Miracle-dz/UniFAR-FTUs huggingface dataset:
Instrew: leveraging LLVM for high performance dynamic binary instrumentation

Dynamic binary instrumentation frameworks are popular tools to enhance programs with additional analysis, debugging, or profiling facilities or to add optimizations or translations without requiring recompilation or access to source code. They analyze the binary code, translate into a---typically low-level---intermediate representation, add the needed instrumentation or transformation and then generate new code on-demand and at run-time. Most tools thereby focus on a fast code rewriting process at the cost of lower quality code, leading to a significant slowdown in the instrumented code. Further, most tools run in the application's address space, making their development cumbersome. We propose a novel dynamic binary instrumentation framework, Instrew, which closes these gaps by (a) leveraging the LLVM compiler infrastructure for high-quality code optimization and generation and (b) enables process isolation between the target code and the instrumenter. Instead of using our own non-portable and low-level intermediate representation, our framework directly lifts the original machine code into LLVM-IR, where instrumentation and behavioral changes may be performed, and from which high quality code can be produced. Results on the SPEC CPU2017 benchmarks show that the rewriting overhead is only 1/5 of the overhead incurred using the state-of-the-art toolchain Valgrind.
Renal-protective effect of dexmedetomidine during cardiac surgery with cardiopulmonary bypass: a prospective, randomized, double-blind, placebo-controlled study

Background and objectives Postcardiac surgery-associated acute kidney injury (AKI) is associated with up to 60% mortality rates of all cardiac surgery patients. This study aimed to study the renal-protective effect of dexmedetomidine in reducing the incidence of AKI following cardiac surgery. Patients and methods A total of 40 patients scheduled for cardiac surgery with cardiopulmonary bypass (CPB) were randomly allocated into two equal groups. In the study group, dexmedetomidine was given as an infusion of 0.4 μg/kg/h from induction of anesthesia till the end of surgery while in the control group, the patients received an equal volume of normal saline. The primary outcome of this study was the level of serum neutrophil gelatinase-associated lipocalin. The secondary outcomes were serum creatinine, hemodynamic parameters, operative time, aortic cross-clamp time, CPB time, and duration of ICU stay. Results Intraoperative and postoperative time variables and number of patients who developed hypotension were comparable between groups. Bradycardia developed more frequently in the dexmedetomidine group than in the placebo group. Serum neutrophil gelatinase-associated lipocalin after 2 h showed a statistically significant difference between groups. Serum creatinine showed no statistically significant difference between groups. Conclusion Dexmedetomidine could have a protective role in renal function during cardiac surgery using the CPB.
Neurological deterioration in a patient with lung cancer and brain metastasis

A 52‐year‐old male, known tobacco chewer for 15 years, with no comorbidities was evaluated for complaints of breathlessness on exertion and found to have left lower lobe mass lesion with bilateral pleural effusion and mediastinal and right supraclavicular lymphadenopathy. Pleural fluid cytology and biopsy from the right supraclavicular lymph node revealed adenocarcinoma with epidermal growth factor receptor (EGFR) exon 19 deletion positive. He was diagnosed with cT2N3M1a adenocarcinoma of the lung, Stage IVA as per the American Joint Committee on Cancer, 8th edition. He was treated on a clinical trial and received gefitinib with chemotherapy,[1] consisting of four cycles of 3‐weekly pemetrexed and carboplatin, followed by 11 cycles of maintenance pemetrexed with sustained partial response. Post 11 cycles, he developed a headache and was found to have a brain metastasis in the right occipital region [Figure 1a and b]. He was treated with whole‐brain radiotherapy (WBRT) at a dose of 20 Gy in five fractions, 4 Gy per fraction in November 2018. Since he had progressed only in the brain and had stable disease extracranially, he continued on maintenance pemetrexed along with gefitinib, with the last cycle (cycle 21) administered on August 1, 2019.
Should every cholecystectomy specimen be sent for histopathology to identify incidental gall bladder cancer?

It is interesting to note that many cases of gall bladder cancer are seen to have concomitant gall stone disease. [4,5] Most published literature on the subject report a concomitant presence of gall stones in 60-70% of all cases of GBC. In all such cases, the gall bladder is seen on ultrasound to have a thickened wall, which may not be too different as compared to chronic cholecystitis on ultrasound or even cross-sectional imaging.
Mycosis Fungoides: A Clinicopathological Study of 60 Cases from a Tertiary Care Center

Background: Mycosis fungoides (MF) is the most common primary cutaneous lymphoma. It affects usually the covered areas of the body in elderly males in 6th and 7th decades of life. Atypical dermal lymphoid infiltrate is seen along with epidermotropism. Nuclei of neoplastic cells are convoluted. The neoplastic cells demonstrate positivity for CD3 (Pan T) immunohistochemical stain. Majority show increased CD4 to CD8 ratio. The present study was done to study the clinicopathological features, which might be of help in reaching a correct diagnosis in these cases. Materials and Methods: A retrospective descriptive study was conducted on 60 reported cases of MF. The retrieved slides were reviewed for clinical and histopathological features and immunohistochemical profile. Results: The ages ranged from 20–84 years, mean age was 47 years. Majority (75%) of patients were male. Trunk and extremities were the sites most commonly affected. There was significant inverse correlation between epidermal thickness and tumor stage (P = 0.02). Thickened epidermis was seen in patch stage and thickness reduced with progressing stage. The intensity of dermal infiltrate and cell size was also statistically significantly linked to stage progression (P < 0.001 each). In addition, proliferation index also correlated significantly with tumor stage (P = 0.002). Conclusion: Clinical information and histological features are equally important in the accurate diagnosis of MF. Papillary dermal fibrosis is a useful diagnostic clue. CD4:CD8 ratio is not increased in all cases; it may be decreased or remain unchanged.
Ablation of DJ-1 Enhances Oxidative Stress by Disturbing the Function of Mitochondria in Epidermal Melanocytes

Background: Oxidative stress is implicated in the pathogenesis of vitiligo. The function of DJ-1 in oxidative damage of melanocytes is still elusive. Aims: The aim of this study was to investigate the role of DJ-1 in oxidative damage of melanocytes. Material and Methods: The expression of DJ-1 in melanocytes was studied by reverse transcription-quantitative polymerase chain reaction and Western blot. Short-interfering RNAs (siRNA) were employed to downregulate DJ-1. The cells were pooled into three groups: mock group (cells with transfection reagent), negative control (NC) group (negative siRNA control), and siRNA group. After H2O2treatment for 24 h, the morphological changes, cell viability, apoptosis, intracellular reactive oxygen species (ROS) levels, mitochondrial membrane potential (MMP), and mitochondrial respiration were measured in different groups. Results: DJ-1 was highly expressed in PIG1 melanocytes. DJ-1 knockdown rendered PIG1 melanocytes more susceptible to oxidative stress. Loss of DJ-1 led to apoptosis of PIG1 cells by impairing the function of mitochondria, including morphological abnormalities, ROS accumulation, depolarization of MMP, less adenosine-triphosphate (ATP) production, and less proton leak. Conclusions: DJ-1 plays a role in maintaining the antioxidative capacity in epidermal melanocytes.
Morphometry of the C2 Pedicle and Lamina in Thai Patients

Background: Traumatic upper cervical spine leads to instability and neurological deficit. At present, C2 (axis) pedicle or lamina screws for fixation are popular because further external immobilization is not needed. However, these techniques demand experience inserting the screws and carry the risk of vertebral artery or spinal cord injury. In some patients, the C2 screws cannot be inserted because of limited C2 size. Objective: To determine the width, length, height, and angle in the C2 pedicle and lamina in the Thai population. Materials and Methods: Patient data were collected from the Picture Archiving and Communication System at the Faculty of Medicine, Prince of Songkla University from January 2016 to December 2017. The C2 parameters, i.e., width, length, height, and angle of the pedicle and lamina were recorded. Results: The CT C-spine scans of 270 patients were enrolled. The mean Thai C2 pedicle dimensions were width 5.51 mm, length 23.78 mm, angle 39.04°, and height 8.64 mm. The mean C2 lamina dimensions were width 5.88 mm, length 32.17 mm, angle 49.46°, and height 12.27 mm. Twenty-four patients from the 270 patients (8.8%) had a pedicle width <3.5 mm but all patients had a lamina width ≥3.5 mm. Conclusion: In the Thai samples, 8.8% had a C2 pedicle width <3.5 mm which would not allow insertion of screws; however, they could be replaced with lamina screws since the lamina width was ≥3.5 mm. In this study, all of the patients who could not be inserted pedicle can be replaced with lamina screws inserted.
The efficacy and safety of first-line therapy for the epidermal growth factor receptor mutant non-small cell lung cancer in older versus younger patients: A pooled analysis of two randomized controlled trials

Background: There is a scarcity of data to guide the management of older patients with cancer. We therefore conducted this study to compare the outcomes and toxicities in older versus younger patients with an epidermal growth factor receptor (EGFR)-positive non-small cell lung cancer (NSCLC). Patients and Methods: For this pooled analysis, we utilized the individual patient databases of two prospective, first-line Phase III randomized controlled trials in patients with EGFR-mutant advanced NSCLC. The therapies in the two trials included gefitinib alone, pemetrexed/carboplatin, followed by maintenance pemetrexed and the combination of gefitinib with pemetrexed/carboplatin chemotherapy. We evaluated the progression-free survival (PFS) and overall survival (OS) of older patients (=/> 60 years) as compared to younger patients. Grade 3 or worse adverse events were also compared. Results: A total of 640 patients were included in this analysis, of which 156 (24.3%) were 60 years or older. The median PFS with first-line therapy was 8.5 months (95% confidence interval [CI], 7.8–9.2) in younger versus 9 months (95% CI, 6.7–11.4) in older patients (hazard ratio [HR], 2.3; 95% CI, 0.8–6.7; P = 0.575). The median OS of younger patients was 23.2 months (95% CI, 20.6–25.6) compared to 19 months (95% CI, 14.2–23.7) in older patients (HR, 1.18; 95 CI, 0.89–1.54, P = 0.234). On comparing older with younger patients for various known prognostic factors, there was no difference in OS based on any of the factors. On comparing the toxicities between the younger and older patients in the combination group, there was no difference in Grade 3 or 4 toxicities between younger and older patients except higher incidence of diarrhea in older patients (24.4% versus 9.3%, P = 0.010). Conclusions: In patients with EGFR-mutated NSCLC, similar survival and toxicities were found in patients aged 60 years or older as compared to younger patients with Eastern Cooperative Oncology Group Performance Status of 0–2, except for a higher incidence of diarrhea in older patients.
Transpalpebral Approach for Microsurgical Removal of Tuberculum Sellae Meningiomas

Background: The evolution of skull base approaches associated with individualization of surgical corridor and minimizing the collateral damage. Achieving the radical removal of tumor and preserving the neurological status of the patient is possible, both with the traditional approaches and keyhole approaches. Our work presents experience using the transpalpebral approach (TPA) for microsurgical removal of tuberculum sellae meningioma (TSM). Materials and Methods: A total of 15 patients with meningiomas underwent microsurgical removal of TSM through TPA. Ten patients were women and five were men. The standard preoperative diagnostic protocol includes magnetic resonance imaging with contrast enhancement, brain computed tomography for neuronavigation. We assess surgical complications, functional and cosmetic outcomes, and surgical parameters, including the time of surgery and intraoperative blood loss. Results: Visual impairment was finding in 100% patients, including slight decrease of vision (46,7%, seven patients), partial vision field loss (six patients, 40%), and serious visual impairment (two patients 13.3%). Visual improvement was noted in ten cases (66.7%), there was no improvement in four cases (26.7%), and one case (6.6%) had transient visual worsening for 4 days and slow improvement in 1 month. Headache disappeared in three patients (50%). There were no cases of cerebrospinal fluid leak. Transient frontal hypoesthesia was noted in all patients (100%) without permanent deficit. Transient palsy of the frontal muscle was noted in four patients for 4–6 months. Histological examination revealed WHO Grade I meningioma in 14 cases and in 1 case WHO Grade II meningioma. No deaths were identified in follow-up at 12 months. The average value of the Modified Rankin Scale was 1.4. The mean length of stay in hospital was 5. Conclusion: TPA is technically difficult and requires some experience to work in deep structures in a small surgical corridor. This technique can be good alternative to traditional fronto-lateral, supraorbital keyhole craniotomies, and endoscopic endonasal approaches.
Prevalence of Vitamin D deficiency in treatment-naive individual consecutive cancer patients

Background: There is a lack of information regarding Vitamin D deficiency in treatment-naive cancer patients. Aim: The aim of this was to study the prevalence of Vitamin D deficiency in cancer patients. Objectives: The objective was to measure the extent of Vitamin D insufficiency and deficiency in treatment-naive consecutive individual cancer patients from Eastern India. Materials and Methods: All consecutive new patients seen between April 2019 and September 2019 were offered a baseline test to measure serum 25-hydroxy Vitamin D [25 (OH) D] levels along with routine investigations. Vitamin D insufficiency was diagnosed when serum 25 (OH) D level was between 20 and 30 ng/mL, whereas patients with a level <20 ng/mL were designated as Vitamin D deficient. Patients with a Vitamin D level <10 ng/mL were termed as having severe Vitamin D deficiency. Descriptive statistics and frequency distribution were used in SPSS software, and Pearson's Chi-squared test was used to compare between the categorical variables. Results: Of 252 patients, 140 (56%) were female; median age was 51 years (range, 19–84 years) and 204 (81%) were diagnosed with solid organ malignancies. Mean (±standard deviation) Vitamin D level was 18.94 (±10.4). 169/252 (67%) had Vitamin D deficiency, whereas another 52/252 (21%) had Vitamin D insufficiency. Among these, 44/169 (26%) had severe Vitamin D deficiency. Females were more deficient compared to males, 76% versus 55% (P = 0.002). Vitamin D deficiency in younger (<50 years) and older (>50 years) population was 73% and 61% (P = 0.144); while that in solid versus hematolymphoid malignancies was 69% versus 58% (P = 0.173). In the three most common tumors, namely breast (21%), colorectal (8%), and ovary (8%), Vitamin D deficiency was noted in 75% of patients in each group. Vitamin D deficiency was the highest (84%) in esophageal and stomach cancer patients. Conclusion: More than two-thirds of Indian cancer patients are Vitamin D deficient. Patients with upper gastrointestinal, breast, colorectal, and ovarian cancers and female patients are the most vulnerable groups.
Authors' reply to Chaturvedi, Khaddar, and Bhat et al.

Our original article[1] published on quality of life and the needs of Indian advanced cancer patients receiving palliative care has received very interesting reviews and comments including an editorial on the topic. [2] We thank Dr Chaturvedi who has rightly indicated the need for quality of life distribution of patients into poor, satisfactory, and good categories. [3] In addition, we would rather state that there is a specific item in the reported tool expressing patient’s satisfaction with their general physicians (GPs) in the tool. The availability of palliative care physicians is grossly lacking in India. So, the present care of advanced cancer patients is by a variable group of physicians and nurses, as the GP system does not exist for palliative care in our country. As stated earlier, we agree with the view of doctors facing challenges and ethical dilemmas in providing palliative care in Indian settings. This correlates with the outcome of our study for needs and satisfaction for the palliative care. We agree with the fact that a tool focusing on specific needs of the Indian population would better depict the needs and problems. However, no validated tools for our Indian population have been made, and this needs future research in this context.
Health related quality of life and needs speak a global language that seek local solutions

The authors have used popular, validated tools such as the PNPC questionnaire to elicit a detailed measure of patients’ needs. Of note, fatigue and need to be informed of treatment options and side effects were prominent. This finding in the Indian population mirrors that of prior reviews in Western literature in patients and caregivers. [2] As the authors elaborate in their discussion of findings of surveys in various countries, the assessment of needs can inform future plans to expand the woefully inadequate state of access to palliative care services in the present day.
Origins of Nonnative Populations of Bufo japonicus formosus (Amphibia: Bufonidae) in Hokkaido, Japan, as Inferred by a Molecular Approach

Abstract: The Eastern-Japanese common toad, Bufo japonicus formosus, is distributed from southern Hokkaido to Kinki district of northeastern Honshu, Japan. However, Hokkaido populations are suspected to be nonnative and derived from relatively recent artificial introduction from Honshu. To clarify the origin of Hokkaido populations, we analyzed sequence variations of the mitochondrial cytochrome b gene in the toads from Hokkaido and compared the sequence data from previous studies. We obtained ten haplotypes from six sites on Hokkaido. Samples from the sites located along Ishikari river system, Asahikawa, Ebetsu, and Ishikari cities, had six haplotypes. Only one haplotype was obtained in Sapporo city and it was genetically far from Ishikari river's ones. Hakodate and Muroran cities samples had one and two haplotypes, respectively. All ten haplotypes from Hokkaido were genetically identical or close to haplotype data from Kanto district or Shizuoka Prefecture, mid-eastern Honshu, far from Hokkaido. Therefore, the toad populations of Hokkaido were considered to be nonnative and multiple introductions from eastern Honshu to Hokkaido were implied.
Morphological Re-Examination of the Endemic Paraguayan Snake Phalotris nigrilatus Ferrarezzi, 1993 (Serpentes: Colubridae: Elapomorphini), with Notes on Its Ecology and Conservation Status

Abstract: The colubrid snake Phalotris nigrilatus is endemic to San Pedro Department (Paraguay) and is known from a very few historical specimens. We analyze morphological variation and geographic distribution of P. nigrilatus on the basis of currently available specimens, including long-overlooked museum material. Also, we briefly report for the first time its live coloration and behavior on the basis of a recently collected individual. Results of morphological and geographic analyses lead to a slight revision of diagnosis and an argument for a higher conservation priority for this species.
Development of 22 Microsatellite Markers for Assessing Hybridization in the Genus Gekko (Squamata: Gekkonidae)

Abstract: Gekko yakuensis and G. tawaensis, both endemic to western Japan, are threatened by genetic introgression from G. hokouensis and G. japonicus, respectively. To know detailed situation of their hybridizations for planning relevant conservation measures, development of sensitive genetic markers is desired. We here developed microsatellite markers based on the sequences obtained from G. hokouensis using 454 GS Junior sequencer, and tested stability of PCR amplification and species-specificity of alleles at each locus using G. hokouensis, G. yakuensis, G. japonicus, and G. tawaensis. The results showed that 22 loci were almost constantly amplified in more than one species. We further confirmed that there were fixed or nearly fixed allelic displacement between G. hokouensis and G. yakuensis, and between G. japonicus and G. tawaensis at 14 loci. Thus, these 22 loci are considered to be useful for evaluation of hybridizations between these pairs of species.
Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity

The need for definitive answers probably explains our natural tendency to seek simplicity. The reductionist “bulk” approach, in which a mean behavior is attributed to a heterogeneous cell population, fulfills this need by considerably helping the conceptualization of complex biological processes. However, the limits of this methodology are becoming increasingly clear as models seek to explain biological events occurring in vivo, where heterogeneity is the rule. Research in the HIV-1 field is no exception: the challenges encountered in the development of preventive and curative anti-HIV-1 strategies may well originate in part from inadequate assumptions built on bulk technologies, highlighting the need for new perspectives. The emergence of diverse single-cell technologies set the stage for potential breakthrough discoveries, as heterogeneous processes can now be investigated with an unprecedented depth in topics as diverse as HIV-1 tropism, dynamics of the replication cycle, latency, viral reservoirs and immune control. In this review, we summarize recent advances in the HIV-1 field made possible by single-cell technologies, and contextualize their importance.