second, we use individualized single-cell gene co-expression networks to make personalized predictions. These innovations let us predict gene function and drug response for individual patients. Taken together, our work shows promise that single-cell co-expression data could be combined in heterogeneous information networks to facilitate precision medicine.
Association of cerebrospinal fluid protein biomarkers with outcomes in patients with traumatic and non-traumatic acute brain injury: systematic review of the literature
Authors: Santacruz Carlos A. , Vincent Jean-Louis , Bader Andres , Rincón-Gutiérrez Luis A. , Dominguez-Curell Claudia , Communi David , Taccone Fabio S. 
Published: August 2021

Abstract
Background
Acute brain injuries are associated with high mortality rates and poor long-term functional outcomes. Measurement of cerebrospinal fluid (CSF) biomarkers in patients with acute brain injuries may help elucidate some of the pathophysiological pathways involved in the prognosis of these patients.

Methods
We performed a systematic search and descriptive review using the MEDLINE database and the PubMed interface from inception up to June 29, 2021, to retrieve observational studies in which the relationship between CSF concentrations of protein biomarkers and neurological outcomes was reported in patients with acute brain injury [traumatic brain injury, subarachnoid hemorrhage, acute ischemic stroke, status epilepticus or post-cardiac arrest]. We classified the studies according to whether or not biomarker concentrations were associated with neurological outcomes. The methodological quality of the studies was evaluated using the Newcastle–Ottawa quality assessment scale.

Results
Of the 39 studies that met our criteria, 30 reported that the biomarker concentration was associated with neurological outcome and 9 reported no association. In TBI, increased extracellular concentrations of biomarkers related to neuronal cytoskeletal disruption, apoptosis and inflammation were associated with the severity of acute brain injury, early mortality and worse long-term functional outcome. Reduced concentrations of protein biomarkers related to impaired redox function were associated with increased risk of neurological deficit. In non-traumatic acute brain injury, concentrations of CSF protein biomarkers related to dysregulated inflammation and apoptosis were associated with a greater risk of vasospasm and a larger volume of brain ischemia. There was a high risk of bias across the studies.

Conclusion
In patients with acute brain injury, altered CSF concentrations of protein biomarkers related to cytoskeletal damage, inflammation, apoptosis and oxidative stress may be predictive of worse neurological outcomes.
Genetic and phylogeographic evidence for Jewish Holocaust victims at the Sobibór death camp
Authors: Diepenbroek Marta , Amory Christina , Niederstätter Harald , Zimmermann Bettina , Szargut Maria , Zielińska Grażyna , Dür Arne , Teul Iwona , Mazurek Wojciech , Persak Krzysztof , Ossowski Andrzej , Parson Walther 
Published: August 2021

AbstractSix million Jews were killed by Nazi Germany and its collaborators during World War II. Archaeological excavations in the area of the death camp in Sobibór, Poland, revealed ten sets of human skeletal remains presumptively assigned to Polish victims of the totalitarian regimes. However, their genetic analyses indicate that the remains are of Ashkenazi Jews murdered as part of the mass extermination of European Jews by the Nazi regime and not of otherwise hypothesised non-Jewish partisan combatants. In accordance with traditional Jewish rite, the remains were reburied in the presence of a Rabbi at the place of their discovery.
Lifestyle-dependent microglial plasticity: training the brain guardians
Authors: Augusto-Oliveira Marcus , Verkhratsky Alexei 
Published: August 2021

AbstractLifestyle is one of the most powerful instruments shaping mankind; the lifestyle includes many aspects of interactions with the environment, from nourishment and education to physical activity and quality of sleep. All these factors taken in complex affect neuroplasticity and define brain performance and cognitive longevity. In particular, physical exercise, exposure to enriched environment and dieting act through complex modifications of microglial cells, which change their phenotype and modulate their functional activity thus translating lifestyle events into remodelling of brain homoeostasis and reshaping neural networks ultimately enhancing neuroprotection and cognitive longevity.
Life cycle impact assessment of biofuels derived from sweet sorghum in the U.S.
Authors: Morrissey Karla G. , Thoma Greg , López Dora E. 
Published: August 2021

Abstract
Background
The objective of this study was to evaluate the environmental impact of the production of a range of liquid biofuels produced from the combination of fermenting sorghum stalk juice (bioethanol) and the pyrolysis/hydrotreatment of residual bagasse (renewable gasoline and diesel). Life cycle impact assessment (LCIA) was performed on a farm-to-wheels system that included: (i) sorghum farming, (ii) juice extraction, (iii) juice fermenting, (iv) bagasse pretreatment, (v) bagasse thermochemical treatment (pyrolysis, hydroprocessing, and steam reforming), and (vi) typical passenger vehicle operation. LCIA results were compared to those of petroleum fuels providing the equivalent functional unit—cumulative kilometers driven by spark ignition direct injection (SIDI) vehicles utilizing either renewable gasoline or ‘bioE85—a blend of bioethanol and renewable gasoline,’ and a compression ignition direct injection (CIDI) vehicle utilizing renewable diesel produced from 76 tons of harvested sweet sorghum (1 ha).

Results
Sweet sorghum biofuels resulted in a 48% reduction climate change impact and a 52% reduction in fossil fuel depletion. Additionally, reduced impacts in ozone depletion and eutrophication were found (67% and 47%, respectively). Petroleum fuels had lower impacts for the categories of non-carcinogenic health impact, smog, respiratory effects, and ecotoxicity, showing tradeoffs between sorghum and petroleum fuels.

Conclusion
Overall, sorghum biofuels provide advantages in environmental impact categories including global warming potential, fossil fuel depletion and eutrophication, showing potential for sorghum as a promising second-generation feedstock for fuel.
Tailoring renewable materials via plant biotechnology
Authors: de Vries Lisanne , Guevara-Rozo Sydne , Cho MiJung , Liu Li-Yang , Renneckar Scott , Mansfield Shawn D. 
Published: August 2021

AbstractPlants inherently display a rich diversity in cell wall chemistry, as they synthesize an array of polysaccharides along with lignin, a polyphenolic that can vary dramatically in subunit composition and interunit linkage complexity. These same cell wall chemical constituents play essential roles in our society, having been isolated by a variety of evolving industrial processes and employed in the production of an array of commodity products to which humans are reliant. However, these polymers are inherently synthesized and intricately packaged into complex structures that facilitate plant survival and adaptation to local biogeoclimatic regions and stresses, not for ease of deconstruction and commercial product development. Herein, we describe evolving techniques and strategies for altering the metabolic pathways related to plant cell wall biosynthesis, and highlight the resulting impact on chemistry, architecture, and polymer interactions. Furthermore, this review illustrates how these unique targeted cell wall modifications could significantly extend the number, diversity, and value of products generated in existing and emerging biorefineries. These modifications can further target the ability for processing of engineered wood into advanced high performance materials. In doing so, we attempt to illuminate the complex connection on how polymer chemistry and structure can be tailored to advance renewable material applications, using all the chemical constituents of plant-derived biopolymers, including pectins, hemicelluloses, cellulose, and lignins.
Long-term dynamics of trematode infections in common birds that use farmlands as their feeding habitats
Authors: Sitko Jiljí , Heneberg Petr 
Published: August 2021

AbstractBackgroundThe biodiversity of farmland habitats is witnessing unprecedented change, mostly in declines and simplification of assemblages that were established during centuries of the use of traditional agricultural techniques. In Central Europe, conspicuous changes are evident in populations of common farmland birds, in strong contrast to forest birds in the same region. However, there is a lack of information on longitudinal changes in trematodes that are associated with common farmland birds, despite the fact that diversity of trematodes is directly linked to the preservation of long-established food webs and habitat use adaptations of their hosts.MethodsWe analyzed the population trends of trematodes for the period 1963–2020 in six bird species that use Central European farmlands as their predominant feeding habitats. Namely, we examinedFalco tinnunculus,Vanellus vanellus, winter populations ofButeo buteo,Ciconia ciconia, extravilan population ofPica pica, andAsio otus, all originating from the Czech Republic.ResultsWe observed dramatic population losses of all trematode species inC. ciconiaandV. vanellus; the changes were less prominent in the other examined hosts. Importantly, the declines in prevalence and intensity of infection affected all previously dominant species. These includedTylodelphys excavataandChaunocephalus feroxinC. ciconia,Lyperosomum petiolatuminP. pica,Strigea strigisinA. otus,Neodiplostomum attenuatumandStrigea falconisinB. buteo(χ2testP < 0.001 each), andEchinoparyphium agnatum andUvitellina adelphainV. vanellus(completely absent in 2011–2000). In contrast, the frequency and spectrum of isolated records of trematode species did not change to any large extent except those inV. vanellus.ConclusionsThe analysis of six unrelated common bird species that use farmlands as their feeding habitats revealed a previously unreported collapse of previously dominant trematode species. The previously dominant trematode species declined in terms of both prevalence and intensity of infection. The causes of the observed declines are unclear; of note is, however, that some of the broadly used agrochemicals, such as azole fungicides, are well known for their antihelminthic activity. Further research is needed to provide direct evidence for effects of field-realistic concentrations of azole fungicides on the survival and fitness of trematodes.Graphical abstract
Spinning straw into gold: description of a disruptive rheumatology research platform inspired by the COVID-19 pandemic
Authors: Boekel L. , Hooijberg F. , Vogelzang E. H. , Klarenbeek P. L. , Bos W. H. , Tas S. W. , Wolbink G. J. 
Published: August 2021

AbstractClinical research projects often use traditional methods in which data collection and signing informed consent forms rely on patients’ visits to the research institutes. However, during challenging times when the medical community is in dire need of information, such as the current COVID-19 pandemic, it becomes more urgent to use digital platforms that can rapidly collect data on large numbers of patients. In the current manuscript, we describe a novel digital rheumatology research platform, consisting of almost 5000 patients with autoimmune diseases and healthy controls, that was set up rapidly during the COVID-19 pandemic, but which is sustainable for the future. Using this platform, uniform patient data can be collected via questionnaires and stored in a single database readily available for analysis. In addition, the platform facilitates two-way communication between patients and researchers, so patients become true research partners. Furthermore, blood collection via a finger prick for routine and specific laboratory measurements has been implemented in this large cohort of patients, which may not only be applicable for research settings but also for clinical care. Finally, we discuss the challenges and potential future applications of our platform, including supplying tailored information to selected patient groups and facilitation of patient recruitment for clinical trials.
Neuromyelitis optica and concomitant pulmonary tuberculosis: a case report
Authors: Saied Zakaria , Nabli Fatma , Rachdi Amine , Jeridi Cyrine , Douma Bissene , Belal Samir , Ben Sassi Samia 
Published: August 2021

Abstract
Background
Concomitant diagnosis of neuromyelitis optica spectrum disease and pulmonary tuberculosis has rarely been reported.

Case report
We report a case involving a young Tunisian male patient who developed dry cough followed, 2 months later, by weakness in the lower limbs. The findings of central nervous system imaging and anti-aquaporin-4 antibody positivity were compatible with the diagnosis of neuromyelitis optica spectrum disease. Constellation of the clinical and the typical radiological pulmonary findings in our patient, coming from an endemic region, allowed the diagnosis of pulmonary tuberculosis, although sputum smear examination for acid-fast bacilli and cultures was negative. The patient received anti-tuberculous polytherapy associated with immunomodulation, consisting of methylprednisolone and intravenous immunoglobulins. Pulmonary infection symptoms initially improved but with no motor recovery. The patient suddenly died at home 4 months after the onset of the first symptoms. Current data regarding the clinical presentation of this underreported concomitant or associated condition, the possible pathophysiological mechanisms, and the therapeutic options were reviewed.

Conclusions
This case underscores the necessity to understand the exact mechanism of these coincident entities and to clarify the best immunomodulatory choice since immunosuppression targeting neuromyelitis optica spectrum disease can lead to dissemination of pulmonary tuberculosis.
Elevated intracranial pressure requiring decompressive craniectomy in a child with progressive primary angiitis of the central nervous system: a case report
Authors: Al-Mansour Lama S. , AlRasheed Abdulrahman A. , AlEnezi Khaled R. , AlAli Hamza M. 
Published: August 2021

Abstract
Background
Elevated intracranial pressure is a potentially catastrophic complication of neurologic injury in children. Successful management of elevated intracranial pressure requires prompt recognition and therapy directed at both reducing intracranial pressure and reversing its underlying cause. A rare condition that causes elevated intracranial pressure is childhood primary angiitis of the central nervous system, which is a rare inflammatory central nervous system disease that poses diagnostic and therapeutic challenges. To our knowledge, this is the first reported case of angiography-positive progressive childhood primary angiitis of the central nervous system requiring decompressive hemicraniectomy for refractory elevated intracranial pressure in children.

Case presentation
We report the case of a 5-year-old Saudi girl who presented to the pediatric emergency department with fever and new-onset status epilepticus. She had elevated inflammatory markers with radiological and histopathological evidence of angiography-positive progressive childhood primary angiitis of the central nervous system, complicated by elevated intracranial pressure. Despite medical management for both childhood primary angiitis of the central nervous system and elevated intracranial pressure, her neurological status continued to deteriorate and the elevated intracranial pressure became refractory. She developed right uncal, right subfalcine, and tonsillar herniation requiring decompressive hemicraniectomy with a favorable neurological outcome.

Conclusion
Decompressive craniectomy might be considered in cases of angiography-positive progressive childhood primary angiitis of the central nervous system with elevated intracranial pressure refractory to medication. A multidisciplinary approach for the decision of decompressive craniectomy is advised to ensure patient safety and avoid possible morbidities and mortality.